1
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Senn KA, Hoskins AA. Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1866. [PMID: 38972853 DOI: 10.1002/wrna.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pre-mRNA splicing, the removal of introns and ligation of flanking exons, is a crucial step in eukaryotic gene expression. The spliceosome, a macromolecular complex made up of five small nuclear RNAs (snRNAs) and dozens of proteins, assembles on introns via a complex pathway before catalyzing the two transesterification reactions necessary for splicing. All of these steps have the potential to be highly regulated to ensure correct mRNA isoform production for proper cellular function. While Saccharomyces cerevisiae (yeast) has a limited set of intron-containing genes, many of these genes are highly expressed, resulting in a large number of transcripts in a cell being spliced. As a result, splicing regulation is of critical importance for yeast. Just as in humans, yeast splicing can be influenced by protein components of the splicing machinery, structures and properties of the pre-mRNA itself, or by the action of trans-acting factors. It is likely that further analysis of the mechanisms and pathways of splicing regulation in yeast can reveal general principles applicable to other eukaryotes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Katherine Anne Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Ng AYE, Chan SN, Pek JW. Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep 2024; 43:114228. [PMID: 38735045 DOI: 10.1016/j.celrep.2024.114228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore.
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3
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Kitamura D, Taniguchi K, Nakamura M, Igaki T. In vivo evidence for homeostatic regulation of ribosomal protein levels in Drosophila. Cell Struct Funct 2024; 49:11-20. [PMID: 38199250 DOI: 10.1247/csf.23088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
The ribosome is a molecular machine essential for protein synthesis, which is composed of approximately 80 different ribosomal proteins (Rps). Studies in yeast and cell culture systems have revealed that the intracellular level of Rps is finely regulated by negative feedback mechanisms or ubiquitin-proteasome system, which prevents over- or under-abundance of Rps in the cell. However, in vivo evidence for the homeostatic regulation of intracellular Rp levels has been poor. Here, using Drosophila genetics, we show that intracellular Rp levels are regulated by proteasomal degradation of excess Rps that are not incorporated into the ribosome. By establishing an EGFP-fused Rp gene system that can monitor endogenously expressed Rp levels, we found that endogenously expressed EGFP-RpS20 or -RpL5 is eliminated from the cell when RpS20 or RpL5 is exogenously expressed. Notably, the level of endogenously expressed Hsp83, a housekeeping gene, was not affected by exogenous expression of Hsp83, suggesting that the strict negative regulation of excess protein is specific for intracellular Rps. Further analyses revealed that the maintenance of cellular Rp levels is not regulated at the transcriptional level but by proteasomal degradation of excess free Rps as a protein quality control mechanism. Our observations provide not only the in vivo evidence for the homeostatic regulation of Rp levels but also a novel genetic strategy to study in vivo regulation of intracellular Rp levels and its role in tissue homeostasis via cell competition.Key words: ribosomal protein, proteasomal degradation, Drosophila.
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Affiliation(s)
- Daiki Kitamura
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University
| | | | - Mai Nakamura
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University
| | - Tatsushi Igaki
- Laboratory of Genetics, Graduate School of Biostudies, Kyoto University
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4
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Roy KR, Gabunilas J, Neutel D, Ai M, Yeh Z, Samson J, Lyu G, Chanfreau GF. Splicing factor Prp18p promotes genome-wide fidelity of consensus 3'-splice sites. Nucleic Acids Res 2023; 51:12428-12442. [PMID: 37956322 PMCID: PMC10711555 DOI: 10.1093/nar/gkad968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The fidelity of splice site selection is critical for proper gene expression. In particular, proper recognition of 3'-splice site (3'SS) sequences by the spliceosome is challenging considering the low complexity of the 3'SS consensus sequence YAG. Here, we show that absence of the Prp18p splicing factor results in genome-wide activation of alternative 3'SS in S. cerevisiae, including highly unusual non-YAG sequences. Usage of these non-canonical 3'SS in the absence of Prp18p is enhanced by upstream poly(U) tracts and by their potential to interact with the first intronic nucleoside, allowing them to dock in the spliceosome active site instead of the normal 3'SS. The role of Prp18p in 3'SS fidelity is facilitated by interactions with Slu7p and Prp8p, but cannot be fulfilled by Slu7p, identifying a unique role for Prp18p in 3'SS fidelity. This fidelity function is synergized by the downstream proofreading activity of the Prp22p helicase, but is independent from another late splicing helicase, Prp43p. Our results show that spliceosomes exhibit remarkably relaxed 3'SS sequence usage in the absence of Prp18p and identify a network of spliceosomal interactions centered on Prp18p which are required to promote the fidelity of the recognition of consensus 3'SS sequences.
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Affiliation(s)
- Kevin R Roy
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Dean Neutel
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Michelle Ai
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Zoe Yeh
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Joyce Samson
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Guochang Lyu
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
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5
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Weinstein HN, Hu K, Fish L, Chen YA, Allegakoen P, Hui KSF, Pham JH, Baco MB, Song H, Giacomelli AO, Vazquez F, Ghandi M, Goodarzi H, Huang FW. RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570873. [PMID: 38106152 PMCID: PMC10723389 DOI: 10.1101/2023.12.10.570873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Microsatellite instability high (MSI-H) tumors are malignant tumors that, despite harboring a high mutational burden, often have intact TP53. One of the most frequent mutations in MSI-H tumors is a frameshift mutation in RPL22, a ribosomal protein. Here, we identified RPL22 as a modulator of MDM4 splicing through an alternative splicing switch in exon 6. RPL22 loss increases MDM4 exon 6 inclusion, cell proliferation, and augments resistance to the MDM inhibitor Nutlin-3a. RPL22 represses expression of its paralog, RPL22L1, by mediating the splicing of a cryptic exon corresponding to a truncated transcript. Therefore, damaging mutations in RPL22 drive oncogenic MDM4 induction and reveal a common splicing circuit in MSI-H tumors that may inform therapeutic targeting of the MDM4-p53 axis and oncogenic RPL22L1 induction.
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Affiliation(s)
- Hannah N.W. Weinstein
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Kevin Hu
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Lisa Fish
- Department of Biochemistry and Biophysics, University of California; San Francisco, USA
| | - Yih-An Chen
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Paul Allegakoen
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Keliana S. F. Hui
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | - Julia H. Pham
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | | | - Hanbing Song
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
| | | | | | | | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California; San Francisco, USA
| | - Franklin W. Huang
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Bakar Computational Health Sciences Institute, Institute for Human Genetics, University of California; San Francisco, USA
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6
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Milenkovic I, Santos Vieira HG, Lucas MC, Ruiz-Orera J, Patone G, Kesteven S, Wu J, Feneley M, Espadas G, Sabidó E, Hübner N, van Heesch S, Völkers M, Novoa EM. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res 2023; 51:5301-5324. [PMID: 36882085 PMCID: PMC10287911 DOI: 10.1093/nar/gkad121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
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Affiliation(s)
- Ivan Milenkovic
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Scott Kesteven
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Michael Feneley
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
- Charité -Universitätsmedizin, D-10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, D-13347 Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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7
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Roy KR, Gabunilas J, Neutel D, Ai M, Samson J, Lyu G, Chanfreau GF. Spliceosomal mutations decouple 3' splice site fidelity from cellular fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523824. [PMID: 36711521 PMCID: PMC9882110 DOI: 10.1101/2023.01.12.523824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The fidelity of splice site selection is thought to be critical for proper gene expression and cellular fitness. In particular, proper recognition of 3'-splice site (3'SS) sequences by the spliceosome is a daunting task considering the low complexity of the 3'SS consensus sequence YAG. Here we show that inactivating the near-essential splicing factor Prp18p results in a global activation of alternative 3'SS, many of which harbor sequences that highly diverge from the YAG consensus, including some highly unusual non-AG 3'SS. We show that the role of Prp18p in 3'SS fidelity is promoted by physical interactions with the essential splicing factors Slu7p and Prp8p and synergized by the proofreading activity of the Prp22p helicase. Strikingly, structure-guided point mutations that disrupt Prp18p-Slu7p and Prp18p-Prp8p interactions mimic the loss of 3'SS fidelity without any impact on cellular growth, suggesting that accumulation of incorrectly spliced transcripts does not have a major deleterious effect on cellular viability. These results show that spliceosomes exhibit remarkably relaxed fidelity in the absence of Prp18p, and that new 3'SS sampling can be achieved genome-wide without a major negative impact on cellular fitness, a feature that could be used during evolution to explore new productive alternative splice sites.
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8
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Pillet B, Méndez-Godoy A, Murat G, Favre S, Stumpe M, Falquet L, Kressler D. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. eLife 2022; 11:74255. [PMID: 35357307 PMCID: PMC8970588 DOI: 10.7554/elife.74255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/22/2022] [Indexed: 12/17/2022] Open
Abstract
The biogenesis of eukaryotic ribosomes involves the ordered assembly of around 80 ribosomal proteins. Supplying equimolar amounts of assembly-competent ribosomal proteins is complicated by their aggregation propensity and the spatial separation of their location of synthesis and pre-ribosome incorporation. Recent evidence has highlighted that dedicated chaperones protect individual, unassembled ribosomal proteins on their path to the pre-ribosomal assembly site. Here, we show that the co-translational recognition of Rpl3 and Rpl4 by their respective dedicated chaperone, Rrb1 or Acl4, reduces the degradation of the encoding RPL3 and RPL4 mRNAs in the yeast Saccharomyces cerevisiae. In both cases, negative regulation of mRNA levels occurs when the availability of the dedicated chaperone is limited and the nascent ribosomal protein is instead accessible to a regulatory machinery consisting of the nascent-polypeptide-associated complex and the Caf130-associated Ccr4-Not complex. Notably, deregulated expression of Rpl3 and Rpl4 leads to their massive aggregation and a perturbation of overall proteostasis in cells lacking the E3 ubiquitin ligase Tom1. Taken together, we have uncovered an unprecedented regulatory mechanism that adjusts the de novo synthesis of Rpl3 and Rpl4 to their actual consumption during ribosome assembly and, thereby, protects cells from the potentially detrimental effects of their surplus production. Living cells are packed full of molecules known as proteins, which perform many vital tasks the cells need to survive and grow. Machines called ribosomes inside the cells use template molecules called messenger RNAs (or mRNAs for short) to produce proteins. The newly-made proteins then have to travel to a specific location in the cell to perform their tasks. Some newly-made proteins are prone to forming clumps, so cells have other proteins known as chaperones that ensure these clumps do not form. The ribosomes themselves are made up of several proteins, some of which are also prone to clumping as they are being produced. To prevent this from happening, cells control how many ribosomal proteins they make, so there are just enough to form the ribosomes the cell needs at any given time. Previous studies found that, in yeast, two ribosomal proteins called Rpl3 and Rpl4 each have their own dedicated chaperone to prevent them from clumping. However, it remained unclear whether these chaperones are also involved in regulating the levels of Rpl3 and Rpl4. To address this question, Pillet et al. studied both of these dedicated chaperones in yeast cells. The experiments showed that the chaperones bound to their target proteins (either units of Rpl3 or Rpl4) as they were being produced on the ribosomes. This protected the template mRNAs the ribosomes were using to produce these proteins from being destroyed, thus allowing further units of Rpl3 and Rpl4 to be produced. When enough Rpl3 and Rpl4 units were made, there were not enough of the chaperones to bind them all, leaving the mRNA templates unprotected. This led to the destruction of the mRNA templates, which decreased the numbers of Rpl3 and Rpl4 units being produced. The work of Pillet et al. reveals a feedback mechanism that allows yeast to tightly control the levels of Rpl3 and Rpl4. In the future, these findings may help us understand diseases caused by defects in ribosomal proteins, such as Diamond-Blackfan anemia, and possibly also neurodegenerative diseases caused by clumps of proteins forming in cells. The next step will be to find out whether the mechanism uncovered by Pillet et al. also exists in human and other mammalian cells.
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Affiliation(s)
- Benjamin Pillet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Guillaume Murat
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Sébastien Favre
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Metabolomics and Proteomics Platform, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, University of Fribourg, Fribourg, Switzerland
| | - Dieter Kressler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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9
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [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: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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10
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Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A. Control of ribosomal protein synthesis by the Microprocessor complex. Sci Signal 2021; 14:14/671/eabd2639. [PMID: 33622983 DOI: 10.1126/scisignal.abd2639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosome biogenesis in eukaryotes requires the coordinated production and assembly of 80 ribosomal proteins and four ribosomal RNAs (rRNAs), and its rate must be synchronized with cellular growth. Here, we showed that the Microprocessor complex, which mediates the first step of microRNA processing, potentiated the transcription of ribosomal protein genes by eliminating DNA/RNA hybrids known as R-loops. Nutrient deprivation triggered the nuclear export of Drosha, a key component of the Microprocessor complex, and its subsequent degradation by the E3 ubiquitin ligase Nedd4, thereby reducing ribosomal protein production and protein synthesis. In mouse erythroid progenitors, conditional deletion of Drosha led to the reduced production of ribosomal proteins, translational inhibition of the mRNA encoding the erythroid transcription factor Gata1, and impaired erythropoiesis. This phenotype mirrored the clinical presentation of human "ribosomopathies." Thus, the Microprocessor complex plays a pivotal role in synchronizing protein synthesis capacity with cellular growth rate and is a potential drug target for anemias caused by ribosomal insufficiency.
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Affiliation(s)
- Xuan Jiang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amit Prabhakar
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie M Van der Voorn
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medical Physiology, University Medical Center Utrecht, Utrecht, 3584 CM, Netherlands
| | - Prajakta Ghatpande
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chuwen Lin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Giorgio Lagna
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
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11
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Roy B, Granas D, Bragg F, Cher JAY, White MA, Stormo GD. Autoregulation of yeast ribosomal proteins discovered by efficient search for feedback regulation. Commun Biol 2020; 3:761. [PMID: 33311538 PMCID: PMC7732827 DOI: 10.1038/s42003-020-01494-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 11/15/2020] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional autoregulation of gene expression is common in bacteria but many fewer examples are known in eukaryotes. We used the yeast collection of genes fused to GFP as a rapid screen for examples of feedback regulation in ribosomal proteins by overexpressing a non-regulatable version of a gene and observing the effects on the expression of the GFP-fused version. We tested 95 ribosomal protein genes and found a wide continuum of effects, with 30% showing at least a 3-fold reduction in expression. Two genes, RPS22B and RPL1B, showed over a 10-fold repression. In both cases the cis-regulatory segment resides in the 5’ UTR of the gene as shown by placing that segment of the mRNA upstream of GFP alone and demonstrating it is sufficient to cause repression of GFP when the protein is over-expressed. Further analyses showed that the intron in the 5’ UTR of RPS22B is required for regulation, presumably because the protein inhibits splicing that is necessary for translation. The 5’ UTR of RPL1B contains a sequence and structure motif that is conserved in the binding sites of Rpl1 orthologs from bacteria to mammals, and mutations within the motif eliminate repression. Here, the authors screen for feedback regulation of ribosomal proteins by overexpressing a non- regulatable version of a gene and observing its effects on the expression of the GFP-fused version. They find that 30% show at least a 3-fold reduction in expression and two genes show a 10-fold reduction with the regulatory site being in the 5’ untranslated region of the gene.
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Affiliation(s)
- Basab Roy
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - David Granas
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Fredrick Bragg
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Jonathan A Y Cher
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Michael A White
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gary D Stormo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, 63110, USA.
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12
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Weathers I, Gabunilas J, Samson J, Roy K, Chanfreau GF. Protocol for High-Resolution Mapping of Splicing Products and Isoforms by RT-PCR Using Fluorescently Labeled Primers. STAR Protoc 2020; 1:100140. [PMID: 33377034 PMCID: PMC7757285 DOI: 10.1016/j.xpro.2020.100140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe an RT-PCR protocol that allows high-resolution mapping of splicing products and isoforms using fluorescently labeled primers. Each species contains one fluorescent group allowing a direct comparison of the different isoforms despite size differences. A custom-size ladder enables the precise determination of cDNA lengths and discrimination of isoforms differing by less than five nucleotides on polyacrylamide gels. This protocol also allows the detection of products from in vitro splicing reactions, circumventing the need to use radiolabeled transcripts. For complete details on the use and execution of this protocol, please refer to Gabunilas and Chanfreau (2016).
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Affiliation(s)
- Indya Weathers
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Joyce Samson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Guillaume F. Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
- Corresponding author
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13
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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14
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Müller-McNicoll M, Rossbach O, Hui J, Medenbach J. Auto-regulatory feedback by RNA-binding proteins. J Mol Cell Biol 2020; 11:930-939. [PMID: 31152582 PMCID: PMC6884704 DOI: 10.1093/jmcb/mjz043] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) are key regulators in post-transcriptional control of gene expression. Mutations that alter their activity or abundance have been implicated in numerous diseases such as neurodegenerative disorders and various types of cancer. This highlights the importance of RBP proteostasis and the necessity to tightly control the expression levels and activities of RBPs. In many cases, RBPs engage in an auto-regulatory feedback by directly binding to and influencing the fate of their own mRNAs, exerting control over their own expression. For this feedback control, RBPs employ a variety of mechanisms operating at all levels of post-transcriptional regulation of gene expression. Here we review RBP-mediated autogenous feedback regulation that either serves to maintain protein abundance within a physiological range (by negative feedback) or generates binary, genetic on/off switches important for e.g. cell fate decisions (by positive feedback).
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Affiliation(s)
- Michaela Müller-McNicoll
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 13, D-60438 Frankfurt am Main, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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15
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Ianiri G, Fang YF, Dahlmann TA, Clancey SA, Janbon G, Kück U, Heitman J. Mating-Type-Specific Ribosomal Proteins Control Aspects of Sexual Reproduction in Cryptococcus neoformans. Genetics 2020; 214:635-649. [PMID: 31882399 PMCID: PMC7054023 DOI: 10.1534/genetics.119.302740] [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: 09/19/2019] [Accepted: 12/21/2019] [Indexed: 12/31/2022] Open
Abstract
The MAT locus of Cryptococcus neoformans has a bipolar organization characterized by an unusually large structure, spanning over 100 kb. MAT genes have been characterized by functional genetics as being involved in sexual reproduction and virulence. However, classical gene replacement failed to achieve mutants for five MAT genes (RPL22, RPO41, MYO2, PRT1, and RPL39), indicating that they are likely essential. In the present study, targeted gene replacement was performed in a diploid strain for both the α and a alleles of the ribosomal genes RPL22 and RPL39 Mendelian analysis of the progeny confirmed that both RPL22 and RPL39 are essential for viability. Ectopic integration of the RPL22 allele of opposite MAT identity in the heterozygous RPL22a/rpl22αΔ or RPL22α/rpl22aΔ mutant strains failed to complement their essential phenotype. Evidence suggests that this is due to differential expression of the RPL22 genes, and an RNAi-dependent mechanism that contributes to control RPL22a expression. Furthermore, via CRISPR/Cas9 technology, the RPL22 alleles were exchanged in haploid MATα and MATa strains of C. neoformans These RPL22 exchange strains displayed morphological and genetic defects during bilateral mating. These results contribute to elucidating functions of C. neoformans essential mating type genes that may constitute a type of imprinting system to promote inheritance of nuclei of both mating types.
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Affiliation(s)
- Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Yufeng Francis Fang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, 75015 Paris, France
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
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16
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Levi O, Arava Y. mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels. PLoS Biol 2019; 17:e3000274. [PMID: 31100060 PMCID: PMC6542539 DOI: 10.1371/journal.pbio.3000274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/30/2019] [Accepted: 05/02/2019] [Indexed: 12/25/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are well studied for their role in binding and charging tRNAs with cognate amino acids. Recent RNA interactome studies had suggested that these enzymes can also bind polyadenylated RNAs. Here, we explored the mRNA repertoire bound by several yeast aaRSs. RNA immunoprecipitation (RIP) followed by deep sequencing revealed unique sets of mRNAs bound by each aaRS. Interestingly, for every tested aaRSs, a preferential association with its own mRNA was observed, suggesting an autoregulatory process. Self-association of histidyl-tRNA synthetase (HisRS) was found to be mediated primarily through binding to a region predicted to fold into a tRNAHis anticodon-like structure. Introducing point mutations that are expected to disassemble this putative anticodon mimic alleviated self-association, concomitant with increased synthesis of the protein. Finally, we found that increased cellular levels of uncharged tRNAHis lead to reduced self-association and increased HisRS translation, in a manner that depends on the anticodon-like element. Together, these results reveal a novel post-transcriptional autoregulatory mechanism that exploits binding mimicry to control mRNA translation according to tRNA demands. Better known for their enzymatic role in charging tRNAs with their cognate amino acids, this study shows that tRNA synthetases also bind mRNAs, regulating translation in order to balance the production of a tRNA synthetase with the level of its cognate tRNA.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yoav Arava
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
- * E-mail:
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17
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Taggart JC, Li GW. Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes. Cell Syst 2018; 7:580-589.e4. [PMID: 30553725 PMCID: PMC6659121 DOI: 10.1016/j.cels.2018.11.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/05/2018] [Accepted: 11/18/2018] [Indexed: 01/02/2023]
Abstract
Constituents of multiprotein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here, we quantified the production rates of multiprotein complexes in unicellular and multicellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities, which occur for a large fraction of ribosome footprints and distort quantitation accuracy in eukaryotes, we found that obligate components of multiprotein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution toward quantitative control at every step in the central dogma.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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18
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Mageeney CM, Kearse MG, Gershman BW, Pritchard CE, Colquhoun JM, Ware VC. Functional interplay between ribosomal protein paralogues in the eRpL22 family in Drosophila melanogaster. Fly (Austin) 2018; 12:143-163. [PMID: 30465696 DOI: 10.1080/19336934.2018.1549419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Duplicated ribosomal protein (RP) genes in the Drosophila melanogaster eRpL22 family encode structurally-divergent and differentially-expressed rRNA-binding RPs. eRpL22 is expressed ubiquitously and eRpL22-like expression is tissue-restricted with highest levels in the adult male germline. We explored paralogue functional equivalence using the GAL4-UAS system for paralogue knockdown or overexpression and a conditional eRpL22-like knockout in a heat- shock flippase/FRT line. Ubiquitous eRpL22 knockdown with Actin-GAL4 resulted in embryonic lethality, confirming eRpL22 essentiality. eRpL22-like knockdown (60%) was insufficient to cause lethality; yet, conditional eRpL22-like knockout at one hour following egg deposition caused lethality within each developmental stage. Therefore, each paralogue is essential. Variation in timing of heat-shock-induced eRpL22-like knockout highlighted early embryogenesis as the critical period where eRpL22-like expression (not compensated for by eRpL22) is required for normal development of several organ systems, including testis development and subsequent sperm production. To determine if eRpL22-like can substitute for eRpL22, we used Actin-GAL4 for ubiquitous eRpL22 knockdown and eRpL22-like-FLAG (or FLAG-eRpL22: control) overexpression. Emergence of adults demonstrated that ubiquitous eRpL22-like-FLAG or FLAG-eRpL22 expression eliminates embryonic lethality resulting from eRpL22 depletion. Adults rescued by eRpL22-like-FLAG (but not by FLAG-eRpL22) overexpression had reduced fertility and longevity. We conclude that eRpL22 paralogue roles are not completely interchangeable and include functionally-diverse roles in development and spermatogenesis. Testis-specific paralogue knockdown revealed molecular phenotypes, including increases in eRpL22 protein and mRNA levels following eRpL22-like depletion, implicating a negative crosstalk mechanism regulating eRpL22 expression. Paralogue depletion unmasked mechanisms, yet to be defined that impact paralogue co-expression within germ cells.
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Affiliation(s)
| | - Michael G Kearse
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
| | - Brett W Gershman
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
| | | | | | - Vassie C Ware
- a Department of Biological Sciences , Lehigh University , Bethlehem , PA , USA
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19
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Abrhámová K, Nemčko F, Libus J, Převorovský M, Hálová M, Půta F, Folk P. Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast. PLoS One 2018; 13:e0190685. [PMID: 29304067 PMCID: PMC5755908 DOI: 10.1371/journal.pone.0190685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 12/19/2017] [Indexed: 01/04/2023] Open
Abstract
Ribosomal protein genes (RPGs) in Saccharomyces cerevisiae are a remarkable regulatory group that may serve as a model for understanding genetic redundancy in evolutionary adaptations. Most RPGs exist as pairs of highly conserved functional paralogs with divergent untranslated regions and introns. We examined the roles of introns in strains with various combinations of intron and gene deletions in RPL22, RPL2, RPL16, RPL37, RPL17, RPS0, and RPS18 paralog pairs. We found that introns inhibited the expression of their genes in the RPL22 pair, with the RPL22B intron conferring a much stronger effect. While the WT RPL22A/RPL22B mRNA ratio was 93/7, the rpl22aΔi/RPL22B and RPL22A/rpl22bΔi ratios were >99/<1 and 60/40, respectively. The intron in RPL2A stimulated the expression of its own gene, but the removal of the other introns had little effect on expression of the corresponding gene pair. Rpl22 protein abundances corresponded to changes in mRNAs. Using splicing reporters containing endogenous intron sequences, we demonstrated that these effects were due to the inhibition of splicing by Rpl22 proteins but not by their RNA-binding mutant versions. Indeed, only WT Rpl22A/Rpl22B proteins (but not the mutants) interacted in a yeast three-hybrid system with an RPL22B intronic region between bp 165 and 236. Transcriptome analysis showed that both the total level of Rpl22 and the A/B ratio were important for maintaining the WT phenotype. The data presented here support the contention that the Rpl22B protein has a paralog-specific role. The RPL22 singleton of Kluyveromyces lactis, which did not undergo whole genome duplication, also responded to Rpl22-mediated inhibition in K. lactis cells. Vice versa, the overproduction of the K. lactis protein reduced the expression of RPL22A/B in S. cerevisiae. The extraribosomal function of of the K. lactis Rpl22 suggests that the loop regulating RPL22 paralogs of S. cerevisiae evolved from autoregulation.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Filip Nemčko
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Libus
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Hálová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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20
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Segev N, Gerst JE. Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins. J Cell Biol 2017; 217:117-126. [PMID: 29118025 PMCID: PMC5748985 DOI: 10.1083/jcb.201706059] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/19/2017] [Accepted: 10/17/2017] [Indexed: 12/23/2022] Open
Abstract
Ribosomal proteins exist mainly as paralog pairs in eukaryotes, yet the reasons for maintaining duplication are unclear. By using a novel proteomic approach, Segev and Gerst show paralog-specific regulation of the translation of mitochondrial proteins using specialized ribosomes. Genome duplication in eukaryotes created paralog pairs of ribosomal proteins (RPs) that show high sequence similarity/identity. However, individual paralogs can confer vastly different effects upon cellular processes, e.g., specific yeast paralogs regulate actin organization, bud site selection, and mRNA localization, although how specificity is conferred is unknown. Changes in the RP composition of ribosomes might allow for specialized translation of different subsets of mRNAs, yet it is unclear whether specialized ribosomes exist and if paralog specificity controls translation. Using translatome analyses, we show that the translation of mitochondrial proteins is highly down-regulated in yeast lacking RP paralogs required for normal mitochondrial function (e.g., RPL1b). Although RPL1a and RPL1b encode identical proteins, Rpl1b-containing ribosomes confer more efficient translation of respiration-related proteins. Thus, ribosomes varying in RP composition may confer specialized functions, and RP paralog specificity defines a novel means of translational control.
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Affiliation(s)
- Nadav Segev
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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21
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Mathew V, Tam AS, Milbury KL, Hofmann AK, Hughes CS, Morin GB, Loewen CJR, Stirling PC. Selective aggregation of the splicing factor Hsh155 suppresses splicing upon genotoxic stress. J Cell Biol 2017; 216:4027-4040. [PMID: 28978642 PMCID: PMC5716266 DOI: 10.1083/jcb.201612018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 07/17/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022] Open
Abstract
Upon genotoxic stress, dynamic relocalization events control DNA repair as well as alterations of the transcriptome and proteome, enabling stress recovery. How these events may influence one another is only partly known. Beginning with a cytological screen of genome stability proteins, we find that the splicing factor Hsh155 disassembles from its partners and localizes to both intranuclear and cytoplasmic protein quality control (PQC) aggregates under alkylation stress. Aggregate sequestration of Hsh155 occurs at nuclear and then cytoplasmic sites in a manner that is regulated by molecular chaperones and requires TORC1 activity signaling through the Sfp1 transcription factor. This dynamic behavior is associated with intron retention in ribosomal protein gene transcripts, a decrease in splicing efficiency, and more rapid recovery from stress. Collectively, our analyses suggest a model in which some proteins evicted from chromatin and undergoing transcriptional remodeling during stress are targeted to PQC sites to influence gene expression changes and facilitate stress recovery.
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Affiliation(s)
- Veena Mathew
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Karissa L Milbury
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Analise K Hofmann
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Christopher S Hughes
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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22
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Awad AM, Venkataramanan S, Nag A, Galivanche AR, Bradley MC, Neves LT, Douglass S, Clarke CF, Johnson TL. Chromatin-remodeling SWI/SNF complex regulates coenzyme Q 6 synthesis and a metabolic shift to respiration in yeast. J Biol Chem 2017; 292:14851-14866. [PMID: 28739803 DOI: 10.1074/jbc.m117.798397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/17/2017] [Indexed: 12/13/2022] Open
Abstract
Despite its relatively streamlined genome, there are many important examples of regulated RNA splicing in Saccharomyces cerevisiae Here, we report a role for the chromatin remodeler SWI/SNF in respiration, partially via the regulation of splicing. We find that a nutrient-dependent decrease in Snf2 leads to an increase in splicing of the PTC7 transcript. The spliced PTC7 transcript encodes a mitochondrial phosphatase regulator of biosynthesis of coenzyme Q6 (ubiquinone or CoQ6) and a mitochondrial redox-active lipid essential for electron and proton transport in respiration. Increased splicing of PTC7 increases CoQ6 levels. The increase in PTC7 splicing occurs at least in part due to down-regulation of ribosomal protein gene expression, leading to the redistribution of spliceosomes from this abundant class of intron-containing RNAs to otherwise poorly spliced transcripts. In contrast, a protein encoded by the nonspliced isoform of PTC7 represses CoQ6 biosynthesis. Taken together, these findings uncover a link between Snf2 expression and the splicing of PTC7 and establish a previously unknown role for the SWI/SNF complex in the transition of yeast cells from fermentative to respiratory modes of metabolism.
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Affiliation(s)
- Agape M Awad
- From the Department of Chemistry and Biochemistry.,the Molecular Biology Institute, and
| | - Srivats Venkataramanan
- the Molecular Biology Institute, and.,the Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, California 90095
| | - Anish Nag
- From the Department of Chemistry and Biochemistry.,the Molecular Biology Institute, and
| | - Anoop Raj Galivanche
- the Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, California 90095
| | - Michelle C Bradley
- From the Department of Chemistry and Biochemistry.,the Molecular Biology Institute, and
| | - Lauren T Neves
- the Molecular Biology Institute, and.,the Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, California 90095
| | - Stephen Douglass
- the Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, California 90095
| | - Catherine F Clarke
- From the Department of Chemistry and Biochemistry, .,the Molecular Biology Institute, and
| | - Tracy L Johnson
- the Molecular Biology Institute, and .,the Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, California 90095
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Gillespie A, Gabunilas J, Jen JC, Chanfreau GF. Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae. RNA (NEW YORK, N.Y.) 2017; 23:466-472. [PMID: 28053271 PMCID: PMC5340910 DOI: 10.1261/rna.060004.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/22/2016] [Indexed: 05/29/2023]
Abstract
The RNA exosome is a conserved multiprotein complex that achieves a large number of processive and degradative functions in eukaryotic cells. Recently, mutations have been mapped to the gene encoding one of the subunits of the exosome, EXOSC3 (yeast Rrp40p), which results in pontocerebellar hypoplasia with motor neuron degeneration in human patients. However, the molecular impact of these mutations in the pathology of these diseases is not well understood. To investigate the molecular consequences of mutations in EXOSC3 that lead to neurological diseases, we analyzed the effect of three of the mutations that affect conserved residues of EXOSC3/Rrp40p (G31A, G191C, and W238R; G8A, G148C, and W195R, respectively, in human and yeast) in S. cerevisiae We show that the severity of the phenotypes of these mutations in yeast correlate with that of the disease in human patients, with the W195R mutant showing the strongest growth and RNA processing phenotypes. Furthermore, we show that these mutations affect more severely pre-ribosomal RNA processing functions of the exosome rather than other nuclear processing or surveillance functions. These results suggest that delayed or defective pre-rRNA processing might be the primary defect responsible for the pathologies detected in patients with mutations affecting EXOSC3 function in residues conserved throughout eukaryotes.
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Affiliation(s)
- Abby Gillespie
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
| | - Joanna C Jen
- Department of Neurology, University of California, Los Angeles, California 90095-1763, USA
- Department of Neurobiology, University of California, Los Angeles, California 90095-1763, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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Fasken MB, Corbett AH. Links between mRNA splicing, mRNA quality control, and intellectual disability. RNA & DISEASE 2016; 3:e1448. [PMID: 27868086 PMCID: PMC5113822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
In recent years, the impairment of RNA binding proteins that play key roles in the post-transcriptional regulation of gene expression has been linked to numerous neurological diseases. These RNA binding proteins perform critical mRNA processing steps in the nucleus, including splicing, polyadenylation, and export. In many cases, these RNA binding proteins are ubiquitously expressed raising key questions about why only brain function is impaired. Recently, mutations in the ZC3H14 gene, encoding an evolutionarily conserved, polyadenosine RNA binding protein, have been linked to a nonsyndromic form of autosomal recessive intellectual disability. Thus far, research on ZC3H14 and its Nab2 orthologs in budding yeast and Drosophila reveals that ZC3H14/Nab2 is important for mRNA processing and neuronal patterning. Two recent studies now provide evidence that ZC3H14/Nab2 may function in the quality control of mRNA splicing and export and could help to explain the molecular defects that cause neuronal dysfunction and lead to an inherited form of intellectual disability. These studies on ZC3H14/Nab2 reveal new clues to the puzzle of why loss of the ubiquitously expressed ZC3H14 protein specifically affects neurons.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
| | - Anita H Corbett
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
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The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA. Mol Cell Biol 2016; 36:2697-2714. [PMID: 27528618 PMCID: PMC5064217 DOI: 10.1128/mcb.00402-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate post-transcriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This work reveals that nab2 mutant cells accumulate intron-containing pre-mRNA in vivo We extend this analysis to identify genetic interactions between mutant alleles of nab2 and genes encoding the splicing factor, MUD2, and the RNA exosome, RRP6, with in vivo consequences of altered pre-mRNA splicing and poly(A) tail length control. As further evidence linking Nab2 proteins to splicing, an unbiased proteomic analysis of vertebrate Nab2, ZC3H14, identifies physical interactions with numerous components of the spliceosome. We validated the interaction between ZC3H14 and U2AF2/U2AF65 Taking all the findings into consideration, we present a model where Nab2/ZC3H14 interacts with spliceosome components to allow proper coupling of splicing with subsequent mRNA processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to exit the nucleus and escape Rrp6-dependent degradation.
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