1
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Martín-Villanueva S, Galmozzi CV, Ruger-Herreros C, Kressler D, de la Cruz J. The Beak of Eukaryotic Ribosomes: Life, Work and Miracles. Biomolecules 2024; 14:882. [PMID: 39062596 PMCID: PMC11274626 DOI: 10.3390/biom14070882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Ribosomes are not totally globular machines. Instead, they comprise prominent structural protrusions and a myriad of tentacle-like projections, which are frequently made up of ribosomal RNA expansion segments and N- or C-terminal extensions of ribosomal proteins. This is more evident in higher eukaryotic ribosomes. One of the most characteristic protrusions, present in small ribosomal subunits in all three domains of life, is the so-called beak, which is relevant for the function and regulation of the ribosome's activities. During evolution, the beak has transitioned from an all ribosomal RNA structure (helix h33 in 16S rRNA) in bacteria, to an arrangement formed by three ribosomal proteins, eS10, eS12 and eS31, and a smaller h33 ribosomal RNA in eukaryotes. In this review, we describe the different structural and functional properties of the eukaryotic beak. We discuss the state-of-the-art concerning its composition and functional significance, including other processes apparently not related to translation, and the dynamics of its assembly in yeast and human cells. Moreover, we outline the current view about the relevance of the beak's components in human diseases, especially in ribosomopathies and cancer.
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Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carla V. Galmozzi
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carmen Ruger-Herreros
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Dieter Kressler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland;
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
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2
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Alruwaili MM, Zonneville J, Naranjo MN, Serio H, Melendy T, Straubinger RM, Gillard B, Foster BA, Rajan P, Attwood K, Chatley S, Iyer R, Fountzilas C, Bakin AV. A synergistic two-drug therapy specifically targets a DNA repair dysregulation that occurs in p53-deficient colorectal and pancreatic cancers. Cell Rep Med 2024; 5:101434. [PMID: 38387463 PMCID: PMC10982975 DOI: 10.1016/j.xcrm.2024.101434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 12/06/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
The tumor-suppressor p53 is commonly inactivated in colorectal cancer and pancreatic ductal adenocarcinoma, but existing treatment options for p53-mutant (p53Mut) cancer are largely ineffective. Here, we report a therapeutic strategy for p53Mut tumors based on abnormalities in the DNA repair response. Investigation of DNA repair upon challenge with thymidine analogs reveals a dysregulation in DNA repair response in p53Mut cells that leads to accumulation of DNA breaks. Thymidine analogs do not interrupt DNA synthesis but induce DNA repair that involves a p53-dependent checkpoint. Inhibitors of poly(ADP-ribose) polymerase (PARPis) markedly enhance DNA double-strand breaks and cell death induced by thymidine analogs in p53Mut cells, whereas p53 wild-type cells respond with p53-dependent inhibition of the cell cycle. Combinations of trifluorothymidine and PARPi agents demonstrate superior anti-neoplastic activity in p53Mut cancer models. These findings support a two-drug combination strategy to improve outcomes for patients with p53Mut cancer.
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Affiliation(s)
- Mohammed M Alruwaili
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Medical Laboratory Technology, College of Applied Medical Science, Northern Border University, Arar City, Saudi Arabia
| | - Justin Zonneville
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Maricris N Naranjo
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Hannah Serio
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Thomas Melendy
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214, USA
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Bryan Gillard
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Barbara A Foster
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Priyanka Rajan
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Kristopher Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sarah Chatley
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Renuka Iyer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Christos Fountzilas
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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3
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Dönig J, Mende H, Davila Gallesio J, Wagner K, Hotz P, Schunck K, Piller T, Hölper S, Uhan S, Kaulich M, Wirth M, Keller U, Tascher G, Bohnsack KE, Müller S. Characterization of nucleolar SUMO isopeptidases unveils a general p53-independent checkpoint of impaired ribosome biogenesis. Nat Commun 2023; 14:8121. [PMID: 38065954 PMCID: PMC10709353 DOI: 10.1038/s41467-023-43751-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Ribosome biogenesis is a multi-step process, in which a network of trans-acting factors ensures the coordinated assembly of pre-ribosomal particles in order to generate functional ribosomes. Ribosome biogenesis is tightly coordinated with cell proliferation and its perturbation activates a p53-dependent cell-cycle checkpoint. How p53-independent signalling networks connect impaired ribosome biogenesis to the cell-cycle machinery has remained largely enigmatic. We demonstrate that inactivation of the nucleolar SUMO isopeptidases SENP3 and SENP5 disturbs distinct steps of 40S and 60S ribosomal subunit assembly pathways, thereby triggering the canonical p53-dependent impaired ribosome biogenesis checkpoint. However, inactivation of SENP3 or SENP5 also induces a p53-independent checkpoint that converges on the specific downregulation of the key cell-cycle regulator CDK6. We further reveal that impaired ribosome biogenesis generally triggers the downregulation of CDK6, independent of the cellular p53 status. Altogether, these data define the role of SUMO signalling in ribosome biogenesis and unveil a p53-independent checkpoint of impaired ribosome biogenesis.
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Affiliation(s)
- Judith Dönig
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Hannah Mende
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Kristina Wagner
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Paul Hotz
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Kathrin Schunck
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
- PharmBioTec gGmbH, Schiffweiler, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
- Sanofi AG, Frankfurt, Germany
| | - Soraya Hölper
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
- Sanofi AG, Frankfurt, Germany
| | - Sara Uhan
- Department of Hematology, Oncology and Cancer Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Max Delbrück Center, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Max Delbrück Center, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Max Delbrück Center, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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4
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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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5
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Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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Szaflarski W, Leśniczak-Staszak M, Sowiński M, Ojha S, Aulas A, Dave D, Malla S, Anderson P, Ivanov P, Lyons SM. Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity. Nucleic Acids Res 2022; 50:1033-1051. [PMID: 34928368 PMCID: PMC8789083 DOI: 10.1093/nar/gkab1231] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 01/20/2023] Open
Abstract
The production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here, we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but is independently regulated. Failure to coordinately control ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils how the rapid translational shut-off in response to stress coordinates with rRNA synthesis production to maintain nucleolar integrity.
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Affiliation(s)
- Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
| | - Marta Leśniczak-Staszak
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
| | - Mateusz Sowiński
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań, Poland
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
- The Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
| | - Anaïs Aulas
- Predictive Oncology Laboratory, Cancer Research Center of Marseille (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Dhwani Dave
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
- The Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
| | - Paul Anderson
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
- The Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
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7
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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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8
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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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9
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Zonneville J, Wang M, Alruwaili MM, Smith B, Melnick M, Eng KH, Melendy T, Park BH, Iyer R, Fountzilas C, Bakin AV. Selective therapeutic strategy for p53-deficient cancer by targeting dysregulation in DNA repair. Commun Biol 2021; 4:862. [PMID: 34253820 PMCID: PMC8275734 DOI: 10.1038/s42003-021-02370-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Breast carcinomas commonly carry mutations in the tumor suppressor p53, although therapeutic efforts to target mutant p53 have previously been unfruitful. Here we report a selective combination therapy strategy for treatment of p53 mutant cancers. Genomic data revealed that p53 mutant cancers exhibit high replication activity and express high levels of the Base-Excision Repair (BER) pathway, whereas experimental testing showed substantial dysregulation in BER. This defect rendered accumulation of DNA damage in p53 mutant cells upon treatment with deoxyuridine analogues. Notably, inhibition of poly (ADP-ribose) polymerase (PARP) greatly enhanced this response, whereas normal cells responded with activation of the p53-p21 axis and cell cycle arrest. Inactivation of either p53 or p21/CDKN1A conferred the p53 mutant phenotype. Preclinical animal studies demonstrated a greater anti-neoplastic efficacy of the drug combination (deoxyuridine analogue and PARP inhibitor) than either drug alone. This work illustrates a selective combination therapy strategy for p53 mutant cancers that will improve survival rates and outcomes for thousands of breast cancer patients.
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Affiliation(s)
- Justin Zonneville
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Moyi Wang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mohammed M Alruwaili
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Brandon Smith
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Megan Melnick
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Thomas Melendy
- Department of Microbiology & Immunology and Biochemistry, University at Buffalo, Buffalo, NY, USA
| | - Ben Ho Park
- The Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renuka Iyer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christos Fountzilas
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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10
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Urbonaite G, Lee JTH, Liu P, Parada GE, Hemberg M, Acar M. A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Commun Biol 2021; 4:822. [PMID: 34193958 PMCID: PMC8245502 DOI: 10.1038/s42003-021-02320-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
Stochastic gene expression leads to inherent variability in expression outcomes even in isogenic single-celled organisms grown in the same environment. The Drop-Seq technology facilitates transcriptomic studies of individual mammalian cells, and it has had transformative effects on the characterization of cell identity and function based on single-cell transcript counts. However, application of this technology to organisms with different cell size and morphology characteristics has been challenging. Here we present yeastDrop-Seq, a yeast-optimized platform for quantifying the number of distinct mRNA molecules in a cell-specific manner in individual yeast cells. Using yeastDrop-Seq, we measured the transcriptomic impact of the lifespan-extending compound mycophenolic acid and its epistatic agent guanine. Each treatment condition had a distinct transcriptomic footprint on isogenic yeast cells as indicated by distinct clustering with clear separations among the different groups. The yeastDrop-Seq platform facilitates transcriptomic profiling of yeast cells for basic science and biotechnology applications.
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Affiliation(s)
- Guste Urbonaite
- Systems Biology Institute, Yale University, West Haven, CT, USA.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Ping Liu
- Systems Biology Institute, Yale University, West Haven, CT, USA.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. .,Evergrande Center for Immunologic Disease, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Murat Acar
- Systems Biology Institute, Yale University, West Haven, CT, USA. .,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA. .,Department of Physics, Yale University, New Haven, CT, USA.
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11
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Martín-Villanueva S, Gutiérrez G, Kressler D, de la Cruz J. Ubiquitin and Ubiquitin-Like Proteins and Domains in Ribosome Production and Function: Chance or Necessity? Int J Mol Sci 2021; 22:ijms22094359. [PMID: 33921964 PMCID: PMC8122580 DOI: 10.3390/ijms22094359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin is a small protein that is highly conserved throughout eukaryotes. It operates as a reversible post-translational modifier through a process known as ubiquitination, which involves the addition of one or several ubiquitin moieties to a substrate protein. These modifications mark proteins for proteasome-dependent degradation or alter their localization or activity in a variety of cellular processes. In most eukaryotes, ubiquitin is generated by the proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor, or as a single N-terminal moiety to ribosomal proteins, which are practically invariably eL40 and eS31. Herein, we summarize the contribution of the ubiquitin moiety within precursors of ribosomal proteins to ribosome biogenesis and function and discuss the biological relevance of having maintained the explicit fusion to eL40 and eS31 during evolution. There are other ubiquitin-like proteins, which also work as post-translational modifiers, among them the small ubiquitin-like modifier (SUMO). Both ubiquitin and SUMO are able to modify ribosome assembly factors and ribosomal proteins to regulate ribosome biogenesis and function. Strikingly, ubiquitin-like domains are also found within two ribosome assembly factors; hence, the functional role of these proteins will also be highlighted.
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Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41009 Seville, Spain;
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
| | - Gabriel Gutiérrez
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
- Correspondence: (D.K.); (J.d.l.C.); Tel.: +41-26-300-86-45 (D.K.); +34-955-923-126 (J.d.l.C.)
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41009 Seville, Spain;
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
- Correspondence: (D.K.); (J.d.l.C.); Tel.: +41-26-300-86-45 (D.K.); +34-955-923-126 (J.d.l.C.)
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12
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Zhao J, Yang Y, Fan Y, Yi J, Zhang C, Gu Z, Pan W, Gu J, Liao W, Fang W. Ribosomal Protein L40e Fused With a Ubiquitin Moiety Is Essential for the Vegetative Growth, Morphological Homeostasis, Cell Cycle Progression, and Pathogenicity of Cryptococcus neoformans. Front Microbiol 2020; 11:570269. [PMID: 33224112 PMCID: PMC7674629 DOI: 10.3389/fmicb.2020.570269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/20/2020] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin is a highly conserved protein required for various fundamental cellular processes in eukaryotes. Herein, we first report the contribution of the ubiquitin fusion protein Ubi1 (a ubiquitin monomer fused with the ribosome protein L40e, Rpl40e) in the growth and pathogenicity of Cryptococcus neoformans. UBI1 deletion resulted in severe growth restriction of C. neoformans, whose growth rate was positively correlated with UBI1 expression level. The growth defect of the ubi1Δ strain could be closely associated with its morphological abnormalities, such as its reduced ribosome particles. In addition, the ubi1Δ mutant also displayed increased cell ploidy, cell cycle arrest, and decreased intracellular survival inside macrophages. All these phenotypes were reversed by the reconstitution of the full-length UBI1 gene or RPL40a domain. Mouse survival and fungal burden assays further revealed a severely attenuated pathogenicity for the ubi1Δ mutant, which is probably associated with its reduced stress tolerance and the induction of T-helper 1-type immune response. Taken together, Ubi1 is required for maintaining the vegetative growth, morphological homeostasis, cell cycle progression, and pathogenicity in vivo of C. neoformans. The pleiotropic roles of Ubi1 are dependent on the presence of Rpl40e and associated with its regulation of cryptococcal ribosome biogenesis.
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Affiliation(s)
- Jingyu Zhao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yali Yang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Department of Dermatology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibin Fan
- Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jiu Yi
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chao Zhang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhongkai Gu
- The Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Julin Gu
- Department of Dermatology, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wei Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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13
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Babaylova ES, Kolobova AV, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data. Biochimie 2020; 177:68-77. [DOI: 10.1016/j.biochi.2020.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023]
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14
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Abstract
Pheochromocytoma (PCC) is a rare, mostly benign tumour of the adrenal medulla. Hereditary PCC accounts for ~35% of cases and has been associated with germline mutations in several cancer susceptibility genes (e.g., KIF1B, SDHB, VHL, SDHD, RET). We performed whole-exome sequencing in a family with four PCC-affected patients in two consecutive generations and identified a potential novel candidate pathogenic variant in the REXO2 gene that affects splicing (c.531-1G>T (NM 015523.3)), which co-segregated with the phenotype in the family. REXO2 encodes for RNA exonuclease 2 protein and localizes to 11q23, a chromosomal region displaying allelic imbalance in PCC. REXO2 protein has been associated with DNA repair, replication and recombination processes and thus its inactivation may contribute to tumorigenesis. While the study suggests that this novel REXO2 gene variant underlies PCC in this family, additional functional studies are required in order to establish the putative role of the REXO2 gene in PCC predisposition.
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15
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Lin YL, Chung CL, Chen MH, Chen CH, Fang SC. SUMO Protease SMT7 Modulates Ribosomal Protein L30 and Regulates Cell-Size Checkpoint Function. THE PLANT CELL 2020; 32:1285-1307. [PMID: 32060174 PMCID: PMC7145494 DOI: 10.1105/tpc.19.00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/02/2020] [Accepted: 02/11/2020] [Indexed: 05/10/2023]
Abstract
Proliferating cells actively coordinate growth and cell division to ensure cell-size homeostasis; however, the underlying mechanism through which size is controlled is poorly understood. Defect in a SUMO protease protein, suppressor of mat3 7 (SMT7), has been shown to reduce cell division number and increase cell size of the small-size mutant mating type locus 3-4 (mat3-4), which contains a defective retinoblastoma tumor suppressor-related protein of Chlamydomonas (Chlamydomonas reinhardtii). Here we describe development of an in vitro SUMOylation system using Chlamydomonas components and use it to provide evidence that SMT7 is a bona fide SUMO protease. We further demonstrate that the SUMO protease activity is required for supernumerous mitotic divisions of the mat3-4 cells. In addition, we identified RIBOSOMAL PROTEIN L30 (RPL30) as a prime SMT7 target and demonstrated that its SUMOylation is an important modulator of cell division in mat3-4 cells. Loss of SMT7 caused elevated SUMOylated RPL30 levels. Importantly, overexpression of the translational fusion version of RPL30-SUMO4, which mimics elevation of the SUMOylated RPL30 protein in mat3-4, caused a decrease in mitotic division and recapitulated the size-increasing phenotype of the smt7-1 mat3-4 cells. In summary, our study reveals a novel mechanism through which a SUMO protease regulates cell division in the mat3-4 mutant of Chlamydomonas and provides yet another important example of the role that protein SUMOylation can play in regulating key cellular processes, including cell division.
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Affiliation(s)
- Yen-Ling Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 402, Taiwan
| | - Chin-Lin Chung
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Hui Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 741, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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16
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Cell trapping microfluidic chip made of Cyclo olefin polymer enabling two concurrent cell biology experiments with long term durability. Biomed Microdevices 2020; 22:20. [DOI: 10.1007/s10544-020-0474-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Zonneville J, Wong V, Limoge M, Nikiforov M, Bakin AV. TAK1 signaling regulates p53 through a mechanism involving ribosomal stress. Sci Rep 2020; 10:2517. [PMID: 32054925 PMCID: PMC7018718 DOI: 10.1038/s41598-020-59340-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/22/2020] [Indexed: 01/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is among the most aggressive forms of breast cancer with limited therapeutic options. TAK1 is implicated in aggressive behavior of TNBC, while means are not fully understood. Here, we report that pharmacological blockade of TAK1 signaling hampered ribosome biogenesis (RBG) by reducing expression of RBG regulators such as RRS1, while not changing expression of ribosomal core proteins. Notably, TAK1 blockade upregulated expression of p53 target genes in cell lines carrying wild type (wt) TP53 but not in p53-mutant cells, suggesting involvement of ribosomal stress in the response. Accordingly, p53 activation by blockade of TAK1 was prevented by depletion of ribosomal protein RPL11. Further, siRNA-mediated depletion of TAK1 or RELA resulted in RPL11-dependent activation of p53 signaling. Knockdown of RRS1 was sufficient to disrupt nucleolar structures and resulted in activation of p53. TCGA data showed that TNBCs express high levels of RBG regulators, and elevated RRS1 levels correlate with unfavorable prognosis. Cytotoxicity data showed that TNBC cell lines are more sensitive to TAK1 inhibitor compared to luminal and HER2+ cell lines. These results show that TAK1 regulates p53 activation by controlling RBG factors, and the TAK1-ribosome axis is a potential therapeutic target in TNBC.
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Affiliation(s)
- Justin Zonneville
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, 14263, USA
| | - Vincent Wong
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Michelle Limoge
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, 14263, USA
| | - Mikhail Nikiforov
- Department of Cancer Biology, Wake Forest University, Winston-Salem, NC, 27101, USA
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, 14263, USA.
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18
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Rahman N, Shamsuzzaman M, Lindahl L. Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5. PLoS One 2020; 15:e0222479. [PMID: 31986150 PMCID: PMC6984702 DOI: 10.1371/journal.pone.0222479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Inhibition of the synthesis of an essential ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception and this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for the formation of their cognate subunit, it would be predicted that accumulation of extra-ribosomal uL18/L5 is specific to restriction of 60S assembly and does not occur abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does lead to accumulation of uL18/L5 outside of the ribosome. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. Our results also show extra-ribosomal uL18/L5 is formed during 60S assembly, not during degradation of mature cytoplasmic 60S subunits. Finally, we propose a model for the accumulation of extra-ribosomal uL18 in response to the abolition of 40S r-proteins.
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Affiliation(s)
- Nusrat Rahman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
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19
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Inhibition of tRNA Gene Transcription by the Immunosuppressant Mycophenolic Acid. Mol Cell Biol 2019; 40:MCB.00294-19. [PMID: 31658995 PMCID: PMC6908259 DOI: 10.1128/mcb.00294-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Mycophenolic acid (MPA) is the active metabolite of mycophenolate mofetil, a drug that is widely used for immunosuppression in organ transplantation and autoimmune diseases, as well as anticancer chemotherapy. It inhibits IMP dehydrogenase, a rate-limiting enzyme in de novo synthesis of guanidine nucleotides. Mycophenolic acid (MPA) is the active metabolite of mycophenolate mofetil, a drug that is widely used for immunosuppression in organ transplantation and autoimmune diseases, as well as anticancer chemotherapy. It inhibits IMP dehydrogenase, a rate-limiting enzyme in de novo synthesis of guanidine nucleotides. MPA treatment interferes with transcription elongation, resulting in a drastic reduction of pre-rRNA and pre-tRNA synthesis, the disruption of the nucleolus, and consequently cell cycle arrest. Here, we investigated the mechanism whereby MPA inhibits RNA polymerase III (Pol III) activity, in both yeast and mammalian cells. We show that MPA rapidly inhibits Pol III by depleting GTP. Although MPA treatment can activate p53, this is not required for Pol III transcriptional inhibition. The Pol III repressor MAF1 is also not responsible for inhibiting Pol III in response to MPA treatment. We show that upon MPA treatment, the levels of selected Pol III subunits decrease, but this is secondary to transcriptional inhibition. Chromatin immunoprecipitation (ChIP) experiments show that Pol III does not fully dissociate from tRNA genes in yeast treated with MPA, even though there is a sharp decrease in the levels of newly transcribed tRNAs. We propose that in yeast, GTP depletion may lead to Pol III stalling.
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20
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Herrera MC, Chymkowitch P, Robertson JM, Eriksson J, Bøe SO, Alseth I, Enserink JM. Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity. Nucleic Acids Res 2019; 46:11698-11711. [PMID: 30247619 PMCID: PMC6294503 DOI: 10.1093/nar/gky846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023] Open
Abstract
tRNA genes are transcribed by RNA polymerase III (RNAPIII). During recent years it has become clear that RNAPIII activity is strictly regulated by the cell in response to environmental cues and the homeostatic status of the cell. However, the molecular mechanisms that control RNAPIII activity to regulate the amplitude of tDNA transcription in normally cycling cells are not well understood. Here, we show that tRNA levels fluctuate during the cell cycle and reveal an underlying molecular mechanism. The cyclin Clb5 recruits the cyclin dependent kinase Cdk1 to tRNA genes to boost tDNA transcription during late S phase. At tDNA genes, Cdk1 promotes the recruitment of TFIIIC, stimulates the interaction between TFIIIB and TFIIIC, and increases the dynamics of RNA polymerase III in vivo. Furthermore, we identified Bdp1 as a putative Cdk1 substrate in this process. Preventing Bdp1 phosphorylation prevented cell cycle-dependent recruitment of TFIIIC and abolished the cell cycle-dependent increase in tDNA transcription. Our findings demonstrate that under optimal growth conditions Cdk1 gates tRNA synthesis in S phase by regulating the RNAPIII machinery, revealing a direct link between the cell cycle and RNAPIII activity.
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Affiliation(s)
- Maria C Herrera
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
| | - Joseph M Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Eriksson
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Stig Ove Bøe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, the Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371, Norway
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21
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Albert B, Kos-Braun IC, Henras AK, Dez C, Rueda MP, Zhang X, Gadal O, Kos M, Shore D. A ribosome assembly stress response regulates transcription to maintain proteome homeostasis. eLife 2019; 8:45002. [PMID: 31124783 PMCID: PMC6579557 DOI: 10.7554/elife.45002] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Given the extremely high level of RP synthesis in rapidly growing cells, alteration of any step in the ribosome assembly process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. Here, we show that arrest of ribosome biogenesis in the budding yeast Saccharomyces cerevisiae triggers rapid activation of a highly specific stress pathway that coordinately upregulates Hsf1 target genes and downregulates RP genes. Activation of Hsf1 target genes requires neo-synthesis of RPs, which accumulate in an insoluble fraction and presumably titrate a negative regulator of Hsf1, the Hsp70 chaperone. RP aggregation is also coincident with that of the RP gene activator Ifh1, a transcription factor that is rapidly released from RP gene promoters. Our data support a model in which the levels of newly synthetized RPs, imported into the nucleus but not yet assembled into ribosomes, work to continuously balance Hsf1 and Ifh1 activity, thus guarding against proteotoxic stress during ribosome assembly. When yeast cells are growing at top speed, they can make 2,000 new ribosomes every minute. These enormous molecular assemblies are the protein-making machines of the cell. Building new ribosomes is one of the most energy-demanding parts of cell growth and, if the process goes wrong, the results can be catastrophic. The proteins that make up the ribosomes themselves are sticky. Left unattended, they start to form toxic clumps inside the compartment that houses most of the cell’s DNA, the nucleus. A protein called Heat shock factor 1, or Hsf1 for short, plays an important role in the cell's quality control systems. It helps to manage sticky proteins by switching on genes that break down protein clumps and prevent new clumps from forming. Hsf1 levels start to rise whenever cells are struggling to keep up with protein production. If it is half-finished ribosomes that are causing the problem, cells can stop making ribosome proteins. The protein in charge of this in yeast is Ifh1. It is a transcription factor that sits at the front of the genes for ribosome proteins, switching them on. When yeast cells get stressed, Ifh1 drops away from the genes within minutes, switching them off again. Yet how this happens, and how it links to Hsf1, is a mystery. To start to provide some answers, Albert et al. disrupted the production of ribosomes in yeast cells and examined the consequences. This revealed a new rescue response, that they named the “ribosome assembly stress response”. Both Hsf1 and Ifh1 are sensitive to the build-up of unfinished ribosomes in the nucleus. As expected, Hsf1 activated when ribosome proteins started to build up, and switched on the genes needed to manage the protein clumps. The effect on Isfh1, however, was unexpected. When the unassembled ribosome proteins started to build up, it was the clumps themselves that pulled the Ifh1 proteins off the genes. The unassembled ribosomes proteins seemed to be stopping their own production. Low levels of clumped ribosome proteins in the nuclei of unstressed cells also helped to keep Hsf1 active and pull Ifh1 off the ribosome genes. It is possible that this provides continual protection against a toxic protein build-up. These findings are not only important for understanding yeast cells; cancer cells also need to produce ribosomes at a very high rate to sustain their rapid growth. They too might be prone to stresses that interrupt their ribosome assembly. As such, understanding more about this process could one day lead to new therapies to target cancer cells.
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Affiliation(s)
- Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | | | - Anthony K Henras
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Christophe Dez
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Maria Paula Rueda
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Xu Zhang
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Olivier Gadal
- Centre de Biologie Intégrative, Université Paul Sabatier, Toulouse, France
| | - Martin Kos
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
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22
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Płonka M, Wawrzycka D, Wysocki R, Boguta M, Cieśla M. Coupling of RNA polymerase III assembly to cell cycle progression in Saccharomyces cerevisiae. Cell Cycle 2019; 18:500-510. [PMID: 30760101 DOI: 10.1080/15384101.2019.1578134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Assembly of the RNA polymerases in both yeast and humans is proposed to occur in the cytoplasm prior to their nuclear import. Our previous studies identified a cold-sensitive mutation, rpc128-1007, in the yeast gene encoding the second largest Pol III subunit, Rpc128. rpc128-1007 is associated with defective assembly of Pol III complex and, in consequence, decreased level of tRNA synthesis. Here, we show that rpc128-1007 mutant cells remain largely unbudded and larger than wild type cells. Flow cytometry revealed that most rpc128-1007 mutant cells have G1 DNA content, suggesting that this mutation causes pronounced cell cycle delay in the G1 phase. Increased expression of gene encoding Rbs1, the Pol III assembly/import factor, could counteract G1 arrest observed in the rpc128-1007 mutant and restore wild type morphology of mutant cells. Concomitantly, cells lacking Rbs1 show a mild delay in G1 phase exit, indicating that Rbs1 is required for timely cell cycle progression. Using the double rpc128-1007 maf1Δ mutant in which tRNA synthesis is recovered, we confirmed that the Pol III assembly defect associated with rpc128-1007 is a primary cause of cell cycle arrest. Together our results indicate that impairment of Pol III complex assembly is coupled to cell cycle inhibition in the G1 phase.
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Affiliation(s)
- Marta Płonka
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
| | - Donata Wawrzycka
- b Department of Genetics and Cell Physiology, Institute of Experimental Biology , University of Wrocław , Wrocław , Poland
| | - Robert Wysocki
- b Department of Genetics and Cell Physiology, Institute of Experimental Biology , University of Wrocław , Wrocław , Poland
| | - Magdalena Boguta
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
| | - Małgorzata Cieśla
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
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23
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Leśniewska E, Cieśla M, Boguta M. Repression of yeast RNA polymerase III by stress leads to ubiquitylation and proteasomal degradation of its largest subunit, C160. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:25-34. [PMID: 30342998 DOI: 10.1016/j.bbagrm.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/04/2018] [Accepted: 10/12/2018] [Indexed: 12/29/2022]
Abstract
Respiratory growth and various stress conditions repress RNA polymerase III (Pol III) transcription in Saccharomyces cerevisiae. Here we report a degradation of the largest Pol III catalytic subunit, C160 as a consequence of Pol III transcription repression. We observed C160 degradation in response to transfer of yeast from fermentation to respiration conditions, as well as treatment with rapamycin or inhibition of nucleotide biosynthesis. We also detected ubiquitylated forms of C160 and demonstrated that C160 protein degradation is dependent on proteasome activity. A comparable time-course study of Pol III repression upon metabolic shift from fermentation to respiration shows that the transcription inhibition is correlated with Pol III dissociation from chromatin but that the degradation of C160 subunit is a downstream event. Despite blocking degradation of C160 by proteasome, Pol III-transcribed genes are under proper regulation. We postulate that the degradation of C160 is activated under stress conditions to reduce the amount of existing Pol III complex and prevent its de novo assembly.
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Affiliation(s)
- Ewa Leśniewska
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Małgorzata Cieśla
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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24
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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
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Affiliation(s)
- Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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25
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Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae. Genetics 2017; 207:1441-1456. [PMID: 29046400 PMCID: PMC5714458 DOI: 10.1534/genetics.117.300388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/12/2017] [Indexed: 11/26/2022] Open
Abstract
Transposons can impact the host genome by altering gene expression and participating in chromosome rearrangements. Therefore, organisms evolved different ways to minimize the level of transposition. In Saccharomyces cerevisiae and its close relative S. paradoxus, Ty1 copy number control (CNC) is mediated by the self-encoded restriction factor p22, which is derived from the GAG capsid gene and inhibits virus-like particle (VLP) assembly and function. Based on secondary screens of Ty1 cofactors, we identified LOC1, a RNA localization/ribosome biogenesis gene that affects Ty1 mobility predominantly in strains harboring Ty1 elements. Ribosomal protein mutants rps0bΔ and rpl7aΔ displayed similar CNC-specific phenotypes as loc1Δ, suggesting that ribosome biogenesis is critical for CNC. The level of Ty1 mRNA and Ty1 internal (Ty1i) transcripts encoding p22 was altered in these mutants, and displayed a trend where the level of Ty1i RNA increased relative to full-length Ty1 mRNA. The level of p22 increased in these mutants, and the half-life of p22 also increased in a loc1Δ mutant. Transcriptomic analyses revealed small changes in the level of Ty1 transcripts or efficiency of translation initiation in a loc1Δ mutant. Importantly, a loc1Δ mutant had defects in assembly of Gag complexes and packaging Ty1 RNA. Our results indicate that defective ribosome biogenesis enhances CNC by increasing the level of p22, and raise the possibility for versatile links between VLP assembly, its cytoplasmic environment, and a novel stress response.
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26
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Shamsuzzaman M, Bommakanti A, Zapinsky A, Rahman N, Pascual C, Lindahl L. Analysis of cell cycle parameters during the transition from unhindered growth to ribosomal and translational stress conditions. PLoS One 2017; 12:e0186494. [PMID: 29028845 PMCID: PMC5640253 DOI: 10.1371/journal.pone.0186494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/01/2017] [Indexed: 02/07/2023] Open
Abstract
Abrogation of ribosome synthesis (ribosomal stress) leads to cell cycle arrest. However, the immediate cell response to cessation of ribosome formation and the transition from normal cell proliferation to cell cycle arrest have not been characterized. Furthermore, there are conflicting conclusions about whether cells are arrested in G2/M or G1, and whether the cause is dismantling ribosomal assembly per se, or the ensuing decreased number of translating ribosomes. To address these questions, we have compared the time kinetics of key cell cycle parameters after inhibiting ribosome formation or function in Saccharomyces cerevisiae. Within one-to-two hours of repressing genes for individual ribosomal proteins or Translation Elongation factor 3, configurations of spindles, spindle pole bodies began changing. Actin began depolarizing within 4 hours. Thus the loss of ribosome formation and function is sensed immediately. After several hours no spindles or mitotic actin rings were visible, but membrane ingression was completed in most cells and Ace2 was localized to daughter cell nuclei demonstrating that the G1 stage was reached. Thus cell division was completed without the help of a contractile actin ring. Moreover, cell wall material held mother and daughter cells together resulting in delayed cell separation, suggesting that expression or function of daughter gluconases and chitinases is inhibited. Moreover, cell development changes in very similar ways in response to inhibition of ribosome formation and function, compatible with the notion that decreased translation capacity contributes to arresting the cell cycle after abrogation of ribosome biogenesis. Potential implications for the mechanisms of diseases caused by mutations in ribosomal genes (ribosomopathies) are discussed.
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Affiliation(s)
- Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Ananth Bommakanti
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Aviva Zapinsky
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Nusrat Rahman
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Clarence Pascual
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
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27
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de la Cruz J, Gómez-Herreros F, Rodríguez-Galán O, Begley V, de la Cruz Muñoz-Centeno M, Chávez S. Feedback regulation of ribosome assembly. Curr Genet 2017; 64:393-404. [PMID: 29022131 DOI: 10.1007/s00294-017-0764-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 12/12/2022]
Abstract
Ribosome biogenesis is a crucial process for growth and constitutes the major consumer of cellular resources. This pathway is subjected to very stringent regulation to ensure correct ribosome manufacture with a wide variety of environmental and metabolic changes, and intracellular insults. Here we summarise our current knowledge on the regulation of ribosome biogenesis in Saccharomyces cerevisiae by particularly focusing on the feedback mechanisms that maintain ribosome homeostasis. Ribosome biogenesis in yeast is controlled mainly at the level of the production of both pre-rRNAs and ribosomal proteins through the transcriptional and post-transcriptional control of the TORC1 and protein kinase A signalling pathways. Pre-rRNA processing can occur before or after the 35S pre-rRNA transcript is completed; the switch between these two alternatives is regulated by growth conditions. The expression of both ribosomal proteins and the large family of transacting factors involved in ribosome biogenesis is co-regulated. Recently, it has been shown that the synthesis of rRNA and ribosomal proteins, but not of trans-factors, is coupled. Thus the so-called CURI complex sequesters specific transcription factor Ifh1 to repress ribosomal protein genes when rRNA transcription is impaired. We recently found that an analogue system should operate to control the expression of transacting factor genes in response to actual ribosome assembly performance. Regulation of ribosome biogenesis manages situations of imbalanced ribosome production or misassembled ribosomal precursors and subunits, which have been closely linked to distinct human diseases.
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Affiliation(s)
- Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - María de la Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
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28
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Wu XL, Yang ZW, He L, Dong PD, Hou MX, Meng XK, Zhao HP, Wang ZY, Wang F, Baoluri, Wurenqimuge, Agudamu, Jia YF, Shi L. RRS1 silencing suppresses colorectal cancer cell proliferation and tumorigenesis by inhibiting G2/M progression and angiogenesis. Oncotarget 2017; 8:82968-82980. [PMID: 29137316 PMCID: PMC5669942 DOI: 10.18632/oncotarget.20897] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/26/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. Ribosome biogenesis regulatory protein homolog (RRS1) is an essential factor involved in ribosome biogenesis, while its role in CRC remains largely unclear. Here, we found that RRS1 expression was significantly higher in CRC tissues compared with adjacent normal tissues. RRS1 High expression also predicted poor overall survival of CRC patients. Knockdown of RRS1 induced the G2/M cell cycle arrest, apoptosis and suppressed the proliferation of RKO and HCT-116 CRC cells. Furthermore, angiogenesis was also reduced in CRC cells after RRS1 knockdown. In addition, suppression of RRS1 blunted the tumor formation of CRC cells in nude mice. At the molecular level, silencing of RRS1 decreased the expression of M-phase inducer phosphatase 3 (CDC25C), Cyclin-dependent kinase 1 (CDK1), antigen KI-67 (KI67) and increased the protein level of cyclin-dependent kinase inhibitor 1 (CDKN1A) and tumor suppressor p53 (p53). Taken together, our findings provide evidence that RRS1 may promote the development of colon cancer. Therefore, targeting RRS1 may be a promising therapeutic strategy for CRC patients.
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Affiliation(s)
- Xin-Lin Wu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Zhi-Wen Yang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Li He
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Pei-De Dong
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Ming-Xing Hou
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Xing-Kai Meng
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Hai-Ping Zhao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Zhao-Yang Wang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Feng Wang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Baoluri
- Department of Pathology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China.,Institute of Pathology and Pathophysiology, Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Wurenqimuge
- Department of Pathology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China.,Institute of Pathology and Pathophysiology, Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Agudamu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Yong-Feng Jia
- Department of Pathology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China.,Institute of Pathology and Pathophysiology, Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
| | - Lin Shi
- Department of Pathology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China.,Institute of Pathology and Pathophysiology, Inner Mongolia Medical University, Hohhot 010059, Inner Mongolian Autonomous Region, China
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29
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Rajput P, Pandey V, Kumar V. Stimulation of ribosomal RNA gene promoter by transcription factor Sp1 involves active DNA demethylation by Gadd45-NER pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:953-63. [PMID: 27156884 DOI: 10.1016/j.bbagrm.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/23/2016] [Accepted: 05/04/2016] [Indexed: 01/29/2023]
Abstract
The well-studied Pol II transcription factor Sp1 has not been investigated for its regulatory role in rDNA transcription. Here, we show that Sp1 bound to specific sites on rDNA and localized into the nucleoli during the G1 phase of cell cycle to activate rDNA transcription. It facilitated the recruitment of Pol I pre-initiation complex and impeded the binding of nucleolar remodeling complex (NoRC) to rDNA resulting in the formation of euchromatin active state. More importantly, Sp1 also orchestrated the site-specific binding of Gadd45a-nucleotide excision repair (NER) complex resulting in active demethylation and transcriptional activation of rDNA. Interestingly, knockdown of Sp1 impaired rDNA transcription due to reduced engagement of the Gadd45a-NER complex and hypermethylation of rDNA. Thus, the present study unveils a novel role of Sp1 in rDNA transcription involving promoter demethylation.
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MESH Headings
- A549 Cells
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Nucleolus/metabolism
- DNA Methylation
- DNA Repair
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Epigenesis, Genetic
- Euchromatin/chemistry
- Euchromatin/metabolism
- G1 Phase
- Genes, Reporter
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HCT116 Cells
- HEK293 Cells
- Humans
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- Sp1 Transcription Factor/antagonists & inhibitors
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Transcription, Genetic
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Affiliation(s)
- Pallavi Rajput
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Vijaya Pandey
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Vijay Kumar
- Virology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
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30
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Li Y, Liu D, López-Paz C, Olson BJ, Umen JG. A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division. eLife 2016; 5:e10767. [PMID: 27015111 PMCID: PMC4841777 DOI: 10.7554/elife.10767] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/24/2016] [Indexed: 01/04/2023] Open
Abstract
Proliferating cells actively control their size by mechanisms that are poorly understood. The unicellular green alga Chlamydomonas reinhardtii divides by multiple fission, wherein a ‘counting’ mechanism couples mother cell-size to cell division number allowing production of uniform-sized daughters. We identified a sizer protein, CDKG1, that acts through the retinoblastoma (RB) tumor suppressor pathway as a D-cyclin-dependent RB kinase to regulate mitotic counting. Loss of CDKG1 leads to fewer mitotic divisions and large daughters, while mis-expression of CDKG1 causes supernumerous mitotic divisions and small daughters. The concentration of nuclear-localized CDKG1 in pre-mitotic cells is set by mother cell size, and its progressive dilution and degradation with each round of cell division may provide a link between mother cell-size and mitotic division number. Cell-size-dependent accumulation of limiting cell cycle regulators such as CDKG1 is a potentially general mechanism for size control. DOI:http://dx.doi.org/10.7554/eLife.10767.001 Most cells are programmed to maintain a certain size. This property, known as size control, is achieved by balancing growth and division, such that a cell will only divide after it reaches a certain size. However, and despite years of research, it is largely unknown how cells sense their size (or growth) to be able to divide accordingly. One theory proposes that there is a “sizer” protein inside cells, and that cells measure the abundance of this protein and use it to link cell size to the process of division. However, the existence of such a protein remained unproven. Li, Liu et al. have now used the cells of the green alga Chlamydomonas to identify a candidate sizer protein. Chlamydomonas cells, like many other algae, can grow to become very large mother cells that then divide one or more times in succession to produce many daughter cells. Larger mother cells undergo more divisions than smaller mother cells in order to produce daughter cells of a correct size. Using a range of genetic and biochemical techniques, Li, Liu et al. identified a protein that is produced in Chlamydomonas cells just before they begin to divide. Larger mother cells contain more of this protein than smaller cells and the protein encourages cells to divide. For example, mutant cells that lack this protein divided too few times, while cells that produce too much of it divided too many times. The protein, called CDKG1, belongs to a family of proteins that regulate cell division in many organisms. CDKG1 is a kinase – an enzyme that alters the activity of other proteins by adding a phosphate group on to them. In Chlamydomonas, CDKG1 couples cell size to cell division by altering the activity of an important protein called the retinoblastoma-related protein that controls cell division in numerous organisms. This protein is also frequently disrupted in cancers in humans. These findings shed new light on a molecular pathway for size control. Future work will need to determine how the accumulation of CDKG1 links to the size of a mother cell and how it is inactivated once daughter cells reach the appropriate size. DOI:http://dx.doi.org/10.7554/eLife.10767.002
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Affiliation(s)
- Yubing Li
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Plant Molecular and Cell Biology Program, the Horticultural and Plant Science Department, University of Florida, Gainesville, United States
| | - Dianyi Liu
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Cristina López-Paz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Donald Danforth Plant Science Center, St. Louis, United States
| | - Bradley Jsc Olson
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - James G Umen
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Donald Danforth Plant Science Center, St. Louis, United States
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31
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Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE. The importance of controlling mRNA turnover during cell proliferation. Curr Genet 2016; 62:701-710. [PMID: 27007479 DOI: 10.1007/s00294-016-0594-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
Abstract
Microbial gene expression depends not only on specific regulatory mechanisms, but also on cellular growth because important global parameters, such as abundance of mRNAs and ribosomes, could be growth rate dependent. Understanding these global effects is necessary to quantitatively judge gene regulation. In the last few years, transcriptomic works in budding yeast have shown that a large fraction of its genes is coordinately regulated with growth rate. As mRNA levels depend simultaneously on synthesis and degradation rates, those studies were unable to discriminate the respective roles of both arms of the equilibrium process. We recently analyzed 80 different genomic experiments and found a positive and parallel correlation between both RNA polymerase II transcription and mRNA degradation with growth rates. Thus, the total mRNA concentration remains roughly constant. Some gene groups, however, regulate their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulate their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lower mRNA levels by reducing mRNA stability or the transcription rate, respectively. We critically review here these results and analyze them in relation to their possible extrapolation to other organisms and in relation to the new questions they open.
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Affiliation(s)
- Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - José García-Martínez
- Departamento de Genética, Universitat de València, Burjassot, Spain.,ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Lidia Delgado-Ramos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain. .,ERI Biotecmed, Universitat de València, Burjassot, Spain.
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32
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Zones JM, Blaby IK, Merchant SS, Umen JG. High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. THE PLANT CELL 2015; 27:2743-69. [PMID: 26432862 PMCID: PMC4682324 DOI: 10.1105/tpc.15.00498] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
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Affiliation(s)
- James Matt Zones
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Abstract
A veritable explosion of primary research papers within the past 10 years focuses on nucleolar and ribosomal stress, and for good reason: with ribosome biosynthesis consuming ~80% of a cell’s energy, nearly all metabolic and signaling pathways lead ultimately to or from the nucleolus. We begin by describing p53 activation upon nucleolar stress resulting in cell cycle arrest or apoptosis. The significance of this mechanism cannot be understated, as oncologists are now inducing nucleolar stress strategically in cancer cells as a potential anti-cancer therapy. We also summarize the human ribosomopathies, syndromes in which ribosome biogenesis or function are impaired leading to birth defects or bone narrow failures; the perplexing problem in the ribosomopathies is why only certain cells are affected despite the fact that the causative mutation is systemic. We then describe p53-independent nucleolar stress, first in yeast which lacks p53, and then in other model metazoans that lack MDM2, the critical E3 ubiquitin ligase that normally inactivates p53. Do these presumably ancient p53-independent nucleolar stress pathways remain latent in human cells? If they still exist, can we use them to target >50% of known human cancers that lack functional p53?
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Affiliation(s)
- Allison James
- a Department of Biological Sciences; Louisiana State University; Baton Rouge, LA USA
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Yelick PC, Trainor PA. Ribosomopathies: Global process, tissue specific defects. Rare Dis 2015; 3:e1025185. [PMID: 26442198 PMCID: PMC4590025 DOI: 10.1080/21675511.2015.1025185] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 01/01/2023] Open
Abstract
Disruptions in ribosomal biogenesis would be expected to have global and in fact lethal effects on a developing organism. However, mutations in ribosomal protein genes have been shown in to exhibit tissue specific defects. This seemingly contradictory finding - that globally expressed genes thought to play fundamental housekeeping functions can in fact exhibit tissue and cell type specific functions - provides new insight into roles for ribosomes, the protein translational machinery of the cell, in regulating normal development and disease. Furthermore it illustrates the surprisingly dynamic nature of processes regulating cell type specific protein translation. In this review, we discuss our current knowledge of a variety of ribosomal protein mutations associated with human disease, and models to better understand the molecular mechanisms associated with each. We use specific examples to emphasize both the similarities and differences between the effects of various human ribosomal protein mutations. Finally, we discuss areas of future study that are needed to further our understanding of the role of ribosome biogenesis in normal development, and possible approaches that can be used to treat debilitating ribosomopathy diseases.
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Affiliation(s)
| | - Paul A Trainor
- Stowers Institute ; Kansas City, MO USA ; University of Kansas Medical Center ; Kansas City, KS USA
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