201
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Filipek K, Michalec-Wawiórka B, Boguszewska A, Kmiecik S, Tchórzewski M. Phosphorylation of the N-terminal domain of ribosomal P-stalk protein uL10 governs its association with the ribosome. FEBS Lett 2020; 594:3002-3019. [PMID: 32668052 DOI: 10.1002/1873-3468.13885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/25/2022]
Abstract
The uL10 protein is the main constituent of the ribosomal P-stalk, anchoring the whole stalk to the ribosome through interactions with rRNA. The P-stalk is the core of the GTPase-associated center (GAC), a critical element for ribosome biogenesis and ribosome translational activity. All P-stalk proteins (uL10, P1, and P2) undergo phosphorylation within their C termini. Here, we show that uL10 has multiple phosphorylation sites, mapped also within the N-terminal rRNA-binding domain. Our results reveal that the introduction of a negative charge within the N terminus of uL10 impairs its association with the ribosome. These findings demonstrate that uL10 N-terminal phosphorylation has regulatory potential governing the uL10 interaction with the ribosome and may control the activity of GAC.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Aleksandra Boguszewska
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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202
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Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Sci Rep 2020; 10:12618. [PMID: 32724211 PMCID: PMC7387497 DOI: 10.1038/s41598-020-69313-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
The ribosome is not only a highly complex molecular machine that translates the genetic information into proteins, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker disuccinimidyl diacetic urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all cross-links, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.
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Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
- Corporate Preclinical R&D, Analytics and Early Formulations Department, CHIESI FARMACEUTICI S.P.A., Via Palermo 26/A, 43122, Parma, Italy
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120, Halle/Saale, Germany.
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
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203
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Abstract
Many organisms, including bacteria, code for multiple paralogues of some ribosomal protein subunits. The relative contribution of these alternative subunits to ribosome function and protein synthesis is unknown and controversial. Many studies on alternative ribosomes have been confounded by isolation of alternative and canonical ribosomes from different strains or growth conditions, potentially confounding results. Here, we show that one form of alternative ribosome from Mycobacterium smegmatis has a distinct translational profile compared with canonical ribosomes purified from an identical cellular context. We also identify a role for alternative ribosomes in iron homeostasis. Given the prevalence of alternative ribosomal genes in diverse organisms, our study suggests that alternative ribosomes may represent a further layer of regulation of gene translation. Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain of M. smegmatis in which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.
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204
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Panda A, Yadav A, Yeerna H, Singh A, Biehl M, Lux M, Schulz A, Klecha T, Doniach S, Khiabanian H, Ganesan S, Tamayo P, Bhanot G. Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic Acids Res 2020; 48:7079-7098. [PMID: 32525984 PMCID: PMC7367157 DOI: 10.1093/nar/gkaa485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 12/26/2022] Open
Abstract
We give results from a detailed analysis of human Ribosomal Protein (RP) levels in normal and cancer samples and cell lines from large mRNA, copy number variation and ribosome profiling datasets. After normalizing total RP mRNA levels per sample, we find highly consistent tissue specific RP mRNA signatures in normal and tumor samples. Multiple RP mRNA-subtypes exist in several cancers, with significant survival and genomic differences. Some RP mRNA variations among subtypes correlate with copy number loss of RP genes. In kidney cancer, RP subtypes map to molecular subtypes related to cell-of-origin. Pan-cancer analysis of TCGA data showed widespread single/double copy loss of RP genes, without significantly affecting survival. In several cancer cell lines, CRISPR-Cas9 knockout of RP genes did not affect cell viability. Matched RP ribosome profiling and mRNA data in humans and rodents stratified by tissue and development stage and were strongly correlated, showing that RP translation rates were proportional to mRNA levels. In a small dataset of human adult and fetal tissues, RP protein levels showed development stage and tissue specific heterogeneity of RP levels. Our results suggest that heterogeneous RP levels play a significant functional role in cellular physiology, in both normal and disease states.
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Affiliation(s)
- Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Anupama Yadav
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huwate Yeerna
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
| | - Amartya Singh
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Michael Biehl
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Nijenborgh 9, NL-9747 AG Groningen, The Netherlands
| | - Markus Lux
- Cognitive Interaction Technology (CITEC), Bielefeld University, Inspiration 1, D-33619 Bielefeld, Germany
| | - Alexander Schulz
- Cognitive Interaction Technology (CITEC), Bielefeld University, Inspiration 1, D-33619 Bielefeld, Germany
| | - Tyler Klecha
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ,08854, USA
| | - Sebastian Doniach
- Department of Applied Physics, Stanford University, Palo Alto, CA 94305, USA
| | | | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Pablo Tamayo
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ,08854, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA
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205
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Mołoń M, Molestak E, Kula-Maximenko M, Grela P, Tchórzewski M. Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle. Cells 2020; 9:cells9071745. [PMID: 32708309 PMCID: PMC7409069 DOI: 10.3390/cells9071745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
Aging is a biological phenomenon common to all living organisms. It is thought that the rate of aging is influenced by diverse factors, in many cases related to the control of energy metabolism, i.e., the so-called pro-longevity effects of starvation. Translation, regarded as the main energy consumption process, lies at the center of interest, as it has a significant impact on the longevity phenomenon. It has been shown that perturbations in the translational apparatus may lead to a lower rate of aging. Therefore, the main aim of this study was to investigate aging in relation to the protein biosynthesis circuit, taking into account the uL11 ribosomal protein as a vital ribosomal element. To this end, we used set of yeast mutants with deleted single uL11A or uL11B genes and a double disruptant uL11AB mutant. We applied an integrated approach analyzing a broad range of biological parameters of yeast mutant cells, especially the longevity phenomenon, supplemented with biochemical and high throughput transcriptomic and metobolomic approaches. The analysis showed that the longevity phenomenon is not fully related to the commonly considered energy restriction effect, thus the slow-down of translation does not represent the sole source of aging. Additionally, we showed that uL11 can be classified as a moonlighting protein with extra-ribosomal function having cell-cycle regulatory potential.
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Affiliation(s)
- Mateusz Mołoń
- Department of Biochemistry and Cell Biology, University of Rzeszów, 35-601 Rzeszów, Poland
- Correspondence: (M.M.); (M.T.); Tel.: +48-17-7855407 (M.M.); +48-81-5375956 (M.T.)
| | - Eliza Molestak
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
| | - Monika Kula-Maximenko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland;
| | - Przemysław Grela
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
- Correspondence: (M.M.); (M.T.); Tel.: +48-17-7855407 (M.M.); +48-81-5375956 (M.T.)
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206
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Lilleorg S, Reier K, Volõnkin P, Remme J, Liiv A. Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli. Sci Rep 2020; 10:11682. [PMID: 32669635 PMCID: PMC7363858 DOI: 10.1038/s41598-020-68582-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023] Open
Abstract
Ribosomes are essential macromolecular complexes conducting protein biosynthesis in all domains of life. Cells can have heterogeneous ribosomes, i.e. ribosomes with various ribosomal RNA and ribosomal protein (r-protein) composition. However, the functional importance of heterogeneous ribosomes has remained elusive. One of the possible sources for ribosome heterogeneity is provided by paralogous r-proteins. In E. coli, ribosomal protein bL31 has two paralogs: bL31A encoded by rpmE and bL31B encoded by ykgM. This study investigates phenotypic effects of these ribosomal protein paralogs using bacterial strains expressing only bL31A or bL31B. We show that bL31A confers higher fitness to E. coli under lower temperatures. In addition, bL31A and bL31B have different effects on translation reading frame maintenance and apparent translation processivity in vivo as demonstrated by dual luciferase assay. In general, this study demonstrates that ribosomal protein paralog composition (bL31A versus bL31B) can affect cell growth and translation outcome.
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Affiliation(s)
- Silva Lilleorg
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Kaspar Reier
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Pavel Volõnkin
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia
| | - Aivar Liiv
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, 51010, Tartu, Estonia.
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207
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Ryu J, Lee C. Regulatory Nucleotide Sequence Signals for Expression of the Genes Encoding Ribosomal Proteins. Front Genet 2020; 11:501. [PMID: 32655613 PMCID: PMC7326009 DOI: 10.3389/fgene.2020.00501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/23/2020] [Indexed: 11/13/2022] Open
Abstract
Ribosomal proteins (RPs) are essential components that translate genetic information from mRNA templates into proteins. Their expressional dysregulation adversely affects the survival and growth of human cells. Nevertheless, little is known about the nucleotide sequences regulating the expression of RPs. Genome-wide associations for expression level of 70 RP genes were conducted across expression stages. Eighteen expression regulatory quantitative trait loci (erQTLs) were identified for protein abundances of 21 RPs (P < 1 × 10-5), but not for their mRNA expression and ribosome occupancy (P > 1 × 10-5). These erQTLs for protein abundance (pQTLs) were all trans-acting. Three of the pQTLs were associated with the expression of long noncoding RNAs (lncRNAs). Target genes of these lncRNAs may produce ribosomal components or may control the metabolic cues for ribosome synthesis. mRNAs of the RP genes extensively interact with miRNAs. The protein-specific erQTLs may become engendered by intensive miRNA controls at the translational stage, which in turn can produce RPs efficient in handling instantaneous cell requirements. This study suggests that the expression levels of RPs may be greatly influenced by trans-acting regulation, presumably via interference of miRNAs and target genes of lncRNAs. Further studies are warranted to examine the molecular functions of pQTLs presented in this study and to understand the underlying regulatory mechanisms of gene expression of RPs.
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Affiliation(s)
- Jihye Ryu
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
| | - Chaeyoung Lee
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
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208
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DiGiuseppe S, Rollins MG, Astar H, Khalatyan N, Savas JN, Walsh D. Proteomic and mechanistic dissection of the poxvirus-customized ribosome. J Cell Sci 2020; 134:jcs246603. [PMID: 32467327 PMCID: PMC7358139 DOI: 10.1242/jcs.246603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
Ribosomes are often viewed as protein synthesis machines that lack intrinsic regulatory capacity. However, studies have established that ribosomes can functionally diversify through changes in the composition of, or post-translational modifications to ribosomal subunit proteins (RPs). We recently found that poxviruses phosphorylate unique sites in the RP, receptor for activated C kinase 1 (RACK1) to enhance viral protein synthesis. Here, we developed approaches for large-scale proteomic analysis of ribosomes isolated from cells infected with different viruses. Beyond RACK1, we identified additional phosphorylation events within RPS2 and RPS28 that arise during poxvirus infection, but not other viruses tested. The modified sites lie within unstructured loop domains that position around the mRNA entry and exit channel, respectively, and site-substitution mutants revealed that each modified residue contributed differently to poxvirus replication. Our findings reveal the broader extent to which poxviruses customize host ribosomes and provide new insights into how ribosomes can functionally diversify.
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Affiliation(s)
- Stephen DiGiuseppe
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Madeline G Rollins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Helen Astar
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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209
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Kerr CH, Skinnider MA, Andrews DDT, Madero AM, Chan QWT, Stacey RG, Stoynov N, Jan E, Foster LJ. Dynamic rewiring of the human interactome by interferon signaling. Genome Biol 2020; 21:140. [PMID: 32539747 PMCID: PMC7294662 DOI: 10.1186/s13059-020-02050-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized. Here, we apply a combination of quantitative proteomic approaches to describe the effects of IFN signaling on the human proteome, and apply protein correlation profiling to map IFN-induced rearrangements in the human protein-protein interaction network. RESULTS We identify > 26,000 protein interactions in IFN-stimulated and unstimulated cells, many of which involve proteins associated with human disease and are observed exclusively within the IFN-stimulated network. Differential network analysis reveals interaction rewiring across a surprisingly broad spectrum of cellular pathways in the antiviral response. We identify IFN-dependent protein-protein interactions mediating novel regulatory mechanisms at the transcriptional and translational levels, with one such interaction modulating the transcriptional activity of STAT1. Moreover, we reveal IFN-dependent changes in ribosomal composition that act to buffer IFN-stimulated gene protein synthesis. CONCLUSIONS Our map of the IFN interactome provides a global view of the complex cellular networks activated during the antiviral response, placing IFN-stimulated genes in a functional context, and serves as a framework to understand how these networks are dysregulated in autoimmune or inflammatory disease.
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Affiliation(s)
- Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Current Address: Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Daniel D T Andrews
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Angel M Madero
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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210
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Barrera A, Olguín V, Vera-Otarola J, López-Lastra M. Cap-independent translation initiation of the unspliced RNA of retroviruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194583. [PMID: 32450258 DOI: 10.1016/j.bbagrm.2020.194583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Retroviruses are a unique family of RNA viruses that utilize a virally encoded reverse transcriptase (RT) to replicate their genomic RNA (gRNA) through a proviral DNA intermediate. The provirus is permanently integrated into the host cell chromosome and is expressed by the host cell transcription, RNA processing, and translation machinery. Retroviral messenger RNAs (mRNAs) entirely resemble a cellular mRNA as they have a 5'cap structure, 5'untranslated region (UTR), an open reading frame (ORF), 3'UTR, and a 3'poly(A) tail. The primary transcription product interacts with the cellular RNA processing machinery and is spliced, exported to the cytoplasm, and translated. However, a proportion of the pre-mRNA subverts typical RNA processing giving rise to the full-length RNA. In the cytoplasm, the full-length retroviral RNA fulfills a dual role acting as mRNA and as the gRNA. Simple retroviruses generate two pools of full-length RNA, one for each purpose. However, complex retroviruses have a single pool of full-length RNA, which is destined for translation or encapsidation. As for eukaryotic mRNAs, translational control of retroviral protein synthesis is mostly exerted at the step of initiation. Interestingly, some retroviral mRNAs, both simple and complex, use a dual mechanism to initiate protein synthesis, a cap-dependent initiation mechanism, or via internal initiation using an internal ribosome entry site (IRES). In this review, we describe and discuss data regarding the molecular mechanism driving the canonical cap-dependent and IRES-mediated translation initiation for retroviral mRNA, focusing the discussion mainly on the most studied retroviral mRNA, the HIV-1 mRNA.
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Affiliation(s)
- Aldo Barrera
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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211
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Stojković V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit. Nucleic Acids Res 2020; 48:2723-2732. [PMID: 31989172 PMCID: PMC7049716 DOI: 10.1093/nar/gkaa037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 01/01/2023] Open
Abstract
Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
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Affiliation(s)
- Vanja Stojković
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alexander G Myasnikov
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280 San Francisco, CA 94158, USA
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212
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Biever A, Glock C, Tushev G, Ciirdaeva E, Dalmay T, Langer JD, Schuman EM. Monosomes actively translate synaptic mRNAs in neuronal processes. Science 2020; 367:367/6477/eaay4991. [PMID: 32001627 DOI: 10.1126/science.aay4991] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/29/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
Abstract
To accommodate their complex morphology, neurons localize messenger RNAs (mRNAs) and ribosomes near synapses to produce proteins locally. However, a relative paucity of polysomes (considered the active sites of translation) detected in electron micrographs of neuronal processes has suggested a limited capacity for local protein synthesis. In this study, we used polysome profiling together with ribosome footprinting of microdissected rodent synaptic regions to reveal a surprisingly high number of dendritic and/or axonal transcripts preferentially associated with monosomes (single ribosomes). Furthermore, the neuronal monosomes were in the process of active protein synthesis. Most mRNAs showed a similar translational status in the cell bodies and neurites, but some transcripts exhibited differential ribosome occupancy in the compartments. Monosome-preferring transcripts often encoded high-abundance synaptic proteins. Thus, monosome translation contributes to the local neuronal proteome.
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Affiliation(s)
- Anne Biever
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Caspar Glock
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | | | - Tamas Dalmay
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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213
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Liberman N, O’Brown ZK, Earl AS, Boulias K, Gerashchenko MV, Wang SY, Fritsche C, Fady PE, Dong A, Gladyshev VN, Greer EL. N6-adenosine methylation of ribosomal RNA affects lipid oxidation and stress resistance. SCIENCE ADVANCES 2020; 6:eaaz4370. [PMID: 32494643 PMCID: PMC7176415 DOI: 10.1126/sciadv.aaz4370] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/27/2020] [Indexed: 05/26/2023]
Abstract
During stress, global translation is reduced, but specific transcripts are actively translated. How stress-responsive mRNAs are selectively translated is unknown. We show that METL-5 methylates adenosine 1717 on 18S ribosomal RNA in C. elegans, enhancing selective ribosomal binding and translation of specific mRNAs. One of these mRNAs, CYP-29A3, oxidizes the omega-3 polyunsaturated fatty acid eicosapentaenoic acid to eicosanoids, key stress signaling molecules. While metl-5-deficient animals grow normally under homeostatic conditions, they are resistant to a variety of stresses. metl-5 mutant worms also show reduced bioactive lipid eicosanoids and dietary supplementation of eicosanoid products of CYP-29A3 restores stress sensitivity of metl-5 mutant worms. Thus, methylation of a specific residue of 18S rRNA by METL-5 selectively enhances translation of cyp-29A3 to increase production of eicosanoids, and blocking this pathway increases stress resistance. This study suggests that ribosome methylation can facilitate selective translation, providing another layer of regulation of the stress response.
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Affiliation(s)
- Noa Liberman
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Zach K. O’Brown
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Scott Earl
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantinos Boulias
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Colette Fritsche
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Paul-Enguerrand Fady
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Anna Dong
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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214
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The rRNA m 6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 2020; 34:715-729. [PMID: 32217665 PMCID: PMC7197354 DOI: 10.1101/gad.333369.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
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215
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Kampen KR, Sulima SO, Vereecke S, De Keersmaecker K. Hallmarks of ribosomopathies. Nucleic Acids Res 2020; 48:1013-1028. [PMID: 31350888 PMCID: PMC7026650 DOI: 10.1093/nar/gkz637] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.
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Affiliation(s)
- Kim R Kampen
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Stijn Vereecke
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
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216
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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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217
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Xu Y, Ruggero D. The Role of Translation Control in Tumorigenesis and Its Therapeutic Implications. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033420] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As a convergent mechanism downstream of most oncogenic signals, control of mRNA translation has emerged as a key driver in establishing and tuning gene expression at specific steps in cancer development. Translation control is the most energetically expensive molecular process in the cell that needs to be modulated upon adaption to limited cellular resources, such as cellular stress. It thereby serves as the Achilles’ heel for cancer cells, particularly in response to changes in the microenvironment as well as to nutrient and metabolic shifts characteristic of cancer cell growth and metastasis. In this review, we discuss emerging discoveries that reveal how cancer cells modulate the translation machinery to adapt to oncogenic stress, the mechanisms that guide mRNA translation specificity in cancer, and how this selective mode of gene regulation provides advantages for cancer progression. We also provide an overview of promising preclinical and clinical efforts aimed at targeting the unique vulnerabilities of cancer cells that rely on the remodeling of mRNA translation for their infinite growth and survival.
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Affiliation(s)
- Yichen Xu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
| | - Davide Ruggero
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94157, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
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218
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Targeting the Human 80S Ribosome in Cancer: From Structure to Function and Drug Design for Innovative Adjuvant Therapeutic Strategies. Cells 2020; 9:cells9030629. [PMID: 32151059 PMCID: PMC7140421 DOI: 10.3390/cells9030629] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
The human 80S ribosome is the cellular nucleoprotein nanomachine in charge of protein synthesis that is profoundly affected during cancer transformation by oncogenic proteins and provides cancerous proliferating cells with proteins and therefore biomass. Indeed, cancer is associated with an increase in ribosome biogenesis and mutations in several ribosomal proteins genes are found in ribosomopathies, which are congenital diseases that display an elevated risk of cancer. Ribosomes and their biogenesis therefore represent attractive anti-cancer targets and several strategies are being developed to identify efficient and specific drugs. Homoharringtonine (HHT) is the only direct ribosome inhibitor currently used in clinics for cancer treatments, although many classical chemotherapeutic drugs also appear to impact on protein synthesis. Here we review the role of the human ribosome as a medical target in cancer, and how functional and structural analysis combined with chemical synthesis of new inhibitors can synergize. The possible existence of oncoribosomes is also discussed. The emerging idea is that targeting the human ribosome could not only allow the interference with cancer cell addiction towards protein synthesis and possibly induce their death but may also be highly valuable to decrease the levels of oncogenic proteins that display a high turnover rate (MYC, MCL1). Cryo-electron microscopy (cryo-EM) is an advanced method that allows the visualization of human ribosome complexes with factors and bound inhibitors to improve our understanding of their functioning mechanisms mode. Cryo-EM structures could greatly assist the foundation phase of a novel drug-design strategy. One goal would be to identify new specific and active molecules targeting the ribosome in cancer such as derivatives of cycloheximide, a well-known ribosome inhibitor.
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219
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Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Curr Opin Chem Biol 2020; 54:70-75. [PMID: 32131038 DOI: 10.1016/j.cbpa.2020.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023]
Abstract
Protein-RNA interactions regulate all aspects of RNA metabolism and are crucial to the function of catalytic ribonucleoproteins. Until recently, the available technologies to capture RNA-bound proteins have been biased toward poly(A) RNA-binding proteins (RBPs) or involve molecular labeling, limiting their application. With the advent of organic-aqueous phase separation-based methods, we now have technologies that efficiently enrich the complete suite of RBPs and enable quantification of RBP dynamics. These flexible approaches to study RBPs and their bound RNA open up new research avenues for systems-level interrogation of protein-RNA interactions.
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Affiliation(s)
- Tom Smith
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Eneko Villanueva
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Rayner M L Queiroz
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Charlotte S Dawson
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Mohamed Elzek
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Erika C Urdaneta
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester, LE1 7BH, UK
| | - Benedikt M Beckmann
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Kathryn S Lilley
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
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220
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221
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Kim E, Jung H. Local mRNA translation in long-term maintenance of axon health and function. Curr Opin Neurobiol 2020; 63:15-22. [PMID: 32087477 DOI: 10.1016/j.conb.2020.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Distal axons, remote from their cell bodies and nuclei, must survive the lifetime of an organism. Recent studies have provided compelling evidence that proteins are locally synthesized in healthy, mature central nervous system axons and presynaptic terminals in vivo. Presynaptic, mitochondrial and ribosomal proteins are locally synthesized in most adult axons of diverse cell types, linking local translation to axon function and survival. Accordingly, inhibiting the intra-axonal translation of key mRNAs or the function of their translational regulators causes dying-back axon degeneration, and human mutations in RNA metabolic pathways are increasingly being associated with neurodegenerative diseases that accompany axon degeneration. Here, we summarize recent relevant findings in a highly simplified 'RNA operon'-based model and discuss open questions and future directions.
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Affiliation(s)
- Eunjin Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hosung Jung
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Department of Anatomy, Brain Research Institute, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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222
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von Kügelgen N, Chekulaeva M. Conservation of a core neurite transcriptome across neuronal types and species. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1590. [PMID: 32059075 DOI: 10.1002/wrna.1590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022]
Abstract
The intracellular localization of mRNAs allows neurons to control gene expression in neurite extensions (axons and dendrites) and respond rapidly to local stimuli. This plays an important role in diverse processes including neuronal growth and synaptic plasticity, which in turn serves as a foundation for learning and memory. Recent high-throughput analyses have revealed that neurites contain hundreds to thousands of mRNAs, but an analysis comparing the transcriptomes derived from these studies has been lacking. Here we analyze 20 datasets pertaining to neuronal mRNA localization across species and neuronal types and identify a conserved set of mRNAs that had robustly localized to neurites in a high number of the studies. The set includes mRNAs encoding for ribosomal proteins and other components of the translation machinery, mitochondrial proteins, cytoskeletal components, and proteins associated with neurite formation. Our combinatorial analysis provides a unique resource for future hypothesis-driven research. This article is categorized under: RNA Export and Localization > RNA Localization RNA Evolution and Genomics > Computational Analyses of RNA RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Nicolai von Kügelgen
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marina Chekulaeva
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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223
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Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
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Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
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224
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Beese CJ, Brynjólfsdóttir SH, Frankel LB. Selective Autophagy of the Protein Homeostasis Machinery: Ribophagy, Proteaphagy and ER-Phagy. Front Cell Dev Biol 2020; 7:373. [PMID: 32039200 PMCID: PMC6985035 DOI: 10.3389/fcell.2019.00373] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic cell has developed intricate machineries that monitor and maintain proteome homeostasis in order to ensure cellular functionality. This involves the carefully coordinated balance between protein synthesis and degradation pathways, which are dynamically regulated in order to meet the constantly changing demands of the cell. Ribosomes, together with the endoplasmic reticulum (ER), are the key drivers of protein synthesis, folding, maturation and sorting, while the proteasome plays a pivotal role in terminating the existence of thousands of proteins that are misfolded, damaged or otherwise obsolete. The synthesis, structure and function of these dedicated machines has been studied for decades, however, much less is understood about the mechanisms that control and execute their own turnover. Autophagy, an evolutionarily conserved catabolic pathway, mediates degradation of a large variety of cytosolic substrates, ranging from single proteins to entire organelles or multi-subunit macromolecular complexes. In this review, we focus on selective autophagy of three key components of the protein homeostasis machinery: ribosomes, ER and proteasomes, through the selective autophagy pathways of ribophagy, ER-phagy, and proteaphagy. We discuss newly discovered mechanisms for the selective clearance of these substrates, which are often stress-dependent and involve specialized signals for cargo recognition by a growing number of receptors. We further discuss the interplay between these pathways and their biological impact on key aspects of proteome homeostasis and cellular function in health and disease.
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Affiliation(s)
- Carsten J Beese
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Lisa B Frankel
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
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225
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Thelen MP, Kye MJ. The Role of RNA Binding Proteins for Local mRNA Translation: Implications in Neurological Disorders. Front Mol Biosci 2020; 6:161. [PMID: 32010708 PMCID: PMC6974540 DOI: 10.3389/fmolb.2019.00161] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
As neurons are one of the most highly polarized cells in our body, they require sophisticated cellular mechanisms to maintain protein homeostasis in their subcellular compartments such as axons and dendrites. When neuronal protein homeostasis is disturbed due to genetic mutations or deletions, this often results in degeneration of neurons leading to devastating outcome such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), and fragile X syndrome (FXS). Ribonucleoprotein (RNP) complexes are macromolecular complexes composed of RNA binding proteins (RBPs) and their target RNAs. RBPs contain RNA binding domains and bind to RNA molecules via specific sequence motifs. RNP complexes have various functions in gene expression including messenger RNA (mRNA) trafficking, RNA processing and silencing. In neurons, RBPs deliver specific sets of mRNAs to subcellular compartments such as axons and dendrites to be locally translated. Mutations or deletions in genes coding for RNPs have been reported as causes for neurological disorders such as SMA, ALS, and FXS. As RBPs determine axonal or dendritic mRNA repertoires as well as proteomes by trafficking selective mRNAs and regulating local protein synthesis, they play a crucial role for neuronal function. In this review, we summarize the role of well-known RBPs, SMN, TDP-43, FUS, and FMRP, and review their function for local protein synthesis in neurons. Furthermore, we discuss their pathological contribution to the neurological disorders.
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Affiliation(s)
| | - Min Jeong Kye
- Institute of Human Genetics, University of Cologne, Cologne, Germany
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226
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Chen PH, Chen YT, Chu TY, Ma TH, Wu MH, Lin HH, Chang YS, Tan BCM, Lo SJ. Nucleolar control by a non-apoptotic p53-caspases-deubiquitinylase axis promotes resistance to bacterial infection. FASEB J 2020; 34:1107-1121. [PMID: 31914708 DOI: 10.1096/fj.201901959r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/11/2022]
Abstract
The nucleolus is best known for its cellular role in regulating ribosome production and growth. More recently, an unanticipated role for the nucleolus in innate immunity has recently emerged whereby downregulation of fibrillarin and nucleolar contraction confers pathogen resistance across taxa. The mechanism of this downregulation, however, remains obscure. Here we report that rather than fibrillarin itself being the proximal factor in this pathway, the key player is a fibrillarin-stabilizing deubiquitinylase USP-33. This was discovered by a candidate-gene search of Caenorhabditis elegans in which CED-3 caspase was revealed to execute targeted cleavage of USP-33, thus destabilizing fibrillarin. We also showed that cep-1 and ced-3 mutant worms altered nucleolar size and decreased antimicrobial peptide gene, spp-1, expression rendering susceptibility to bacterial infection. These phenotypes were reversed by usp-33 knockdown, thus linking the CEP-1-CED-3-USP-33 pathway with nucleolar control and resistance to bacterial infection in worms. Parallel experiments with the human analogs of caspases and USP36 revealed similar roles in coordinating these two processes. In summary, our work outlined a conserved cascade that connects cell death signaling to nucleolar control and innate immune response.
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Affiliation(s)
- Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Ying Chu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Tian-Hsiang Ma
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hsuan Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Hsien Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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227
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Kurylo CM, Parks MM, Juette MF, Zinshteyn B, Altman RB, Thibado JK, Vincent CT, Blanchard SC. Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype. Cell Rep 2020; 25:236-248.e6. [PMID: 30282032 PMCID: PMC6312700 DOI: 10.1016/j.celrep.2018.08.093] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 08/16/2018] [Accepted: 08/30/2018] [Indexed: 11/30/2022] Open
Abstract
Prevailing dogma holds that ribosomes are uniform in composition and function. Here, we show that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to alter the rRNA composition within the actively translating ribosome pool. The most upregulated operon encodes the unique 16S rRNA, rrsH, distinguished by conserved sequence variation within the small ribosomal subunit. rrsH-bearing ribosomes affect the expression of functionally coherent gene sets and alter the levels of the RpoS sigma factor, the master regulator of the general stress response. These impacts are associated with phenotypic changes in antibiotic sensitivity, biofilm formation, and cell motility and are regulated by stress response proteins, RelA and RelE, as well as the metabolic enzyme and virulence-associated protein, AdhE. These findings establish that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosome function, central aspects of gene expression regulation, and cellular physiology. Most organisms encode multiple, distinct copies of rRNA genes, rendering the composition of the ribosome pool intrinsically heterogeneous. Here, Kurylo et al. show that nutrient limitation in E. coli upregulates the expression of ribosomes bearing conserved sequence variation in 16S rRNA that can regulate gene expression and phenotype.
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Affiliation(s)
- Chad M Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Manuel F Juette
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jordana K Thibado
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - C Theresa Vincent
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA.
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228
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Ramos RS, Casati P, Spampinato CP, Falcone Ferreyra ML. Ribosomal Protein RPL10A Contributes to Early Plant Development and Abscisic Acid-Dependent Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:582353. [PMID: 33250910 PMCID: PMC7674962 DOI: 10.3389/fpls.2020.582353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/01/2020] [Indexed: 05/17/2023]
Abstract
Plant ribosomal proteins play universal roles in translation, although they are also involved in developmental processes and hormone signaling pathways. Among Arabidopsis RPL10 family members, RPL10A exhibits the highest expression during germination and early development, suggesting that RPL10A is the main contributor to these processes. In this work, we first analyzed RPL10A expression pattern in Arabidopsis thaliana using transgenic RPL10Apro:GUS plants. The gene exhibits a ubiquitous expression pattern throughout the plant, but it is most strongly expressed in undifferentiated tissues. Interestingly, gene expression was also detected in stomatal cells. We then examined protein function during seedling establishment and abscisic acid (ABA) response. Heterozygous rpl10A mutant plants show decreased ABA-sensitivity during seed germination, are impaired in early seedling and root development, and exhibit reduced ABA-inhibition of stomatal aperture under light conditions. Overexpression of RPL10A does not affect the germination and seedling growth, but RPL10A-overexpressing lines are more sensitive to ABA during early plant development and exhibit higher stomatal closure under light condition both with and without ABA treatment than wild type plants. Interestingly, RPL10A expression is induced by ABA. Together, we conclude that RPL10A could act as a positive regulator for ABA-dependent responses in Arabidopsis plants.
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229
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Heissenberger C, Liendl L, Nagelreiter F, Gonskikh Y, Yang G, Stelzer EM, Krammer TL, Micutkova L, Vogt S, Kreil DP, Sekot G, Siena E, Poser I, Harreither E, Linder A, Ehret V, Helbich TH, Grillari-Voglauer R, Jansen-Dürr P, Koš M, Polacek N, Grillari J, Schosserer M. Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Nucleic Acids Res 2019; 47:11807-11825. [PMID: 31722427 PMCID: PMC7145617 DOI: 10.1093/nar/gkz1043] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 09/27/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
Modifications of ribosomal RNA expand the nucleotide repertoire and thereby contribute to ribosome heterogeneity and translational regulation of gene expression. One particular m5C modification of 25S ribosomal RNA, which is introduced by Rcm1p, was previously shown to modulate stress responses and lifespan in yeast and other small organisms. Here, we report that NSUN5 is the functional orthologue of Rcm1p, introducing m5C3782 into human and m5C3438 into mouse 28S ribosomal RNA. Haploinsufficiency of the NSUN5 gene in fibroblasts from William Beuren syndrome patients causes partial loss of this modification. The N-terminal domain of NSUN5 is required for targeting to nucleoli, while two evolutionary highly conserved cysteines mediate catalysis. Phenotypic consequences of NSUN5 deficiency in mammalian cells include decreased proliferation and size, which can be attributed to a reduction in total protein synthesis by altered ribosomes. Strikingly, Nsun5 knockout in mice causes decreased body weight and lean mass without alterations in food intake, as well as a trend towards reduced protein synthesis in several tissues. Together, our findings emphasize the importance of single RNA modifications for ribosome function and normal cellular and organismal physiology.
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Affiliation(s)
- Clemens Heissenberger
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Lisa Liendl
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Fabian Nagelreiter
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Yulia Gonskikh
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Guohuan Yang
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Elena M Stelzer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Teresa L Krammer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Lucia Micutkova
- Institute for Biomedical Aging Research, University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Vogt
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - David P Kreil
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Gerhard Sekot
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Emilio Siena
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eva Harreither
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Angela Linder
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Viktoria Ehret
- Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Preclinical Imaging Laboratory, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas H Helbich
- Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Preclinical Imaging Laboratory, Medical University of Vienna, 1090 Vienna, Austria
| | - Regina Grillari-Voglauer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Koš
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Johannes Grillari
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
- Christian Doppler Laboratory on Biotechnology of Skin Aging, 1190 Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, 1200 Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
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230
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Tomal A, Kwasniak-Owczarek M, Janska H. An Update on Mitochondrial Ribosome Biology: The Plant Mitoribosome in the Spotlight. Cells 2019; 8:E1562. [PMID: 31816993 PMCID: PMC6953067 DOI: 10.3390/cells8121562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023] Open
Abstract
Contrary to the widely held belief that mitochondrial ribosomes (mitoribosomes) are highly similar to bacterial ones, recent experimental evidence reveals that mitoribosomes do differ significantly from their bacterial counterparts. This review is focused on plant mitoribosomes, but we also highlight the most striking similarities and differences between the plant and non-plant mitoribosomes. An analysis of the composition and structure of mitoribosomes in trypanosomes, yeast, mammals and plants uncovers numerous organism-specific features. For the plant mitoribosome, the most striking feature is the enormous size of the small subunit compared to the large one. Apart from the new structural information, possible functional peculiarities of different types of mitoribosomes are also discussed. Studies suggest that the protein composition of mitoribosomes is dynamic, especially during development, giving rise to a heterogeneous populations of ribosomes fulfilling specific functions. Moreover, convincing data shows that mitoribosomes interact with components involved in diverse mitochondrial gene expression steps, forming large expressosome-like structures.
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Affiliation(s)
| | | | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.T.); (M.K.-O.)
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231
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Belli V, Matrone N, Sagliocchi S, Incarnato R, Conte A, Pizzo E, Turano M, Angrisani A, Furia M. A dynamic link between H/ACA snoRNP components and cytoplasmic stress granules. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118529. [DOI: 10.1016/j.bbamcr.2019.118529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/08/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023]
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232
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Filippova JA, Matveeva AM, Zhuravlev ES, Balakhonova EA, Prokhorova DV, Malanin SJ, Shah Mahmud R, Grigoryeva TV, Anufrieva KS, Semenov DV, Vlassov VV, Stepanov GA. Are Small Nucleolar RNAs "CRISPRable"? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells. Front Pharmacol 2019; 10:1246. [PMID: 31780925 PMCID: PMC6856654 DOI: 10.3389/fphar.2019.01246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/27/2019] [Indexed: 01/20/2023] Open
Abstract
CRISPR technologies are nowadays widely used for targeted knockout of numerous protein-coding genes and for the study of various processes and metabolic pathways in human cells. Most attention in the genome editing field is now focused on the cleavage of protein-coding genes or genes encoding long non-coding RNAs (lncRNAs), while the studies on targeted knockout of intron-encoded regulatory RNAs are sparse. Small nucleolar RNAs (snoRNAs) present a class of non-coding RNAs encoded within the introns of various host genes and involved in post-transcriptional maturation of ribosomal RNAs (rRNAs) in eukaryotic cells. Box C/D snoRNAs direct 2'-O-methylation of rRNA nucleotides. These short RNAs have specific elements in their structure, namely, boxes C and D, and a target-recognizing region. Here, we present the study devoted to CRISPR/Cas9-mediated editing of box C/D snoRNA genes in Gas5. We obtained monoclonal cell lines carrying mutations in snoRNA genes and analyzed the levels of the mutant box C/D snoRNA as well as the 2'-O-methylation status of the target rRNA nucleotide in the obtained cells. Mutations in SNORD75 in the obtained monoclonal cell line were shown to result in aberrant splicing of Gas5 with exclusion of exons 3 to 5, which was confirmed by RT-PCR and RNA-Seq. The obtained results suggest that SNORD75 contains an element for binding of some factors regulating maturation of Gas5 pre-lncRNA. We suggest that METTL3/METTL14 is among such factors, and m6A-methylation pathways are involved in regulation of Gas5 splicing. Our results shell light on the role of SNORDs in regulating splicing of the host gene.
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Affiliation(s)
- Julia A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya M Matveeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenia A Balakhonova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey J Malanin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Raihan Shah Mahmud
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Tatiana V Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ksenia S Anufrieva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Moscow, Russia.,Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry V Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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233
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Shcherbik N, Pestov DG. The Impact of Oxidative Stress on Ribosomes: From Injury to Regulation. Cells 2019; 8:cells8111379. [PMID: 31684095 PMCID: PMC6912279 DOI: 10.3390/cells8111379] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The ribosome is a complex ribonucleoprotein-based molecular machine that orchestrates protein synthesis in the cell. Both ribosomal RNA and ribosomal proteins can be chemically modified by reactive oxygen species, which may alter the ribosome′s functions or cause a complete loss of functionality. The oxidative damage that ribosomes accumulate during their lifespan in a cell may lead to reduced or faulty translation and contribute to various pathologies. However, remarkably little is known about the biological consequences of oxidative damage to the ribosome. Here, we provide a concise summary of the known types of changes induced by reactive oxygen species in rRNA and ribosomal proteins and discuss the existing experimental evidence of how these modifications may affect ribosome dynamics and function. We emphasize the special role that redox-active transition metals, such as iron, play in ribosome homeostasis and stability. We also discuss the hypothesis that redox-mediated ribosome modifications may contribute to adaptive cellular responses to stress.
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Affiliation(s)
- Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
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234
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Wu N, Nguyen XN, Wang L, Appourchaux R, Zhang C, Panthu B, Gruffat H, Journo C, Alais S, Qin J, Zhang N, Tartour K, Catez F, Mahieux R, Ohlmann T, Liu M, Du B, Cimarelli A. The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation. PLoS Pathog 2019; 15:e1008093. [PMID: 31600344 PMCID: PMC6805002 DOI: 10.1371/journal.ppat.1008093] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/22/2019] [Accepted: 09/18/2019] [Indexed: 01/29/2023] Open
Abstract
ISG20 is a broad spectrum antiviral protein thought to directly degrade viral RNA. However, this mechanism of inhibition remains controversial. Using the Vesicular Stomatitis Virus (VSV) as a model RNA virus, we show here that ISG20 interferes with viral replication by decreasing protein synthesis in the absence of RNA degradation. Importantly, we demonstrate that ISG20 exerts a translational control over a large panel of non-self RNA substrates including those originating from transfected DNA, while sparing endogenous transcripts. This activity correlates with the protein's ability to localize in cytoplasmic processing bodies. Finally, these functions are conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our results posit ISG20 as an important defense factor able to discriminate the self/non-self origins of the RNA through translation modulation.
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Affiliation(s)
- Nannan Wu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Shanghai Emerging and Reemerging Infectious Disease Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xuan-Nhi Nguyen
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Li Wang
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Romain Appourchaux
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Chengfei Zhang
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Baptiste Panthu
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Chloé Journo
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Sandrine Alais
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Juliang Qin
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Na Zhang
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Kevin Tartour
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Frédéric Catez
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Renaud Mahieux
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Theophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Mingyao Liu
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bing Du
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail: (BD); (AC)
| | - Andrea Cimarelli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- * E-mail: (BD); (AC)
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235
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Sulima SO, Dinman JD. The Expanding Riboverse. Cells 2019; 8:cells8101205. [PMID: 31590378 PMCID: PMC6829380 DOI: 10.3390/cells8101205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/25/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Subverting the conventional concept of “the” ribosome, a wealth of information gleaned from recent studies is revealing a much more diverse and dynamic ribosomal reality than has traditionally been thought possible. A diverse array of researchers is collectively illuminating a universe of heterogeneous and adaptable ribosomes harboring differences in composition and regulatory capacity: These differences enable specialization. The expanding universe of ribosomes not only comprises an incredible richness in ribosomal specialization between species, but also within the same tissues and even cells. In this review, we discuss ribosomal heterogeneity and speculate how the emerging understanding of the ribosomal repertoire is impacting the biological sciences today. Targeting pathogen-specific and pathological “diseased” ribosomes promises to provide new treatment options for patients, and potential applications for “designer ribosomes” are within reach. Our deepening understanding of and ability to manipulate the ribosome are establishing both the technological and theoretical foundations for major advances for the 21st century and beyond.
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Affiliation(s)
- Sergey O Sulima
- Biopharmaceutical New Technologies (BioNTech) Corporation, 55131 Mainz, Germany.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA .
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236
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Farley-Barnes KI, Ogawa LM, Baserga SJ. Ribosomopathies: Old Concepts, New Controversies. Trends Genet 2019; 35:754-767. [PMID: 31376929 PMCID: PMC6852887 DOI: 10.1016/j.tig.2019.07.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/30/2022]
Abstract
Ribosomopathies are a diverse subset of diseases caused by reduced expression of, or mutations in, factors necessary for making ribosomes, the protein translation machinery in the cell. Despite the ubiquitous need for ribosomes in all cell types, ribosomopathies manifest with tissue-specific defects and sometimes increased cancer susceptibility, but few treatments target the underlying cause. By highlighting new research in the field, we review current hypotheses for the basis of this tissue specificity. Based on new work, we broaden our understanding of the role of ribosome biogenesis in diverse tissue types throughout embryonic development. We also pose the question of whether previously described human conditions such as aging can be at least partially attributed to defects in making ribosomes.
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Affiliation(s)
- Katherine I Farley-Barnes
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lisa M Ogawa
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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237
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Kong J, Han H, Bergalet J, Bouvrette LPB, Hernández G, Moon NS, Vali H, Lécuyer É, Lasko P. A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster. Sci Rep 2019; 9:13779. [PMID: 31551467 PMCID: PMC6760144 DOI: 10.1038/s41598-019-50357-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
In Drosophila melanogaster there are two genes encoding ribosomal protein S5, RpS5a and RpS5b. Here, we demonstrate that RpS5b is required for oogenesis. Females lacking RpS5b produce ovaries with numerous developmental defects that undergo widespread apoptosis in mid-oogenesis. Females lacking germline RpS5a are fully fertile, but germline expression of interfering RNA targeting germline RpS5a in an RpS5b mutant background worsened the RpS5b phenotype and blocked oogenesis before egg chambers form. A broad spectrum of mRNAs co-purified in immunoprecipitations with RpS5a, while RpS5b-associated mRNAs were specifically enriched for GO terms related to mitochondrial electron transport and cellular metabolic processes. Consistent with this, RpS5b mitochondrial fractions are depleted for proteins linked to oxidative phosphorylation and mitochondrial respiration, and RpS5b mitochondria tended to form large clusters and had more heterogeneous morphology than those from controls. We conclude that RpS5b-containing ribosomes preferentially associate with particular mRNAs and serve an essential function in oogenesis.
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Affiliation(s)
- Jian Kong
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hong Han
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Julie Bergalet
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Louis Philip Benoit Bouvrette
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.,Département de Biochimie, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Greco Hernández
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.,Unit of Biomedical Research on Cancer, National Institute of Cancer, Tlalpan, 14080, Mexico City, Mexico
| | - Nam-Sung Moon
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, Faculty of Dentistry, McGill University, Montréal, QC, Canada
| | - Éric Lécuyer
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.
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238
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Abstract
Reporting in Developmental Cell, Cenik et al. (2019) show that the maternal ribosome supply is sufficient for C. elegans embryonic development, arguing against tissue-specific specialized ribosomes in this context. Examination of ribosomal requirement with the genetic tool kit presented in Artiles et al. (2019) suggests a checkpoint that prevents uncoordinated growth.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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239
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Leipheimer J, Bloom ALM, Panepinto JC. Protein Kinases at the Intersection of Translation and Virulence. Front Cell Infect Microbiol 2019; 9:318. [PMID: 31572689 PMCID: PMC6749009 DOI: 10.3389/fcimb.2019.00318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
As free living organisms, fungi are challenged with a variety of environmental insults that threaten their cellular processes. In some cases, these challenges mimic conditions present within mammals, resulting in the accidental selection of virulence factors over evolutionary time. Be it within a host or the soil, fungi must contend with environmental challenges through the production of stress effector proteins while maintaining factors required for viability in any condition. Initiation and upkeep of this balancing act is mainly under the control of kinases that affect the propensity and selectivity of protein translation. This review will focus on kinases in pathogenic fungi that facilitate a virulence phenotype through translational control.
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Affiliation(s)
- Jay Leipheimer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - John C Panepinto
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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240
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Zhang Y, Shi J, Rassoulzadegan M, Tuorto F, Chen Q. Sperm RNA code programmes the metabolic health of offspring. Nat Rev Endocrinol 2019; 15:489-498. [PMID: 31235802 PMCID: PMC6626572 DOI: 10.1038/s41574-019-0226-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Mammalian sperm RNA is increasingly recognized as an additional source of paternal hereditary information beyond DNA. Environmental inputs, including an unhealthy diet, mental stresses and toxin exposure, can reshape the sperm RNA signature and induce offspring phenotypes that relate to paternal environmental stressors. Our understanding of the categories of sperm RNAs (such as tRNA-derived small RNAs, microRNAs, ribosomal RNA-derived small RNAs and long non-coding RNAs) and associated RNA modifications is expanding and has begun to reveal the functional diversity and information capacity of these molecules. However, the coding mechanism endowed by sperm RNA structures and by RNA interactions with DNA and other epigenetic factors remains unknown. How sperm RNA-encoded information is decoded in early embryos to control offspring phenotypes also remains unclear. Complete deciphering of the 'sperm RNA code' with regard to metabolic control could move the field towards translational applications and precision medicine, and this may lead to prevention of intergenerational transmission of obesity and type 2 diabetes mellitus susceptibility.
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Affiliation(s)
- Yunfang Zhang
- Medical Center of Hematology, The Xinqiao Hospital of Army Medical University, Chongqing, China
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | | | - Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA.
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241
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Chaillou T. Ribosome specialization and its potential role in the control of protein translation and skeletal muscle size. J Appl Physiol (1985) 2019; 127:599-607. [DOI: 10.1152/japplphysiol.00946.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ribosome is typically viewed as a supramolecular complex with constitutive and invariant capacity in mediating translation of mRNA into protein. This view has been challenged by recent research revealing that ribosome composition could be heterogeneous, and this heterogeneity leads to functional ribosome specialization. This review presents the idea that ribosome heterogeneity results from changes in its various components, including variations in ribosomal protein (RP) composition, posttranslational modifications of RPs, changes in ribosomal-associated proteins, alternative forms of rRNA, and posttranscriptional modifications of rRNAs. Ribosome heterogeneity could be orchestrated at several levels and may depend on numerous factors, such as the subcellular location, cell type, tissue specificity, the development state, cell state, ribosome biogenesis, RP turnover, physiological stimuli, and circadian rhythm. Ribosome specialization represents a completely new concept for the regulation of gene expression. Specialized ribosomes could modulate several aspects of translational control, such as mRNA translation selectivity, translation initiation, translational fidelity, and translation elongation. Recent research indicates that the expression of Rpl3 is markedly increased, while that of Rpl3l is highly reduced during mouse skeletal muscle hypertrophy. Moreover, Rpl3l overexpression impairs the growth and myogenic fusion of myotubes. Although the function of Rpl3 and Rpl3l in the ribosome remains to be clarified, these findings suggest that ribosome specialization may be potentially involved in the control of protein translation and skeletal muscle size. Limited data concerning ribosome specialization are currently available in skeletal muscle. Future investigations have the potential to delineate the function of specialized ribosomes in skeletal muscle.
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Affiliation(s)
- Thomas Chaillou
- School of Health Sciences, Örebro University, Örebro, Sweden
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242
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Kandala D, Del Piano A, Minati L, Clamer M. Targeting Translation Activity at the Ribosome Interface with UV-Active Small Molecules. ACS OMEGA 2019; 4:10336-10345. [PMID: 31460127 PMCID: PMC6648492 DOI: 10.1021/acsomega.9b00366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Puromycin is a well-known antibiotic that is used to study the mechanism of protein synthesis and to monitor ribosome activity due to its incorporation into nascent peptide chains. However, puromycin effects outside the ribosome catalytic core remain unexplored. Here, we developed two analogues (3PB and 3PC) of the 3'-end of tyrosylated-tRNA that can efficiently interact with several proteins associated with ribosomes. We biochemically characterized the binding of these analogues and globally mapped the direct small molecule-protein interactions in living cells using clickable and photoreactive puromycin-like probes in combination with in-depth mass spectrometry. We identified a list of proteins targeted by the molecules during ribosome activity (e.g., GRP78), and we addressed possible uses of the probes to sense the activity of protein synthesis and to capture associated RNA. By coupling genome-wide RNA sequencing methods with these molecules, the characterization of unexplored translational control mechanisms will be feasible.
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243
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Anda S, Grallert B. Cell-Cycle-Dependent Regulation of Translation: New Interpretations of Old Observations in Light of New Approaches. Bioessays 2019; 41:e1900022. [PMID: 31210378 DOI: 10.1002/bies.201900022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/29/2019] [Indexed: 12/22/2022]
Abstract
It is a long-standing view that global translation varies during the cell cycle and is much lower in mitosis than in other cell-cycle phases. However, the central papers in the literature are not in agreement about the extent of downregulation in mitosis, ranging from a dramatic decrease to only a marginal reduction. Herein, it is argued that the discrepancy derives from technical challenges. Cell-cycle-dependent variations are most conveniently studied in synchronized cells, but the synchronization methods by themselves often evoke stress responses that, in turn, affect translation rates. Further, it is argued that previously reported cell-cycle-dependent changes in the global translation rate to a large extent reflect responses to the synchronization methods. Recent findings strongly suggest that the global translation rate is not regulated in a cell-cycle-dependent manner. Novel techniques allowing a genome-wide analysis of translational profiles suggest that the extent and importance of selective translational regulation associated with cell-cycle transitions have been underestimated. Therefore, the main question is which messenger RNAs (mRNAs) are translated, rather than whether the global translation rate is decreased.
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Affiliation(s)
- Silje Anda
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
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244
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Timsit Y, Bennequin D. Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives. Int J Mol Sci 2019; 20:ijms20122911. [PMID: 31207893 PMCID: PMC6627100 DOI: 10.3390/ijms20122911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
In the past few decades, studies on translation have converged towards the metaphor of a “ribosome nanomachine”; they also revealed intriguing ribosome properties challenging this view. Many studies have shown that to perform an accurate protein synthesis in a fluctuating cellular environment, ribosomes sense, transfer information and even make decisions. This complex “behaviour” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. We analyse here the significance of this analogy and establish a preliminary link between two fields: ribosome structure-function studies and the analysis of information processing systems. This cross-disciplinary analysis opens new perspectives about the mechanisms of information transfer and processing in ribosomes and may provide new conceptual frameworks for the understanding of the behaviours of unicellular organisms.
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Affiliation(s)
- Youri Timsit
- Mediterranean Institute of Oceanography UM 110, Aix-Marseille Université, CNRS, IRD, Campus de Luminy, 13288 Marseille, France.
| | - Daniel Bennequin
- Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG) Université Paris Diderot, bâtiment Sophie-Germain, 8, place Aurélie Nemours, 75013 Paris, France.
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245
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Mageeney CM, Ware VC. Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster. Mol Biol Cell 2019; 30:2240-2253. [PMID: 31188709 PMCID: PMC6743460 DOI: 10.1091/mbc.e19-02-0086] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The functional significance of ribosome heterogeneity in development and differentiation is relatively unexplored. We present the first in vivo evidence of ribosome heterogeneity playing a role in specific mRNA translation in a multicellular eukaryote. Eukaryotic-specific ribosomal protein paralogues eRpL22 and eRpL22-like are essential in development and required for sperm maturation and fertility in Drosophila. eRpL22 and eRpL22-like roles in spermatogenesis are not completely interchangeable. Flies depleted of eRpL22 and rescued by eRpL22-like overexpression have reduced fertility, confirming that eRpL22-like cannot substitute fully for eRpL22 function, and that paralogues have functionally distinct roles, not yet defined. We investigated the hypothesis that specific RNAs differentially associate with eRpL22 or eRpL22-like ribosomes, thereby establishing distinct ribosomal roles. RNA-seq identified 12,051 transcripts (mRNAs/noncoding RNAs) with 50% being enriched on specific polysome types. Analysis of ∼10% of the most abundant mRNAs suggests ribosome specialization for translating groups of mRNAs expressed at specific stages of spermatogenesis. Further, we show enrichment of “model” eRpL22-like polysome-associated testis mRNAs can occur outside the germline within S2 cells transfected with eRpL22-like, indicating that germline-specific factors are not required for selective translation. This study reveals specialized roles in translation for eRpL22 and eRpL22-like ribosomes in germline differentiation.
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Affiliation(s)
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
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246
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Rodriguez CM, Chun SY, Mills RE, Todd PK. Translation of upstream open reading frames in a model of neuronal differentiation. BMC Genomics 2019; 20:391. [PMID: 31109297 PMCID: PMC6528255 DOI: 10.1186/s12864-019-5775-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Upstream open reading frames (uORFs) initiate translation within mRNA 5' leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling (RP) studies suggest that translating ribosomes are pervasive within 5' leaders across model systems. However, the significance of this observation remains unclear. To explore a role for uORF usage in a model of neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. RESULTS Using a spectral coherence algorithm (SPECtre), we identify 4954 consistently translated uORFs across 31% of all neuroblastoma transcripts. These uORFs predominantly utilize non-AUG initiation codons and exhibit translational efficiencies (TE) comparable to annotated coding regions. On a population basis, the global impact of both AUG and non-AUG initiated uORFs on basal CDS translation were small, even when analysis is limited to conserved and consistently translated uORFs. However, uORFs did alter the translation of a subset of genes, including the Diamond-Blackfan Anemia associated ribosomal gene RPS24. With retinoic acid induced differentiation, we observed an overall positive correlation in translational shifts between uORF/CDS pairs. However, CDSs downstream of uORFs show smaller shifts in TE with differentiation relative to CDSs without a predicted uORF, suggesting that uORF translation buffers cell state dependent fluctuations in CDS translation. CONCLUSION This work provides insights into the dynamic relationships and potential regulatory functions of uORF/CDS pairs in a model of neuronal differentiation.
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Affiliation(s)
- Caitlin M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Sang Y Chun
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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247
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Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? RNA (NEW YORK, N.Y.) 2019; 25:521-538. [PMID: 30733326 PMCID: PMC6467006 DOI: 10.1261/rna.069823.118] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
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Affiliation(s)
- Max B Ferretti
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
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248
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Andreyeva EN, Ogienko AA, Yushkova AA, Popova JV, Pavlova GA, Kozhevnikova EN, Ivankin AV, Gatti M, Pindyurin AV. Non3 is an essential Drosophila gene required for proper nucleolus assembly. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nucleolus is a dynamic non-membrane-bound nuclear organelle, which plays key roles not only in ribosome biogenesis but also in many other cellular processes. Consistent with its multiple functions, the nucleolus has been implicated in many human diseases, including cancer and degenerative pathologies of the nervous system and heart. Here, we report the characterization of the Drosophila Non3 (Novel nucleolar protein 3) gene, which encodes a protein homologous to the human Brix domain-containing Rpf2 that has been shown to control ribosomal RNA (rRNA) processing. We used imprecise P-element excision to generate four new mutant alleles in the Non3 gene. Complementation and phenotypic analyses showed that these Non3 mutations can be arranged in an allelic series that includes both viable and lethal alleles. The strongest lethal allele (Non3∆600) is a genetically null allele that carries a large deletion of the gene and exhibits early lethality when homozygous. Flies heterozygous for Non3∆600 occasionally exhibit a mild reduction in the bristle size, but develop normally and are fertile. However, heteroallelic combinations of viable Non3 mutations (Non3197, Non3310 and Non3259) display a Minute-like phenotype, consisting in delayed development and short and thin bristles, suggesting that they are defective in ribosome biogenesis. We also demonstrate that the Non3 protein localizes to the nucleolus of larval brain cells and it is required for proper nucleolar localization of Fibrillarin, a protein important for post-translational modification and processing of rRNAs. In summary, we generated a number of genetic and biochemical tools that were exploited for an initial characterization of Non3, and will be instrumental for future functional studies on this gene and its protein product.
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Affiliation(s)
| | - A. A. Ogienko
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - A. A. Yushkova
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University
| | - J. V. Popova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - E. N. Kozhevnikova
- Institute of Molecular and Cellular Biology, SB RAS; Institute of Cytology and Genetics, SB RAS
| | | | - M. Gatti
- Institute of Molecular and Cellular Biology, SB RAS; IBPM CNR and Department of Biology and Biotechnology, Sapienza University of Rome
| | - A. V. Pindyurin
- Institute of Molecular and Cellular Biology, SB RAS; Novosibirsk State University; Institute of Cytology and Genetics, SB RAS
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Sulima SO, Kampen KR, De Keersmaecker K. Cancer Biogenesis in Ribosomopathies. Cells 2019; 8:E229. [PMID: 30862070 PMCID: PMC6468915 DOI: 10.3390/cells8030229] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/23/2022] Open
Abstract
Ribosomopathies are congenital diseases with defects in ribosome assembly and are characterized by elevated cancer risks. Additionally, somatic mutations in ribosomal proteins have recently been linked to a variety of cancers. Despite a clear correlation between ribosome defects and cancer, the molecular mechanisms by which these defects promote tumorigenesis are unclear. In this review, we focus on the emerging mechanisms that link ribosomal defects in ribosomopathies to cancer progression. This includes functional "onco-specialization" of mutant ribosomes, extra-ribosomal consequences of mutations in ribosomal proteins and ribosome assembly factors, and effects of ribosomal mutations on cellular stress and metabolism. We integrate some of these recent findings in a single model that can partially explain the paradoxical transition from hypo- to hyperproliferation phenotypes, as observed in ribosomopathies. Finally, we discuss the current and potential strategies, and the associated challenges for therapeutic intervention in ribosome-mutant diseases.
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim R Kampen
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
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