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Yang J, Ma Y, Li B, Xi Z, Zhang L, Wang Y, Feng W. Roles of Nucleolar Factor RCL1 in Itraconazole Resistance of Clinical Candida albicans Under Different Stress Conditions. Infect Drug Resist 2024; 17:769-777. [PMID: 38433785 PMCID: PMC10908289 DOI: 10.2147/idr.s431024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Purpose RNA terminal phosphate cyclase like 1 (RCL1) undergoes overexpression during the immune response of Candida albicans following drug treatment. This study aims to investigate the expression levels of RCL1 in C. albicans under various stress conditions. Methods Fifteen itraconazole (ITR)-resistant strains of clinical C. albicans, and one standard strain were employed for RCL1 sequencing, and mutations in RCL1 were analyzed. Subsequently, 14 out of the 15 ITR-resistant clinical strains and 14 clinical strains sensitive to ITR, fluconazole (FCA) as well as voriconazole (VRC) were cultured under diverse conditions. The expression of RCL1 ITR-resistant and sensitive C. albicans was then assessed using real-time quantitative PCR (RT-qPCR) assays. Results Compared to the standard strain, three missense mutations (C6A, G10A, and A11T) were identified in the RCL1 gene of ITR-resistant C. albicans through successful forward sequencing. Additionally, using successful reverse sequencing, one synonymous mutation (C1T) and four missense mutations (C1T, A3T, A7G, and T8G) were found in the RCL1 gene of ITR-resistant C. albicans. RCL1 expression was significantly higher in ITR-resistant C. albicans than in sensitive strains under standard conditions (37°C, 0.03% CO2, pH 4.0). Low temperature (25°C) increased RCL1 expression in sensitive C. albicans while decreasing it in ITR-resistant strains. Elevated CO2 concentrations (5% CO2) had a negligible effect on RCL1 expression in sensitive C. albicans, but effectively reduced RCL1 level in ITR-resistant strains. Furthermore, a medium with a pH of 7 decreased the expression of RCL1 in both resistant and sensitive C. albicans. Conclusion This study demonstrated that RCL1 mutations in ITR-resistant C. albicans, and variations in culture conditions significantly influence RCL1 expression in both ITR-resistant and sensitive C. albicans, thereby inducing alterations in the dimorphism of C. albicans.
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Affiliation(s)
- Jing Yang
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Yan Ma
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Bo Li
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Zhiqin Xi
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Li Zhang
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Yuxi Wang
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
| | - Wenli Feng
- Department of Dermatovenereology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, People’s Republic of China
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, S Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. RNA (NEW YORK, N.Y.) 2024; 30:149-170. [PMID: 38071476 PMCID: PMC10798247 DOI: 10.1261/rna.079866.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after the addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during cotranscriptional splicing in Plad-B using single-molecule intron tracking to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between the binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten the characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Asako Tan
- Illumina, Inc., Madison, Wisconsin 53719, USA
| | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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3
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Hunter O, Talkish J, Quick-Cleveland J, Igel H, Tan A, Kuersten S, Katzman S, Donohue JP, Jurica M, Ares M. Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.560965. [PMID: 37873484 PMCID: PMC10592967 DOI: 10.1101/2023.10.05.560965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during co-transcriptional splicing in Plad-B using single-molecule intron tracking (SMIT) to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.
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Affiliation(s)
- Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Jen Quick-Cleveland
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | | | | | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - John Paul Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Melissa Jurica
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064
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4
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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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5
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Durand S, Bruelle M, Bourdelais F, Bennychen B, Blin-Gonthier J, Isaac C, Huyghe A, Martel S, Seyve A, Vanbelle C, Adrait A, Couté Y, Meyronet D, Catez F, Diaz JJ, Lavial F, Ricci EP, Ducray F, Gabut M. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. Nat Commun 2023; 14:356. [PMID: 36690642 PMCID: PMC9870888 DOI: 10.1038/s41467-023-36037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
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Affiliation(s)
- Sébastien Durand
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Marion Bruelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
| | - Fleur Bourdelais
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Inovarion, 75005, Paris, France
| | - Bigitha Bennychen
- Dept. of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Juliana Blin-Gonthier
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - Caroline Isaac
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Aurélia Huyghe
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Sylvie Martel
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Antoine Seyve
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Vanbelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Annie Adrait
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - David Meyronet
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Catez
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Fabrice Lavial
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - François Ducray
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Mathieu Gabut
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France.
- Institut Convergence Plascan, Lyon, France.
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6
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Choi Y, Lee HH, Park J, Kim S, Choi S, Moon H, Shin J, Kim JE, Choi GJ, Seo YS, Son H. Intron turnover is essential to the development and pathogenicity of the plant pathogenic fungus Fusarium graminearum. Commun Biol 2022; 5:1129. [PMID: 36289323 PMCID: PMC9606315 DOI: 10.1038/s42003-022-04111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Intron lariats excised during the splicing process are rapidly degraded by RNA lariat debranching enzyme (Dbr1) and several exonucleases. Rapid turnover of lariat RNA is essential to cellular RNA homeostasis. However, the functions of Dbr1 have not been investigated in filamentous fungi. Here, we characterized the molecular functions of Dbr1 in Fusarium graminearum, a major fungal plant pathogen. Deletion of FgDBR1 resulted in pleiotropic defects in hyphal growth, conidiation, sexual reproduction, and virulence. Through transcriptome analysis, we revealed that the deletion mutant exhibited global accumulation of intron lariats and upregulation of ribosome-related genes. Excessive accumulation of lariat RNA led to reduced overall protein synthesis, causing various phenotypic defects in the absence of FgDBR1. The results of this study demonstrate that a compromised intron turnover process affects development and pathogenesis in this fungus and that Dbr1 function is critical to plant pathogenic fungi. RNA lariat debranching enzyme Dbr1 is required for intron turnover in the fungal plant pathogen <i>Fusarium graminearum <i > , and accumulation of lariat RNA affects its development and pathogenesis.
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Affiliation(s)
- Yejin Choi
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Hyun-Hee Lee
- grid.262229.f0000 0001 0719 8572Department of Integrated Biological Science, Pusan National University, Busan, 46247 Republic of Korea
| | - Jiyeun Park
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sieun Kim
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Soyoung Choi
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Heeji Moon
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jiyoung Shin
- grid.31501.360000 0004 0470 5905Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jung-Eun Kim
- grid.31501.360000 0004 0470 5905Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Gyung Ja Choi
- grid.29869.3c0000 0001 2296 8192Therapeutic & Biotechnology Division, Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114 Republic of Korea
| | - Young-Su Seo
- grid.262229.f0000 0001 0719 8572Department of Integrated Biological Science, Pusan National University, Busan, 46247 Republic of Korea
| | - Hokyoung Son
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea
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7
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Temaj G, Hadziselimovic R, Nefic H, Nuhii N. Ribosome biogenesis and ribosome therapy in cancer cells. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.81706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Introduction: The process of protein synthesis is a vital process for all kingdoms of life. The ribosome is a ribonucleoprotein complex that reads the genetic code, from messenger RNA (mRNA) to produce proteins and to tightly regulate and ensure cells growth. The fact that numerous diseases are caused by defect during the ribosome biogenesis is important to understand this pathway.
Materials and methods: We have analyzed the literature for ribosome biogenesis and its links with different diseases which have been found.
Results and discussion: We have discussed the key aspect of human ribosome biogenesis and its links to diseases. We have also proposed the potential of applying this knowledge to the development of a ribosomal stress-based cancer therapy.
Conclusion: Major challenges in the future will be to determine factors which play a pivotal role during ribosome biogenesis. Therefore, more anti-cancer drugs and gene therapy for genetic diseases will be developed against ribosomal biogenesis in the coming years.
Graphical abstract:
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8
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Hao S, Huang M, Xu X, Wang X, Huo L, Wang L, Gu J. MDN1 Mutation Is Associated With High Tumor Mutation Burden and Unfavorable Prognosis in Breast Cancer. Front Genet 2022; 13:857836. [PMID: 35386280 PMCID: PMC8978890 DOI: 10.3389/fgene.2022.857836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Breast cancer (BRCA) is the most common cancer worldwide and a serious threat to human health. MDN1 mutations have been observed in several cancers. However, the associations of MDN1 mutation with tumor mutation burden (TMB) and prognosis of BRCA have not been investigated. Methods: Genomic, transcriptomic, and clinical data of 973 patients with BRCA from The Cancer Genome Atlas (TCGA) database were analyzed. The clinical attributes of BRCA based on the MDN1 mutation status were assessed by comparing TMB and tumor infiltrating immune cells. Gene ontology analysis and gene set enrichment analysis (GSEA) were conducted to identify the key signaling pathways associated with MDN1 mutation. Moreover, univariate and multivariate Cox regression analyses were performed to assess the association between prognostic factors and survival outcomes. Finally, nomograms were used to determine the predictive value of MDN1 mutation on clinical outcomes in patients with BRCA. Results: MDN1 was found to have a relatively high mutation rate (2.77%). Compared to the MDN1 wild-type patients, the TMB value was significantly higher in MDN1 mutant patients (p < 0.001). Prognostic analysis revealed that MDN1 mutant patients had a worse survival probability than MDN1 wild-type patients (hazard ratio = 2.91; 95% CI:1.07–7.92; p = 0.036). GSEA revealed samples with MDN1 mutation enriched in retinol metabolism, drug metabolism cytochrome P450, glucuronidation, miscellaneous transport, and binding event pathways. Conclusion: MDN1 mutation was found to be associated with high TMB and inferior prognosis, suggesting that MDN1 mutation may play a potential role in prognosis prediction and immunotherapy guidance in BRCA.
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Affiliation(s)
- Shuai Hao
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Miao Huang
- Nursing School, Chongqing Medical University, Chongqing, China
| | - Xiaofan Xu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xulin Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Liqun Huo
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lu Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jun Gu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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9
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Wang R, Amoyel M. mRNA Translation Is Dynamically Regulated to Instruct Stem Cell Fate. Front Mol Biosci 2022; 9:863885. [PMID: 35433828 PMCID: PMC9008482 DOI: 10.3389/fmolb.2022.863885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells preserve tissue homeostasis by replacing the cells lost through damage or natural turnover. Thus, stem cells and their daughters can adopt two identities, characterized by different programs of gene expression and metabolic activity. The composition and regulation of these programs have been extensively studied, particularly by identifying transcription factor networks that define cellular identity and the epigenetic changes that underlie the progressive restriction in gene expression potential. However, there is increasing evidence that post-transcriptional mechanisms influence gene expression in stem cells and their progeny, in particular through the control of mRNA translation. Here, we review the described roles of translational regulation in controlling all aspects of stem cell biology, from the decision to enter or exit quiescence to maintaining self-renewal and promoting differentiation. We focus on mechanisms controlling global translation rates in cells, mTOR signaling, eIF2ɑ phosphorylation, and ribosome biogenesis and how they allow stem cells to rapidly change their gene expression in response to tissue needs or environmental changes. These studies emphasize that translation acts as an additional layer of control in regulating gene expression in stem cells and that understanding this regulation is critical to gaining a full understanding of the mechanisms that underlie fate decisions in stem cells.
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Affiliation(s)
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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10
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Sailer C, Jansen J, Sekulski K, Cruz VE, Erzberger JP, Stengel F. A comprehensive landscape of 60S ribosome biogenesis factors. Cell Rep 2022; 38:110353. [PMID: 35139378 PMCID: PMC8884084 DOI: 10.1016/j.celrep.2022.110353] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/02/2021] [Accepted: 01/19/2022] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic ribosome biogenesis is facilitated and regulated by numerous ribosome biogenesis factors (RBFs). High-resolution cryoelectron microscopy (cryo-EM) maps have defined the molecular interactions of RBFs during maturation, but many transient and dynamic interactions, particularly during early assembly, remain uncharacterized. Using quantitative proteomics and crosslinking coupled to mass spectrometry (XL-MS) data from an extensive set of pre-ribosomal particles, we derive a comprehensive and time-resolved interaction map of RBF engagement during 60S maturation. We localize 22 previously unmapped RBFs to specific biogenesis intermediates and validate our results by mapping the catalytic activity of the methyltransferases Bmt2 and Rcm1 to their predicted nucleolar 60S intermediates. Our analysis reveals the interaction sites for the RBFs Noc2 and Ecm1 and elucidates the interaction map and timing of 60S engagement by the DEAD-box ATPases Dbp9 and Dbp10. Our data provide a powerful resource for future studies of 60S ribosome biogenesis. In this study, Sailer et al. generate a comprehensive and precise timeline of ribosome biogenesis factor (RBF) engagement during 60S maturation and localize previously unmapped RBFs in the yeast Saccharomyces cerevisiae. Overall, their data represent an essential resource for future structural studies of large subunit ribosome biogenesis.
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Affiliation(s)
- Carolin Sailer
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany
| | - Jasmin Jansen
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany
| | - Kamil Sekulski
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Victor E Cruz
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Jan P Erzberger
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany.
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11
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Calvo O, Ansari A, Navarro F. Editorial: The Lesser Known World of RNA Polymerases. Front Mol Biosci 2021; 8:811413. [PMID: 34926588 PMCID: PMC8678064 DOI: 10.3389/fmolb.2021.811413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
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12
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Zou Q, Yang L, Shi R, Qi Y, Zhang X, Qi H. Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis. iScience 2021; 24:103396. [PMID: 34825148 PMCID: PMC8605100 DOI: 10.1016/j.isci.2021.103396] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 01/03/2023] Open
Abstract
Maintaining proteostasis is important for animal development. How proteostasis influences spermatogenesis that generates male gametes, spermatozoa, is not clear. We show that testis-specific paralog of ribosomal large subunit protein RPL39, RPL39L, is required for mouse spermatogenesis. Deletion of Rpl39l in mouse caused reduced proliferation of spermatogonial stem cells, malformed sperm mitochondria and flagella, leading to sub-fertility in males. Biochemical analyses revealed that lack of RPL39L deteriorated protein synthesis and protein quality control in spermatogenic cells, partly due to reduced biogenesis of ribosomal subunits and ribosome homeostasis. RPL39/RPL39L is likely assembled into ribosomes via H/ACA domain containing NOP10 complex early in ribosome biogenesis pathway. Furthermore, Rpl39l null mice exhibited compromised regenerative spermatogenesis after chemical insult and early degenerative spermatogenesis in aging mice. These data demonstrate that maintaining proteostasis is important for spermatogenesis, of which ribosome homeostasis maintained by ribosomal proteins coordinates translation machinery to the regulation of cellular growth. Rpl39l deletion causes reduced spermatogenesis and subfertility in male mice SSC proliferation, mitochondria and sperm flagella compromised in Rpl39l–/– mice Rpl39l deletion affects ribosomal LSU formation and protein quality control Aberrant proteostasis affects spermatogenesis and regeneration
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Affiliation(s)
- Qianxing Zou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lele Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Yuling Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Huayu Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Yueh LY, Tseng YT, Chu CY, Lo KY. The dedicated chaperones of eL43, Puf6 and Loc1, can also bind RPL43 mRNA and regulate the production of this ribosomal protein. J Biochem 2021; 171:85-96. [PMID: 34661244 DOI: 10.1093/jb/mvab110] [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: 06/01/2021] [Accepted: 10/12/2021] [Indexed: 11/14/2022] Open
Abstract
The level of ribosome biogenesis is highly associated with cell growth rate. Because many ribosomal proteins have extraribosomal functions, overexpression or insufficient supply of these proteins may impair cellular growth. Therefore, the supply of ribosomal proteins is tightly controlled in response to rRNA syntheses and environmental stimuli. In our previous study, 2 RNA-binding proteins, Puf6 and Loc1, were identified as dedicated chaperones of the ribosomal protein eL43, with which they associate to maintain its protein level and proper loading. In this study, we demonstrate that Puf6 and Loc1 interact with RPL43 mRNA. Notably, Puf6 and Loc1 usually function as a dimeric complex to bind other mRNAs; however, in this instance, the individual proteins, but not the complex form, can bind RPL43 mRNA. Thus, Puf6 or Loc1 could bind RPL43 mRNA in loc1Δ or puf6Δ, respectively. The binding of Puf6 or Loc1 caused negative effects for eL43 production: decreased RNA stability and translation of RPL43A/B mRNA. The present results suggest that these dedicated chaperones control the protein levels of eL43 from the standpoint of stability and through regulating its production.
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Affiliation(s)
- Le-Yun Yueh
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Yun-Ting Tseng
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Chih-Yi Chu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
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14
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Wahba L, Hansen L, Fire AZ. An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. Dev Cell 2021; 56:2295-2312.e6. [PMID: 34388368 PMCID: PMC8387450 DOI: 10.1016/j.devcel.2021.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
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Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Delgado-Román I, Muñoz-Centeno MC. Coupling Between Cell Cycle Progression and the Nuclear RNA Polymerases System. Front Mol Biosci 2021; 8:691636. [PMID: 34409067 PMCID: PMC8365833 DOI: 10.3389/fmolb.2021.691636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic life is possible due to the multitude of complex and precise phenomena that take place in the cell. Essential processes like gene transcription, mRNA translation, cell growth, and proliferation, or membrane traffic, among many others, are strictly regulated to ensure functional success. Such systems or vital processes do not work and adjusts independently of each other. It is required to ensure coordination among them which requires communication, or crosstalk, between their different elements through the establishment of complex regulatory networks. Distortion of this coordination affects, not only the specific processes involved, but also the whole cell fate. However, the connection between some systems and cell fate, is not yet very well understood and opens lots of interesting questions. In this review, we focus on the coordination between the function of the three nuclear RNA polymerases and cell cycle progression. Although we mainly focus on the model organism Saccharomyces cerevisiae, different aspects and similarities in higher eukaryotes are also addressed. We will first focus on how the different phases of the cell cycle affect the RNA polymerases activity and then how RNA polymerases status impacts on cell cycle. A good example of how RNA polymerases functions impact on cell cycle is the ribosome biogenesis process, which needs the coordinated and balanced production of mRNAs and rRNAs synthesized by the three eukaryotic RNA polymerases. Distortions of this balance generates ribosome biogenesis alterations that can impact cell cycle progression. We also pay attention to those cases where specific cell cycle defects generate in response to repressed synthesis of ribosomal proteins or RNA polymerases assembly defects.
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Affiliation(s)
- Irene Delgado-Román
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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16
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Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae. Noncoding RNA 2021; 7:ncrna7030041. [PMID: 34287362 PMCID: PMC8293398 DOI: 10.3390/ncrna7030041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.
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17
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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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18
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West PT, Peters SL, Olm MR, Yu FB, Gause H, Lou YC, Firek BA, Baker R, Johnson AD, Morowitz MJ, Hettich RL, Banfield JF. Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. MICROBIOME 2021; 9:142. [PMID: 34154658 PMCID: PMC8215838 DOI: 10.1186/s40168-021-01085-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/22/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. RESULTS Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. CONCLUSIONS The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes. Video abstract.
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Affiliation(s)
- Patrick T. West
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Samantha L. Peters
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | | | - Haley Gause
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Brian A. Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Robyn Baker
- Division of Newborn Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA USA
| | - Alexander D. Johnson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Robert L. Hettich
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jillian F. Banfield
- Chan Zuckerberg Biohub, San Francisco, CA USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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19
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Quantitative Proteomic Profiling of Fungal Growth, Development, and Ochratoxin A Production in Aspergillus ochraceus on High- and Low-NaCl Cultures. Toxins (Basel) 2021; 13:toxins13010051. [PMID: 33450861 PMCID: PMC7828334 DOI: 10.3390/toxins13010051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Dry-cured meat products are worldwide food with high-salt content, and filamentous fungi are beneficial to the maturation process. However, some salt-tolerant strains of Aspergillus and Penicillium produce ochratoxin A (OTA) on these products and thus threaten food safety. In our study, proteomic analysis was performed to reveal the mechanism of adaptability to high-salt environment by Aspergillus ochraceus. Twenty g/L and 70 g/L NaCl substrates were used to provide medium- and high-NaCl content environments, respectively. The NaCl addition could induce fungal growth, but only 20 g/L NaCl addition could induce spore production while 70 g/L repressed it. Proteomics analysis identified 2646 proteins in A. ochraceus fc-1, of which 237 and 251 were differentially expressed with 20 g/L and 70 g/L NaCl addition, respectively. Potential factors affecting fungal growth and development were identified by GO and KEGG analyses of biological process, cellular component, and molecular function terms. The results revealed that ergosterol synthesis pathway was significantly upregulated with 20 g/L and 70 g/L NaCl addition. However, fungal growth and development including OTA production were complex processes associated with many factors including nutrient uptake, cell membrane integrity, cell cycle, energy metabolism, intracellular redox homeostasis, protein synthesis and processing, autophagy, and secondary metabolism. Reactive oxygen species may be an important window to understand the mechanism that medium-salt content was conducive to intracellular signal transduction while high-salt content caused oxidative stress. The findings would help to improve the processes and storage conditions of dry-cured meat products.
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20
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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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21
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Hu K. Quick, Coordinated and Authentic Reprogramming of Ribosome Biogenesis during iPSC Reprogramming. Cells 2020; 9:cells9112484. [PMID: 33203179 PMCID: PMC7697288 DOI: 10.3390/cells9112484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/04/2022] Open
Abstract
Induction of pluripotent stem cells (iPSC) by OCT4 (octamer-binding transcription factor 4), SOX2 (SR box 2), KLF4 (Krüppel-Like Factor 4), and MYC (cellular Myelocytomatosis, c-MYC or MYC) (collectively OSKM) is revolutionary, but very inefficient, slow, and stochastic. It is unknown as to what underlies the potency aspect of the multi-step, multi-pathway, and inefficient iPSC reprogramming. Mesenchymal-to-epithelial (MET) transition is known as the earliest pathway reprogrammed. Using the recently established concepts of reprogramome and reprogramming legitimacy, the author first demonstrated that ribosome biogenesis (RB) is globally enriched in terms of human embryonic stem cells in comparison with fibroblasts, the popular starting cells of pluripotency reprogramming. It is then shown that the RB network was reprogrammed quickly in a coordinated fashion. Human iPSCs also demonstrated a more robust ribosome biogenesis. The quick and global reprogramming of ribosome biogenesis was also observed in an independent fibroblast line from a different donor. This study additionally demonstrated that MET did not initiate substantially at the time of proper RB reprogramming. This quick, coordinated and authentic RB reprogramming to the more robust pluripotent state by the OSKM reprogramming factors dramatically contrasts the overall low efficiency and long latency of iPSC reprogramming, and aligns well with the potency aspect of the inefficient OSKM reprogramming.
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Affiliation(s)
- Kejin Hu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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22
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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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23
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Martínez-Fernández V, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Garrido-Godino AI, Rodríguez-Galán O, Jordán-Pla A, Lois S, Triviño JC, de la Cruz J, Navarro F. Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2020; 26:1360-1379. [PMID: 32503921 PMCID: PMC7491330 DOI: 10.1261/rna.075507.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/28/2020] [Indexed: 05/08/2023]
Abstract
Understanding the functional connection that occurs for the three nuclear RNA polymerases to synthesize ribosome components during the ribosome biogenesis process has been the focal point of extensive research. To preserve correct homeostasis on the production of ribosomal components, cells might require the existence of proteins that target a common subunit of these RNA polymerases to impact their respective activities. This work describes how the yeast prefoldin-like Bud27 protein, which physically interacts with the Rpb5 common subunit of the three RNA polymerases, is able to modulate the transcription mediated by the RNA polymerase I, likely by influencing transcription elongation, the transcription of the RNA polymerase III, and the processing of ribosomal RNA. Bud27 also regulates both RNA polymerase II-dependent transcription of ribosomal proteins and ribosome biogenesis regulon genes, likely by occupying their DNA ORFs, and the processing of the corresponding mRNAs. With RNA polymerase II, this association occurs in a transcription rate-dependent manner. Our data also indicate that Bud27 inactivation alters the phosphorylation kinetics of ribosomal protein S6, a readout of TORC1 activity. We conclude that Bud27 impacts the homeostasis of the ribosome biogenesis process by regulating the activity of the three RNA polymerases and, in this way, the synthesis of ribosomal components. This quite likely occurs through a functional connection of Bud27 with the TOR signaling pathway.
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Affiliation(s)
- Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Sergio Lois
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Juan C Triviño
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
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24
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García‐Béjar B, Owens RA, Briones A, Arévalo‐Villena M. Differential distribution and proteomic response of
Saccharomyces cerevisiae
and non‐model yeast species to zinc. Environ Microbiol 2020; 22:4633-4646. [DOI: 10.1111/1462-2920.15206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Beatriz García‐Béjar
- Department of Analytical Chemistry and Food Technology University of Castilla‐La Mancha Ciudad Real 13071 Spain
| | - Rebecca A. Owens
- Department of Biology Maynooth University Maynooth Co. Kildare Ireland
| | - Ana Briones
- Department of Analytical Chemistry and Food Technology University of Castilla‐La Mancha Ciudad Real 13071 Spain
| | - María Arévalo‐Villena
- Department of Analytical Chemistry and Food Technology University of Castilla‐La Mancha Ciudad Real 13071 Spain
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25
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Shu WJ, Chen R, Yin ZH, Li F, Zhang H, Du HN. Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions. Nucleic Acids Res 2020; 48:8360-8373. [PMID: 32619236 PMCID: PMC7470948 DOI: 10.1093/nar/gkaa558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/17/2020] [Accepted: 06/21/2020] [Indexed: 12/24/2022] Open
Abstract
Coordinated regulation of ribosomal RNA (rRNA) synthesis and ribosomal protein gene (RPG) transcription by eukaryotic RNA polymerases (RNAP) is a key requirement for growth control. Although evidence for balance between RNPI-dependent 35S rRNA production and RNAPII-mediated RPG transcription have been described, the molecular basis is still obscure. Here, we found that Rph1 modulates the transcription status of both rRNAs and RPGs in yeast. We show that Rph1 widely associates with RNAPI and RNAPII-transcribed genes. Deletion of RPH1 remarkably alleviates cell slow growth caused by TORC1 inhibition via derepression of rRNA and RPG transcription under nutrient stress conditions. Mechanistically, Rim15 kinase phosphorylates Rph1 upon rapamycin treatment. Phosphorylation-mimetic mutant of Rph1 exhibited more resistance to rapamycin treatment, decreased association with ribosome-related genes, and faster cell growth compared to the wild-type, indicating that Rph1 dissociation from chromatin ensures cell survival upon nutrient stress. Our results uncover the role of Rph1 in coordination of RNA polymerases-mediated transcription to control cell growth under nutrient stress conditions.
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Affiliation(s)
- Wen-Jie Shu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Zhao-Hong Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Feng Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, 3888 Chenhua Road, Shanghai, 201062, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072 China
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26
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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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27
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From Snapshots to Flipbook-Resolving the Dynamics of Ribosome Biogenesis with Chemical Probes. Int J Mol Sci 2020; 21:ijms21082998. [PMID: 32340379 PMCID: PMC7215809 DOI: 10.3390/ijms21082998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
The synthesis of ribosomes is one of the central and most resource demanding processes in each living cell. As ribosome biogenesis is tightly linked with the regulation of the cell cycle, perturbation of ribosome formation can trigger severe diseases, including cancer. Eukaryotic ribosome biogenesis starts in the nucleolus with pre-rRNA transcription and the initial assembly steps, continues in the nucleoplasm and is finished in the cytoplasm. From start to end, this process is highly dynamic and finished within few minutes. Despite the tremendous progress made during the last decade, the coordination of the individual maturation steps is hard to unravel by a conventional methodology. In recent years small molecular compounds were identified that specifically block either rDNA transcription or distinct steps within the maturation pathway. As these inhibitors diffuse into the cell rapidly and block their target proteins within seconds, they represent excellent tools to investigate ribosome biogenesis. Here we review how the inhibitors affect ribosome biogenesis and discuss how these effects can be interpreted by taking the complex self-regulatory mechanisms of the pathway into account. With this we want to highlight the potential of low molecular weight inhibitors to approach the dynamic nature of the ribosome biogenesis pathway.
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28
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Mantilla J, Wang D, Bargiotas I, Wang J, Cao J, Oudre L, Vidal PP. Motor style at rest and during locomotion in human. J Neurophysiol 2020; 123:2269-2284. [PMID: 32319842 DOI: 10.1152/jn.00019.2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Humans exhibit various motor styles that reflect their intra- and interindividual variability when implementing sensorimotor transformations. This opens important questions, such as, At what point should they be readjusted to maintain optimal motor control? Do changes in motor style reveal the onset of a pathological process and can these changes help rehabilitation and recovery? To further investigate the concept of motor style, tests were carried out to quantify posture at rest and motor control in 18 healthy subjects under four conditions: walking at three velocities (comfortable walking, walking at 4 km/h, and race walking) and running at maximum velocity. The results suggest that motor control can be conveniently decomposed into a static component (a stable configuration of the head and column with respect to the gravitational vertical) and dynamic components (head, trunk, and limb movements) in humans, as in quadrupeds, and both at rest and during locomotion. These skeletal configurations provide static markers to quantify the motor style of individuals because they exhibit large variability among subjects. Also, using four measurements (jerk, root mean square, sample entropy, and the two-thirds power law), it was shown that the dynamics were variable at both intra- and interindividual levels during locomotion. Variability increased following a head-to -toe gradient. These findings led us to select dynamic markers that could define, together with static markers, the motor style of a subject. Finally, our results support the view that postural and motor control are subserved by different neuronal networks in frontal, sagittal, and transversal planes.NEW & NOTEWORTHY During human locomotion, motor control can be conveniently decomposed into a static and dynamic components. Variable dynamics were observed at both the intra- and interindividual levels during locomotion. Variability increased following a head-to-toe gradient. Finally, our results support the view that postural and motor control are subserved by different neuronal networks in the frontal, sagittal, and transversal planes.
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Affiliation(s)
- Juan Mantilla
- Université de Paris, CNRS, SSA, École Normale Supérieure Paris-Saclay, Centre Borelli, Paris, France
| | - Danping Wang
- Institute of Information and Control, Hangzhou Dianzi University, Hangzhou, China.,Plateforme Sensorimotricité, CNRS, INSERM, Paris, France
| | - Ioannis Bargiotas
- Université de Paris, CNRS, SSA, École Normale Supérieure Paris-Saclay, Centre Borelli, Paris, France
| | - Junhong Wang
- Institute of Information and Control, Hangzhou Dianzi University, Hangzhou, China
| | - Jiuwen Cao
- Institute of Information and Control, Hangzhou Dianzi University, Hangzhou, China
| | - Laurent Oudre
- L2TI, Sorbonne Paris Nord University, Villetaneuse, France
| | - Pierre-Paul Vidal
- Université de Paris, CNRS, SSA, École Normale Supérieure Paris-Saclay, Centre Borelli, Paris, France.,Institute of Information and Control, Hangzhou Dianzi University, Hangzhou, China
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29
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Ccm1p is a 15S rRNA primary transcript processing factor as elucidated by a novel in vivo system in Saccharomyces cerevisiae. Curr Genet 2020; 66:775-789. [PMID: 32152734 DOI: 10.1007/s00294-020-01064-0] [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: 12/25/2019] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
In Saccharomyces cerevisiae, the mitoribosomal RNA of the minor subunit, 15S rRNA, is transcribed as a bicistronic transcript along with tRNAW. 5' and 3' sequences flanking the mature transcript must be removed by cleavage at the respective junctions before incorporating it into the mitoribosome. An in vivo dose-response triphasic system was created to elucidate the role of Ccm1p in the processing of 15S rRNA: Ccm1p supply ("On"), deprivation ("Off"), and resupply ("Back on"). After 72 h under "Off" status, the cells started to exhibit a complete mutant phenotype as assessed by their lack of growth in glycerol medium, while keeping their mitochondrial DNA integrity (ρ+). Full functionality of mitochondria was reacquired upon "Back on." 15S rRNA levels and phenotype followed the Ccm1p intramitochondrial concentrations throughout the "On-Off-Back on" course. Under "Off" status, cells gradually accumulated unprocessed 5' and 3' junctions, which reached significant levels at 72-96 h, probably due to a saturation of the mitochondrial degradosome (mtEXO). The Ccm1p/mtEXO mutant (Δccm1/Δdss1) showed a copious accumulation of 15S rRNA primary transcript forms, which were cleaved upon Ccm1p resupply. The gene that codes for the RNA component of RNase P was conserved in wild-type and mutant strains. Our results indicate that Ccm1p is crucial in processing the 15S rRNA primary transcript and does not stabilize the already mature 15S rRNA. Consequently, failure of this function in Δccm1 cells results, as it happens to any other unprocessed primary transcripts, in total degradation of 15S rRNA by mtEXO, whose mechanism of action is discussed.
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30
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Ribosome and Translational Control in Stem Cells. Cells 2020; 9:cells9020497. [PMID: 32098201 PMCID: PMC7072746 DOI: 10.3390/cells9020497] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
Embryonic stem cells (ESCs) and adult stem cells (ASCs) possess the remarkable capacity to self-renew while remaining poised to differentiate into multiple progenies in the context of a rapidly developing embryo or in steady-state tissues, respectively. This ability is controlled by complex genetic programs, which are dynamically orchestrated at different steps of gene expression, including chromatin remodeling, mRNA transcription, processing, and stability. In addition to maintaining stem cell homeostasis, these molecular processes need to be rapidly rewired to coordinate complex physiological modifications required to redirect cell fate in response to environmental clues, such as differentiation signals or tissue injuries. Although chromatin remodeling and mRNA expression have been extensively studied in stem cells, accumulating evidence suggests that stem cell transcriptomes and proteomes are poorly correlated and that stem cell properties require finely tuned protein synthesis. In addition, many studies have shown that the biogenesis of the translation machinery, the ribosome, is decisive for sustaining ESC and ASC properties. Therefore, these observations emphasize the importance of translational control in stem cell homeostasis and fate decisions. In this review, we will provide the most recent literature describing how ribosome biogenesis and translational control regulate stem cell functions and are crucial for accommodating proteome remodeling in response to changes in stem cell fate.
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31
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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32
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Nürenberg-Goloub E, Tampé R. Ribosome recycling in mRNA translation, quality control, and homeostasis. Biol Chem 2019; 401:47-61. [DOI: 10.1515/hsz-2019-0279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
Abstract
Protein biosynthesis is a conserved process, essential for life. Ongoing research for four decades has revealed the structural basis and mechanistic details of most protein biosynthesis steps. Numerous pathways and their regulation have recently been added to the translation system describing protein quality control and messenger ribonucleic acid (mRNA) surveillance, ribosome-associated protein folding and post-translational modification as well as human disorders associated with mRNA and ribosome homeostasis. Thus, translation constitutes a key regulatory process placing the ribosome as a central hub at the crossover of numerous cellular pathways. Here, we describe the role of ribosome recycling by ATP-binding cassette sub-family E member 1 (ABCE1) as a crucial regulatory step controlling the biogenesis of functional proteins and the degradation of aberrant nascent chains in quality control processes.
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Affiliation(s)
- Elina Nürenberg-Goloub
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
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33
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Wu G, Yan Y, Wang X, Ren X, Chen X, Zeng S, Wei J, Qian L, Yang X, Ou C, Lin W, Gong Z, Zhou J, Xu Z. CFHR1 is a potentially downregulated gene in lung adenocarcinoma. Mol Med Rep 2019; 20:3642-3648. [PMID: 31485643 PMCID: PMC6755197 DOI: 10.3892/mmr.2019.10644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/08/2019] [Indexed: 02/05/2023] Open
Abstract
There is increasing evidence that human complement factor H‑related protein 1 (CFHR1) plays a crucial role in the development of malignant diseases. However, few studies have identified the roles of CFHR1 in the occurrence and prognosis of lung adenocarcinoma (LADC). In the present study, comprehensive bioinformatic analyses of data obtained from the Oncomine platform, UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) demonstrated that CFHR1 expression is significantly reduced in both LADC tissues and cancer cells. The patients presenting with downregulation of CFHR1 had significantly lower overall survival (OS) and post progression survival (PPS) times. Through analysis of the datasets from Gene Expression Omnibus database, we found that the compound actinomycin D promoted CFHR1 expression, further displaying the cytotoxic effect in the LADC cell line A549. In addition, the expression level of CFHR1 in the cisplatin‑resistant LADC cell line CDDP‑R (derived from H460) was also significantly reduced. Our research demonstrated that low levels of CFHR1 are specifically found in LADC samples, and CFHR1 could serve as a potential therapeutic target for this subset of lung cancers. Determination of the detailed roles of CFHR1 in LADC biology could provide insightful information for further investigations.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jie Wei
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xue Yang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wei Lin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, Otto C, Jühling F, Busch W, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Hoffmann S, Pörtner HO, Luckenbach T, Timofeyev M, Stadler PF. Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods. BMC Genomics 2019; 20:712. [PMID: 31519144 PMCID: PMC6743106 DOI: 10.1186/s12864-019-6024-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Lake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas. To this end, we conducted exposure experiments to increased temperature and the toxic heavy metal cadmium as stressors. Results Here we obtained high-quality de novo transcriptome assemblies, covering mutiple conditions, of three amphipod species, and compared their transcriptomic stress responses. Two of these species, Eulimnogammarus verrucosus and E. cyaneus, are endemic to Lake Baikal, while the Holarctic Gammarus lacustris is a potential invader. Conclusions Both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-6024-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Polina Drozdova
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Lorena Rivarola-Duarte
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.,Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Seeland OT Gatersleben, D-06466, Germany.,Plant Genome and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Denis Axenov-Gribanov
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Stephan Schreiber
- Young Investigator Group Bioinformatics & Transcriptomics, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Anton Gurkov
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Zhanna Shatilina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Kseniya Vereshchagina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Yulia Lubyaga
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Ekaterina Madyarova
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Christian Otto
- ecSeq Bioinformatics GmbH, Sternwartenstraße 29, Leipzig, D-04103, Germany
| | - Frank Jühling
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 3 Rue Koeberlé, Strasbourg, F-67000, France.,Université de Strasbourg, 4 Rue Blaise Pascal, Strasbourg, F-67000, France
| | - Wibke Busch
- Department of Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Lena Jakob
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Magnus Lucassen
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Franz Josef Sartoris
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Jörg Hackermüller
- Young Investigator Group Bioinformatics & Transcriptomics, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Steve Hoffmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Hans-Otto Pörtner
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. .,Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria. .,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, D.C., COL-111321, Colombia. .,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA.
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35
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Boye E, Grallert B. eIF2α phosphorylation and the regulation of translation. Curr Genet 2019; 66:293-297. [PMID: 31485739 DOI: 10.1007/s00294-019-01026-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/27/2022]
Abstract
We discuss novel insight into the role and consequences of the phosphorylation of the translation initiation factor eIF2α in the context of stress responses and cell-cycle regulation. eIF2α is centrally located to regulate translation and its phosphorylation in response to different environmental challenges is one of the best characterized stress-response pathways. In addition to its role in stress management, eIF2α phosphorylation is also linked to cell-cycle progression and memory consolidation in the nervous system. The best known consequences of eIF2α phosphorylation are downregulation of global translation and stimulation of translation of some mRNAs. However, recent evidence shows that (i) eIF2α phosphorylation is not always required for the downregulation of global translation after exposure to stress and (ii) eIF2α phosphorylation does not necessarily lead to the downregulation of global translation. These results suggest that the textbook view of eIF2α phosphorylation needs to be revised and that there must be additional regulatory mechanisms at play.
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Affiliation(s)
- Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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36
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Corsaro D, Venditti D. Putative group I introns in the eukaryote nuclear internal transcribed spacers. Curr Genet 2019; 66:373-384. [PMID: 31463775 DOI: 10.1007/s00294-019-01027-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/17/2019] [Indexed: 11/28/2022]
Abstract
Group I introns are mobile genetic elements that interrupt genes encoding proteins and RNAs. In the rRNA operon, introns can insert in the small subunit (SSU) and large subunit (LSU) of a wide variety of protists and various prokaryotes, but they were never found in the ITS region. In this study, unusually long ITS regions of fungi and closely related unicellular organisms (Polychytrium aggregatum, Mitosporidium daphniae, Amoeboaphelidium occidentale and Nuclearia simplex) were analysed. While the insertion of repeats is responsible for long ITS in other eukaryotes, the increased size of the sequences analysed herein seems rather due to the presence of introns in ITS-1 or ITS-2. The identified insertions can be folded in secondary structures according to group I intron models, and they cluster within introns in conserved core-based phylogeny. In addition, for Mitosporidium, Amoeboaphelidium and Nuclearia, more conventional ITS-2 structures can be deduced once spacer introns are removed. Sequences of five shark species were also analysed for their structure and included in phylogeny because of unpublished work reporting introns in their ITS, obtaining congruent results. Overall, the data presented herein indicate that spacer regions may contain introns.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS, 12 rue du Maconnais, Vandoeuvre-lès-Nancy, 54500, France.
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37
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Bi X, Xu Y, Li T, Li X, Li W, Shao W, Wang K, Zhan G, Wu Z, Liu W, Lu JY, Wang L, Zhao J, Wu J, Na J, Li G, Li P, Shen X. RNA Targets Ribogenesis Factor WDR43 to Chromatin for Transcription and Pluripotency Control. Mol Cell 2019; 75:102-116.e9. [DOI: 10.1016/j.molcel.2019.05.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 01/09/2019] [Accepted: 04/16/2019] [Indexed: 11/30/2022]
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38
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Hannig K, Babl V, Hergert K, Maier A, Pilsl M, Schächner C, Stöckl U, Milkereit P, Tschochner H, Seufert W, Griesenbeck J. The C-terminal region of Net1 is an activator of RNA polymerase I transcription with conserved features from yeast to human. PLoS Genet 2019; 15:e1008006. [PMID: 30802237 PMCID: PMC6415870 DOI: 10.1371/journal.pgen.1008006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/13/2019] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
RNA polymerase I (Pol I) synthesizes ribosomal RNA (rRNA) in all eukaryotes, accounting for the major part of transcriptional activity in proliferating cells. Although basal Pol I transcription factors have been characterized in diverse organisms, the molecular basis of the robust rRNA production in vivo remains largely unknown. In S. cerevisiae, the multifunctional Net1 protein was reported to stimulate Pol I transcription. We found that the Pol I-stimulating function can be attributed to the very C-terminal region (CTR) of Net1. The CTR was required for normal cell growth and Pol I recruitment to rRNA genes in vivo and sufficient to promote Pol I transcription in vitro. Similarity with the acidic tail region of mammalian Pol I transcription factor UBF, which could partly functionally substitute for the CTR, suggests conserved roles for CTR-like domains in Pol I transcription from yeast to human. The production of ribosomes, cellular factories of protein synthesis, is an essential process driving proliferation and cell growth. Ribosome biogenesis is controlled at the level of synthesis of its components, ribosomal proteins and ribosomal RNA. In eukaryotes, RNA polymerase I is dedicated to transcribe the ribosomal RNA. RNA polymerase I has been identified as a potential target for cell proliferation inhibition. Here we describe the C-terminal region of Net1 as an activator of RNA polymerase I transcription in baker’s yeast. In the absence of this activator RNA polymerase I transcription is downregulated and cell proliferation is strongly impaired. Strikingly, this activator might be conserved in human cells, which points to a general mechanism. Our discovery will help to gain a better understanding of the molecular basis of ribosomal RNA synthesis and may have implications in developing strategies to control cellular growth.
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Affiliation(s)
- Katharina Hannig
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Virginia Babl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Kristin Hergert
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Andreas Maier
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Christopher Schächner
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Ulrike Stöckl
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Herbert Tschochner
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Wolfgang Seufert
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
| | - Joachim Griesenbeck
- Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- * E-mail: (PM); (HT); (WS); (JG)
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39
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Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics 2018; 10:1755-1776. [PMID: 30358795 PMCID: PMC6291366 DOI: 10.1039/c8mt00269j] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is an essential cofactor for many proteins. A key mechanism of zinc homeostasis during deficiency is "zinc sparing" in which specific zinc-binding proteins are repressed to reduce the cellular requirement. In this report, we evaluated zinc sparing across the zinc proteome of Saccharomyces cerevisiae. The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. Protein abundance was determined by mass spectrometry. In zinc-replete cells, we detected over 2500 proteins among which 229 were zinc proteins. Based on copy number estimates and binding stoichiometries, a replete cell contains ∼9 million zinc-binding sites on proteins. During zinc deficiency, many zinc proteins decreased in abundance and the zinc-binding requirement decreased to ∼5 million zinc atoms per cell. Many of these effects were due at least in part to changes in mRNA levels rather than simply protein degradation. Measurements of cellular zinc content showed that the level of zinc atoms per cell dropped from over 20 million in replete cells to only 1.7 million in deficient cells. These results confirmed the ability of replete cells to store excess zinc and suggested that the majority of zinc-binding sites on proteins in deficient cells are either unmetalated or mismetalated. Our analysis of two abundant zinc proteins, Fba1 aldolase and Met6 methionine synthetase, supported that hypothesis. Thus, we have discovered widespread zinc sparing mechanisms and obtained evidence of a high accumulation of zinc proteins that lack their cofactor during deficiency.
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Affiliation(s)
- Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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40
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The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr Genet 2018; 65:457-466. [DOI: 10.1007/s00294-018-0912-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022]
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