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Lago JC, Ganzerla MD, Dias ALA, Savietto JP. The Influence of Blue Light Exposure on Reconstructed 3-Dimensional Skin Model: Molecular Changes and Gene Expression Profile. JID INNOVATIONS 2024; 4:100252. [PMID: 38328595 PMCID: PMC10848142 DOI: 10.1016/j.xjidi.2023.100252] [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: 12/13/2021] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 02/09/2024] Open
Abstract
Recent studies have provided information about digital eye strain and the potential damage that blue light from digital devices can cause to the eyes. In this study, we analyzed the influence of blue light exposure on reconstructed 3-dimensional skin model using RNA sequencing to identify the expression of transcripts and abnormal events. Three-dimensional skin was exposed to visible light spectrum and isolated blue wavelength for 1, 2, and 4 hours to represent acute exposure and 1 hour over 4 sequential days to represent repeated exposure, respectively, in this in vitro model. We compared gene expression levels with those of unexposed control. Samples submitted to repeated exposure showed reduced AK2 and DDX47, whereas they showed increased PABPC3 gene expression, revealing a significantly negative impact. RT-PCR validation assay with exposed 3-dimensional skin compared with unexposed control regarding 1 and 4 days of incubation showed increased IL-6 signaling mechanism activation and signal transducer and activator of transcription 3 gene STAT3 gene expression, whereas it showed decreased peroxisome proliferator-activated receptor signaling mechanism activation, suggesting an influence on inflammatory pathways. We also demonstrate upregulated gene expression of KIT, MAPK2, and PI3KC in samples from exposed condition, corroborating previous findings related to pigmentation signaling stimuli. These results reveal, to our knowledge, previously unreported data that enable studies on molecular response correlation of in vitro digital blue light exposure and human skin studies.
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Xue M, Dong L, Zhang H, Li Y, Qiu K, Zhao Z, Gao M, Han L, Chan AKN, Li W, Leung K, Wang K, Pokharel SP, Qing Y, Liu W, Wang X, Ren L, Bi H, Yang L, Shen C, Chen Z, Melstrom L, Li H, Timchenko N, Deng X, Huang W, Rosen ST, Tian J, Xu L, Diao J, Chen CW, Chen J, Shen B, Chen H, Su R. METTL16 promotes liver cancer stem cell self-renewal via controlling ribosome biogenesis and mRNA translation. J Hematol Oncol 2024; 17:7. [PMID: 38302992 PMCID: PMC10835888 DOI: 10.1186/s13045-024-01526-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND While liver cancer stem cells (CSCs) play a crucial role in hepatocellular carcinoma (HCC) initiation, progression, recurrence, and treatment resistance, the mechanism underlying liver CSC self-renewal remains elusive. We aim to characterize the role of Methyltransferase 16 (METTL16), a recently identified RNA N6-methyladenosine (m6A) methyltransferase, in HCC development/maintenance, CSC stemness, as well as normal hepatogenesis. METHODS Liver-specific Mettl16 conditional KO (cKO) mice were generated to assess its role in HCC pathogenesis and normal hepatogenesis. Hydrodynamic tail-vein injection (HDTVi)-induced de novo hepatocarcinogenesis and xenograft models were utilized to determine the role of METTL16 in HCC initiation and progression. A limiting dilution assay was utilized to evaluate CSC frequency. Functionally essential targets were revealed via integrative analysis of multi-omics data, including RNA-seq, RNA immunoprecipitation (RIP)-seq, and ribosome profiling. RESULTS METTL16 is highly expressed in liver CSCs and its depletion dramatically decreased CSC frequency in vitro and in vivo. Mettl16 KO significantly attenuated HCC initiation and progression, yet only slightly influenced normal hepatogenesis. Mechanistic studies, including high-throughput sequencing, unveiled METTL16 as a key regulator of ribosomal RNA (rRNA) maturation and mRNA translation and identified eukaryotic translation initiation factor 3 subunit a (eIF3a) transcript as a bona-fide target of METTL16 in HCC. In addition, the functionally essential regions of METTL16 were revealed by CRISPR gene tiling scan, which will pave the way for the development of potential inhibitor(s). CONCLUSIONS Our findings highlight the crucial oncogenic role of METTL16 in promoting HCC pathogenesis and enhancing liver CSC self-renewal through augmenting mRNA translation efficiency.
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Affiliation(s)
- Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Honghai Zhang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- School of Pharmacy, China Medical University, Shenyang, 110001, Liaoning, China
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wei Liu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Xueer Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lili Ren
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Hongjie Bi
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Laleh Melstrom
- Division of Surgical Oncology, Department of Surgery, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, 91016, USA
| | - Nikolai Timchenko
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Graduate School of Biological Science, City of Hope, Duarte, CA, 91010, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jingyan Tian
- State Key Laboratory of Medical Genomics, Clinical Trial Center, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, 7539, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA.
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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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4
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Bartolec TK, Vázquez-Campos X, Norman A, Luong C, Johnson M, Payne RJ, Wilkins MR, Mackay JP, Low JKK. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Proc Natl Acad Sci U S A 2023; 120:e2219418120. [PMID: 37071682 PMCID: PMC10151615 DOI: 10.1073/pnas.2219418120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
Significant recent advances in structural biology, particularly in the field of cryoelectron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability, or-in the case of complexes-simply not having yet been analyzed. Here, we demonstrate the power of using cross-linking mass spectrometry (XL-MS) for the high-throughput experimental assessment of the structures of proteins and protein complexes. This included those produced by high-resolution but in vitro experimental data, as well as in silico predictions based on amino acid sequence alone. We present the largest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that models of proteins and their complexes predicted by AlphaFold2, and inspired and corroborated by the XL-MS data, offer opportunities to deeply mine the structural proteome and interactome and reveal mechanisms underlying protein structure and function.
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Affiliation(s)
- Tara K. Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Xabier Vázquez-Campos
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
| | - Clement Luong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Marcus Johnson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Richard J. Payne
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW2006, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
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5
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Nazemi-Rafie J, Fatehi F, Hasrak S. A comparative transcriptome analysis of the head of 1 and 9 days old worker honeybees ( Apis mellifera). BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:253-270. [PMID: 36511774 DOI: 10.1017/s0007485322000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The role of bees in the environment, economic, biodiversity and pharmaceutical industries is due to its social behavior, which is oriented from the brain and hypopharyngeal gland that is the center of royal jelly (RJ) production. Limited studies have been performed on the head gene expression profile at the RJ production stage. The aim of this study was to compare the gene expressions in 9 and 1-day-old (DO) honeybee workers in order to achieve better understanding about head gene expression pattern. After sequencing of RNAs, transcriptome and their networks were compared. The head expression profile undergoes various changes. 1662 gene transcripts had differential expressions which 1125 and 537 were up and down regulated, respectively, in 9_DO compared with 1_DO honey bees. The day 1th had more significant role in the expression of genes related to RJ production as major RJ protein 1, 2, 3, 5, 6 and 9 encoding genes, but their maximum secretion occurred at day 9th. All process related to hypopharyngeal glands activities as CYP450 gene, fatty acid synthase gene, vitamin B6 metabolism and some of genes involved in fatty acid elongation and degradation process had an upward trend from 1_DO and were age-dependent. By increasing the age, the activity of pathways related to immune system increased for keeping the health of bees against the chemical compound. The expression of aromatic amino acid genes involved in Phenylalanine, tyrosine and tryptophan biosynthesis pathway are essential for early stage of life. In 9_DO honeybees, the energy supplying, reducing stress, protein production and export pathways have a crucial role for support the body development and the social duties. It can be stated that the activity of honeybee head is focused on energy supply instead of storage, while actively trying to improve the level of cell dynamics for increasing the immunity and reducing stress. Results of current study identified key genes of certain behaviors of honeybee workers. Deeper considering of some pathways will be evaluated in future studies.
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Affiliation(s)
- Javad Nazemi-Rafie
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Foad Fatehi
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Shabnam Hasrak
- Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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6
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Marchena-Cruz E, Camino LP, Bhandari J, Silva S, Marqueta-Gracia JJ, Amdeen SA, Guillén-Mendoza C, García-Rubio ML, Calderón-Montaño JM, Xue X, Luna R, Aguilera A. DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops. Cell Rep 2023; 42:112148. [PMID: 36827184 PMCID: PMC10066596 DOI: 10.1016/j.celrep.2023.112148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.
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Affiliation(s)
- Esther Marchena-Cruz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Lola P Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Jay Bhandari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Sónia Silva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Shahad A Amdeen
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Cristina Guillén-Mendoza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José M Calderón-Montaño
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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7
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DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles. Trends Biochem Sci 2023; 48:244-258. [PMID: 36344372 DOI: 10.1016/j.tibs.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
RNA-dependent DEAD-box ATPases (DDXs) are emerging as major regulators of RNA-containing membrane-less organelles (MLOs). On the one hand, oligomerizing DDXs can promote condensate formation 'in cis', often using RNA as a scaffold. On the other hand, DDXs can disrupt RNA-RNA and RNA-protein interactions and thereby 'in trans' remodel the multivalent interactions underlying MLO formation. In this review, we discuss the best studied examples of DDXs modulating MLOs in cis and in trans. Further, we illustrate how this contributes to the dynamic assembly and turnover of MLOs which might help cells to modulate RNA sequestration and processing in a temporal and spatial manner.
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8
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Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
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Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
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9
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Chen Y, Zeng L, Wang W, Yuan J, Sun R, Yang S. DDX47 promotes cell proliferation and migration in lung adenocarcinoma. Pathol Res Pract 2022; 234:153921. [DOI: 10.1016/j.prp.2022.153921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/17/2022] [Accepted: 04/24/2022] [Indexed: 11/16/2022]
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10
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Latorre‐Muro P, Puigserver P. Atossa
: a royal link between OXPHOS metabolism and macrophage migration. EMBO J 2022; 41:e111290. [PMID: 35466422 PMCID: PMC9194787 DOI: 10.15252/embj.2022111290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/09/2022] Open
Abstract
The ability of immune cells to penetrate affected tissues is highly dependent on energy provided by mitochondria, yet their involvement in promoting migration remains unclear. Recent work by Emtenani et al (2022) describes a nuclear Atossa-Porthos axis that adjusts transcription and translation of a small subset of OXPHOS genes to increase mitochondrial bioenergetics and allow macrophage tissue invasion in flies.
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Affiliation(s)
- Pedro Latorre‐Muro
- Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Department of Cell Biology Harvard Medical School Boston MA USA
| | - Pere Puigserver
- Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Department of Cell Biology Harvard Medical School Boston MA USA
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11
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Martin ET, Blatt P, Nguyen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Dev Cell 2022; 57:883-900.e10. [PMID: 35413237 PMCID: PMC9011129 DOI: 10.1016/j.devcel.2022.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/11/2022] [Accepted: 03/10/2022] [Indexed: 01/26/2023]
Abstract
Ribosomal defects perturb stem cell differentiation, and this is the cause of ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discover that three DExD/H-box proteins govern ribosome biogenesis (RiBi) and Drosophila oogenesis. Loss of these DExD/H-box proteins, which we name Aramis, Athos, and Porthos, aberrantly stabilizes p53, arrests the cell cycle, and stalls germline stem cell (GSC) differentiation. Aramis controls cell-cycle progression by regulating translation of mRNAs that contain a terminal oligo pyrimidine (TOP) motif in their 5' UTRs. We find that TOP motifs confer sensitivity to ribosome levels that are mediated by La-related protein (Larp). One such TOP-containing mRNA codes for novel nucleolar protein 1 (Non1), a conserved p53 destabilizing protein. Upon a sufficient ribosome concentration, Non1 is expressed, and it promotes GSC cell-cycle progression via p53 degradation. Thus, a previously unappreciated TOP motif in Drosophila responds to reduced RiBi to co-regulate the translation of ribosomal proteins and a p53 repressor, coupling RiBi to GSC differentiation.
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Affiliation(s)
- Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Elaine Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sangeetha Selvam
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Hyun Ah M Yoon
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; Albany Medical College, Albany, NY 12208, USA
| | - Tyler Pocchiari
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; SUNY Upstate Medical University, Syracuse, NY 13210-2375, USA
| | - Shamsi Emtenani
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Andrea Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
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12
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Emtenani S, Martin ET, Gyoergy A, Bicher J, Genger JW, Köcher T, Akhmanova M, Guarda M, Roblek M, Bergthaler A, Hurd TR, Rangan P, Siekhaus DE. Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. EMBO J 2022; 41:e109049. [PMID: 35319107 PMCID: PMC9194793 DOI: 10.15252/embj.2021109049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 12/03/2022] Open
Abstract
Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into challenging environments require an energy boost, but what controls this capacity is unclear. Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by CG9005), which supports macrophage invasion into the germband of Drosophila by controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of Porthos, a DEAD‐box protein, and of two metabolic enzymes, lysine‐α‐ketoglutarate reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial bioenergetics. Then Porthos supports ribosome assembly and thereby raises the translational efficiency of a subset of mRNAs, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Mitochondrial respiration measurements, metabolomics, and live imaging indicate that Atossa and Porthos power up OxPhos and energy production to promote the forging of a path into tissues by leading macrophages. Since many crucial physiological responses require increases in mitochondrial energy output, this previously undescribed genetic program may modulate a wide range of cellular behaviors.
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Affiliation(s)
- Shamsi Emtenani
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Elliot T Martin
- Department of Biological Sciences, RNA Institute, University at Albany, Albany, NY, USA
| | - Attila Gyoergy
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Julia Bicher
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Maria Akhmanova
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Mariana Guarda
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Marko Roblek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Prashanth Rangan
- Department of Biological Sciences, RNA Institute, University at Albany, Albany, NY, USA
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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13
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Camborde L, Kiselev A, Pel MJC, Le Ru A, Jauneau A, Pouzet C, Dumas B, Gaulin E. An oomycete effector targets a plant RNA helicase involved in root development and defense. THE NEW PHYTOLOGIST 2022; 233:2232-2248. [PMID: 34913494 DOI: 10.1111/nph.17918] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Oomycete plant pathogens secrete effector proteins to promote disease. The damaging soilborne legume pathogen Aphanomyces euteiches harbors a specific repertoire of Small Secreted Protein effectors (AeSSPs), but their biological functions remain unknown. Here we characterize AeSSP1256. The function of AeSSP1256 is investigated by physiological and molecular characterization of Medicago truncatula roots expressing the effector. A potential protein target of AeSSP1256 is identified by yeast-two hybrid, co-immunoprecipitation, and fluorescent resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) assays, as well as promoter studies and mutant characterization. AeSSP1256 impairs M. truncatula root development and promotes pathogen infection. The effector is localized to the nucleoli rim, triggers nucleoli enlargement and downregulates expression of M. truncatula ribosome-related genes. AeSSP1256 interacts with a functional nucleocytoplasmic plant RNA helicase (MtRH10). AeSSP1256 relocates MtRH10 to the perinucleolar space and hinders its binding to plant RNA. MtRH10 is associated with ribosome-related genes, root development and defense. This work reveals that an oomycete effector targets a plant RNA helicase, possibly to trigger nucleolar stress and thereby promote pathogen infection.
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Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Andrei Kiselev
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Aurélie Le Ru
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Alain Jauneau
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Cécile Pouzet
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
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14
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Wang JX, Ma EB, Zhang JZ, Xing SP. DEAD-Box RNA Helicase DDX47 Maintains Midgut Homeostasis in Locusta migratoria. Int J Mol Sci 2022; 23:ijms23020586. [PMID: 35054771 PMCID: PMC8775783 DOI: 10.3390/ijms23020586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
Tissue homeostasis is critical for maintaining organ shape, size, and function. The condition is regulated by the balance between the generation of new cells and the loss of senescent cells, and it involves many factors and mechanisms. The midgut, an important part of the intestinal tract, is responsible for digestion and nutrient absorption in insects. LmDDX47, the ortholog of DEAD-box helicase 47 from Locusta migratoria, is indispensable for sustaining a normal midgut in the nymphs. However, the underlying cellular and molecular mechanisms remain to be elucidated. In this study, LmDDX47 knockdown resulted in atrophy of the midgut and gastric cecum in both nymph and adult locusts. After LmDDX47 knockdown, the number of regenerative and columnar cells in the midgut was significantly reduced, and cell death was induced in columnar tissue. LmDDX47 was localized to the nucleolus; this was consistent with the reduction in 18S rRNA synthesis in the LmDDX47 knockdown group. In addition, the acetylation and crotonylation levels of midgut proteins were significantly increased. Therefore, LmDDX47 could be a key regulator of midgut homeostasis, regulating 18S rRNA synthesis as well as protein acetylation and crotonylation in the migratory locust.
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Affiliation(s)
- Jun-Xiu Wang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, China; (J.-X.W.); (E.-B.M.); (J.-Z.Z.)
- College of Life Science, Shanxi University, Taiyuan 030006, China
| | - En-Bo Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, China; (J.-X.W.); (E.-B.M.); (J.-Z.Z.)
| | - Jian-Zhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, China; (J.-X.W.); (E.-B.M.); (J.-Z.Z.)
| | - Shu-Ping Xing
- Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, China; (J.-X.W.); (E.-B.M.); (J.-Z.Z.)
- Correspondence:
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15
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Bryant CJ, McCool MA, Abriola L, Surovtseva YV, Baserga SJ. A high-throughput assay for directly monitoring nucleolar rRNA biogenesis. Open Biol 2022; 12:210305. [PMID: 35078352 PMCID: PMC8790372 DOI: 10.1098/rsob.210305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Studies of the regulation of nucleolar function are critical for ascertaining clearer insights into the basic biological underpinnings of ribosome biogenesis (RB), and for future development of therapeutics to treat cancer and ribosomopathies. A number of high-throughput primary assays based on morphological alterations of the nucleolus can indirectly identify hits affecting RB. However, there is a need for a more direct high-throughput assay for a nucleolar function to further evaluate hits. Previous reports have monitored nucleolar rRNA biogenesis using 5-ethynyl uridine (5-EU) in low-throughput. We report a miniaturized, high-throughput 5-EU assay that enables specific calculation of nucleolar rRNA biogenesis inhibition, based on co-staining of the nucleolar protein fibrillarin (FBL). The assay uses two siRNA controls: a negative non-targeting siRNA control and a positive siRNA control targeting RNA Polymerase 1 (RNAP1; POLR1A), and specifically quantifies median 5-EU signal within nucleoli. Maximum nuclear 5-EU signal can also be used to monitor the effects of putative small-molecule inhibitors of RNAP1, like BMH-21, or other treatment conditions that cause FBL dispersion. We validate the 5-EU assay on 68 predominately nucleolar hits from a high-throughput primary screen, showing that 58/68 hits significantly inhibit nucleolar rRNA biogenesis. Our new method establishes direct quantification of nucleolar function in high-throughput, facilitating closer study of RB in health and disease.
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Affiliation(s)
- Carson J. Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Mason A. McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Susan J. Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Genetics, Yale School of Medicine, New Haven, CT, USA,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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16
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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17
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Małecki JM, Odonohue MF, Kim Y, Jakobsson ME, Gessa L, Pinto R, Wu J, Davydova E, Moen A, Olsen JV, Thiede B, Gleizes PE, Leidel SA, Falnes PØ. Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Res 2021; 49:3185-3203. [PMID: 33693809 PMCID: PMC8034639 DOI: 10.1093/nar/gkab088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
Protein methylation occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knockout (KO) cells, identified as 60S ribosomal protein L3 (RPL3). We also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. We found that His-245 in RPL3 carries a 3-methylhistidine (3MH; τ-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be automethylated at His-154, thus further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysome formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Marie-Francoise Odonohue
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Yeji Kim
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation, Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Luca Gessa
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jie Wu
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation, Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Bernd Thiede
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sebastian A Leidel
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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18
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MicroRNA 452 regulates ASB8, NOL8, and CDR2 expression in colorectal cancer cells. Genes Genomics 2021; 43:33-41. [PMID: 33398662 DOI: 10.1007/s13258-020-01016-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND MicroRNAs play important roles in the pathogenesis of human diseases by regulating target gene expression in specific cells or tissues. Previously, we identified microRNA 452 (MIR452), which was specifically up-regulated in early stage human colorectal cancer (CRC) tissue. OBJECTIVE The current study aims to identify and verify the target genes of MIR452 associated with CRC. METHODS A luciferase reporter system was used to confirm the effect of MIR452 on ASB8, NOL8, and CDR2 expression. The expression levels of MIR452 and the target genes were evaluated by quantitative RT-PCR (qRT-PCR) and western blotting. RESULTS We verified the association between MIR452 and three genes, ASB8, NOL8, and CDR2, and showed that their transcripts were down-regulated by MIR452. Up-regulated MIR452 also down-regulated ASB8, NOL8, and CDR2 mRNA and protein levels in CRC cells. CDR2 protein expression was decreased in CRC tissues compared to adjacent non-tumor tissues. CONCLUSIONS These results suggest that ASB8, NOL8, and CDR2 were target genes of MIR452 in CRC cells and that up-regulated MIR452 in CRC tissue regulated ASB8, NOL8, and CDR2 expression during colorectal carcinogenesis.
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19
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Wang T, Li LY, Chen YF, Fu SW, Wu ZW, Du BB, Yang XF, Zhang WS, Hao XY, Guo TK. Ribosome assembly factor URB1 contributes to colorectal cancer proliferation through transcriptional activation of ATF4. Cancer Sci 2020; 112:101-116. [PMID: 32888357 PMCID: PMC7780016 DOI: 10.1111/cas.14643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosome assembly factor URB1 is essential for ribosome biogenesis. However, its latent role in cancer remains unclear. Analysis of The Cancer Genome Atlas database and clinical tissue microarray staining showed that URB1 expression was upregulated in colorectal cancer (CRC) and prominently related to clinicopathological characteristics. Silencing of URB1 hampered human CRC cell proliferation and growth in vitro and in vivo. Microarray screening, ingenuity pathway analysis, and JASPAR assessment indicated that activating transcription factor 4 (ATF4) and X‐box binding protein 1 (XBP1) are potential downstream targets of URB1 and could transcriptionally interact through direct binding. Silencing of URB1 significantly decreased ATF4 and cyclin A2 (CCNA2) expression in vivo and in vitro. Restoration of ATF4 effectively reversed the malignant proliferation phenotype of URB1‐silenced CRC cells. Dual‐luciferase reporter and ChIP assays indicated that XBP1 transcriptionally activated ATF4 by binding with its promoter region. X‐box binding protein 1 colocalized with ATF4 in the nuclei of RKO cells, and ATF4 mRNA expression was positively regulated by XBP1. This study shows that URB1 contributes to oncogenesis and CRC growth through XBP1‐mediated transcriptional activation of ATF4. Therefore, URB1 could be a potential therapeutic target for CRC.
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Affiliation(s)
- Tao Wang
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China.,The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Lai-Yuan Li
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Yi-Feng Chen
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Si-Wu Fu
- The School of Medical College, Northwest Minzu University, Lanzhou, China
| | - Zhi-Wei Wu
- The School of Preclinical Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Bin-Bin Du
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Xiong-Fei Yang
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Wei-Sheng Zhang
- Department of Colorectal Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Xiang-Yong Hao
- Department of General Surgery, Gansu Provincial People's Hospital, Lanzhou, China
| | - Tian-Kang Guo
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Department of General Surgery, Gansu Provincial People's Hospital, Lanzhou, China
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20
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Pinto R, Vågbø CB, Jakobsson ME, Kim Y, Baltissen MP, O'Donohue MF, Guzmán UH, Małecki JM, Wu J, Kirpekar F, Olsen JV, Gleizes PE, Vermeulen M, Leidel SA, Slupphaug G, Falnes PØ. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res 2020; 48:830-846. [PMID: 31799605 PMCID: PMC6954407 DOI: 10.1093/nar/gkz1147] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023] Open
Abstract
RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remained elusive. 28S rRNA carries a single m6A modification, found at position A4220 (alternatively referred to as A4190) within a stem–loop structure, and here we show that the MTase ZCCHC4 is the enzyme responsible for introducing this modification. Accordingly, we found that ZCCHC4 localises to nucleoli, the site of ribosome assembly, and that proteins involved in RNA metabolism are overrepresented in the ZCCHC4 interactome. Interestingly, the absence of m6A4220 perturbs codon-specific translation dynamics and shifts gene expression at the translational level. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.
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Affiliation(s)
- Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Yeji Kim
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Ulises H Guzmán
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Jie Wu
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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21
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Izumikawa K, Ishikawa H, Yoshikawa H, Fujiyama S, Watanabe A, Aburatani H, Tachikawa H, Hayano T, Miura Y, Isobe T, Simpson RJ, Li L, Min J, Takahashi N. LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA. Nucleic Acids Res 2019; 47:10357-10372. [PMID: 31504794 PMCID: PMC6821171 DOI: 10.1093/nar/gkz747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/22/2019] [Accepted: 08/20/2018] [Indexed: 02/06/2023] Open
Abstract
Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine-binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hideaki Ishikawa
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Harunori Yoshikawa
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sally Fujiyama
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Akira Watanabe
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University 53, Shogoin-kawahara-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8507, Japan
| | - Hiroyuki Aburatani
- Laboratory for System Biology and Medicine, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Tachikawa
- Department of Applied Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Hayano
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Japan
| | - Yutaka Miura
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Richard J Simpson
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,La Trobe Institute for Molecular Science (LIMS) LIMS Building 1, Room 412 La Trobe University, Bundoora Victoria 3086, Australia
| | - Li Li
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jinrong Min
- Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nobuhiro Takahashi
- Department of Applied Life Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.,Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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22
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Sekiguchi T, Furuno N, Ishii T, Hirose E, Sekiguchi F, Wang Y, Kobayashi H. RagA, an mTORC1 activator, interacts with a hedgehog signaling protein, WDR35/IFT121. Genes Cells 2019; 24:151-161. [DOI: 10.1111/gtc.12663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Takeshi Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Nobuaki Furuno
- Laboratory for Amphibian Biology, Graduate School of Science Hiroshima University Higashihiroshima Japan
| | - Takashi Ishii
- Department of BiochemistryFukuoka Dental College Fukuoka Japan
| | - Eiji Hirose
- Faculty of Health Promotional Sciences Tokoha University Kitaku, Shizuoka Japan
| | - Fumiko Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Yonggang Wang
- Department of Molecular Biology, Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hideki Kobayashi
- Department of Human Nutrition, Faculty of Contemporary Life ScienceChugoku‐Gakuen University Okayama Japan
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23
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Mahmassani ZS, Reidy PT, McKenzie AI, Stubben C, Howard MT, Drummond MJ. Age-dependent skeletal muscle transcriptome response to bed rest-induced atrophy. J Appl Physiol (1985) 2019; 126:894-902. [PMID: 30605403 DOI: 10.1152/japplphysiol.00811.2018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Short-term muscle disuse induces significant muscle loss in older adults and in some reports may be more accelerated with aging. Identifying muscle transcriptional events in response to bed rest may help identify therapeutic targets to offset muscle loss. Therefore, we compared the muscle transcriptome between young and older adults after bed rest and identified candidate targets related to changes in muscle loss. RNA was sequenced (HiSeq, Illumina; DESeq, R) from muscle biopsies obtained from young [ n = 9; 23 yr (SD 3)] and older [ n = 18; 68 yr (SD 6)] adults before and after 5-day bed rest. Significantly altered pathways in both young and old subjects relating to mechanosensing and cell adhesion (Actin Cytoskeleton Signaling, ILK Signaling, RhoA Signaling, and Integrin Signaling) were altered (activation z score) to a greater extent in old subjects. Hepatic Fibrosis/Hepatic Stellate Cell Activation was the top regulated pathway significantly altered only in the old. Fifty-one differentially regulated genes were only altered in the young after bed rest and resembled a gene expression profile like that in the old at baseline. Inflammation and muscle wasting genes (CXCL2, GADD45A) were uniquely increased in the old after bed rest, and the macrophage gene MAFB decreased in the old and correlated with the change in leg lean mass. In summary, skeletal muscle dysregulation during bed rest in the old may be driven by alterations in molecules related to fibrosis, inflammation, and cell adhesion. This information may aid in the development of mechanistic-based therapies to combat muscle atrophy during short-term disuse. NEW & NOTEWORTHY Using RNA sequencing and bioinformatics approaches, we identified that older adult skeletal muscle was characterized by dysregulated pathways associated with fibrosis, inflammation (upregulated), and cell adhesion and mechanosensing (downregulated) pathways, with a subset of genes differentially regulated in old and young muscle after bed rest that may describe predisposition to muscle loss. Unique upregulated genes only expressed in old muscle after bed rest indicated increased inflammation and muscle wasting (CXCL2, GADD45A) and decreased MAFB correlated with the change in leg lean mass.
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Affiliation(s)
- Ziad S Mahmassani
- Department of Physical Therapy and Athletic Training, University of Utah , Salt Lake City, Utah
| | - Paul T Reidy
- Department of Physical Therapy and Athletic Training, University of Utah , Salt Lake City, Utah
| | - Alec I McKenzie
- Department of Physical Therapy and Athletic Training, University of Utah , Salt Lake City, Utah
| | - Chris Stubben
- Bioinformatics Shared Resource at the Huntsman Cancer Institute , Salt Lake City, Utah
| | - Michael T Howard
- Department of Genetics, University of Utah , Salt Lake City, Utah
| | - Micah J Drummond
- Department of Physical Therapy and Athletic Training, University of Utah , Salt Lake City, Utah
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24
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Okamoto Y, Abe M, Itaya A, Tomida J, Ishiai M, Takaori-Kondo A, Taoka M, Isobe T, Takata M. FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress. FEBS J 2018; 286:139-150. [PMID: 30431240 DOI: 10.1111/febs.14700] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/02/2018] [Accepted: 11/12/2018] [Indexed: 01/19/2023]
Abstract
R-loops, which consist of DNA : RNA hybrids and displaced single-strand DNA, are a major threat to genome stability. We have previously reported that a key Fanconi anemia protein, FANCD2, accumulates on large fragile genes during mild replication stress in a manner depending on R-loops. In this study, we found that FANCD2 suppresses R-loop levels. Furthermore, we identified FANCD2 interactions with RNA processing factors, including hnRNP U and DDX47. Our data suggest that FANCD2, which accumulates with R-loops in chromatin, recruits these factors and thereby promotes efficient processing of long RNA transcripts. This may lead to a reduction in transcription-replication collisions, as detected by PLA between PCNA and RNA Polymerase II, and hence, lowered R-loop levels. We propose that this mechanism might contribute to maintenance of genome stability during mild replication stress.
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Affiliation(s)
- Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masako Abe
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Akiko Itaya
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
| | - Junya Tomida
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan.,National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Japan
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25
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Awasthi S, Chakrapani B, Mahesh A, Chavali PL, Chavali S, Dhayalan A. DDX39B promotes translation through regulation of pre-ribosomal RNA levels. RNA Biol 2018; 15:1157-1166. [PMID: 30176153 DOI: 10.1080/15476286.2018.1517011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
DDX39B, a DExD RNA helicase, is known to be involved in various cellular processes such as mRNA export, splicing and translation. Previous studies showed that the overexpression of DDX39B promotes the global translation but inhibits the mRNA export in a dominant negative manner. This presents a conundrum as to how DDX39B overexpression would increase the global translation if it inhibits the nuclear export of mRNAs. We resolve this by showing that DDX39B affects the levels of pre-ribosomal RNA by regulating its stability as well as synthesis. Furthermore, DDX39B promotes proliferation and colony forming potential of cells and its levels are significantly elevated in diverse cancer types. Thus, increase in DDX39B enhances global translation and cell proliferation through upregulation of pre-ribosomal RNA. This highlights a possible mechanism by which dysregulation of DDX39B expression could lead to oncogenesis.
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Affiliation(s)
- Sharad Awasthi
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Baskar Chakrapani
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Arun Mahesh
- a Department of Biotechnology , Pondicherry University , Puducherry , India
| | - Pavithra L Chavali
- b Structural Studies Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Sreenivas Chavali
- b Structural Studies Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Arunkumar Dhayalan
- a Department of Biotechnology , Pondicherry University , Puducherry , India
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26
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Gu S, Hou P, Liu K, Niu X, Wei B, Mao F, Xu Z. NOL8, the binding protein for beta-catenin, promoted the growth and migration of prostate cancer cells. Chem Biol Interact 2018; 294:40-47. [PMID: 30125550 DOI: 10.1016/j.cbi.2018.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/10/2018] [Accepted: 08/17/2018] [Indexed: 11/29/2022]
Abstract
Overactivation of beta-catenin/TCF signaling in prostate cancer is very common. However, how the beta-catenin/TCF complex is regulated in the nucleus remains largely unknown. In this study, we have shown that NOL8, a binding protein of beta-catenin, enhanced the interaction between beta-catenin and TCF4, and activated beta-catenin/TCF signaling. NOL8 is up-regulated in the prostate cancer, and promoted the growth, migration and colony formation of cancer cells. Knocking down the expression of NOL8 inhibited the growth, migration and colony formation of prostate cancer cells. The molecular mechanism study demonstrated that NOL8 promoted the migration and colony formation of cancer cells by activating beta-catenin/TCF signaling. Taken together, this study demonstrated the oncogenic roles of NOL8 in prostate cancer and suggested that NOL8 might be an important therapeutic target for prostate cancer.
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Affiliation(s)
- Shuo Gu
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Peijin Hou
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Kun Liu
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Xiaobing Niu
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Bingjian Wei
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Fei Mao
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China
| | - Zongyuan Xu
- Department of Urology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, 6 Beijing Road West, Huai'an, 223300, Jiangsu, People's Republic of China.
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27
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Hang R, Wang Z, Deng X, Liu C, Yan B, Yang C, Song X, Mo B, Cao X. Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa. PLANT PHYSIOLOGY 2018; 177:381-397. [PMID: 29555785 PMCID: PMC5933117 DOI: 10.1104/pp.17.01714] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/02/2018] [Indexed: 05/20/2023]
Abstract
Ribosome biogenesis is crucial for plant growth and environmental acclimation. Processing of ribosomal RNAs (rRNAs) is an essential step in ribosome biogenesis and begins with transcription of the rDNA. The resulting precursor-rRNA (pre-rRNA) transcript undergoes systematic processing, where multiple endonucleolytic and exonucleolytic cleavages remove the external and internal transcribed spacers (ETS and ITS). The processing sites and pathways for pre-rRNA processing have been deciphered in Saccharomyces cerevisiae and, to some extent, in Xenopus laevis, mammalian cells, and Arabidopsis (Arabidopsis thaliana). However, the processing sites and pathways remain largely unknown in crops, particularly in monocots such as rice (Oryza sativa), one of the most important food resources in the world. Here, we identified the rRNA precursors produced during rRNA biogenesis and the critical endonucleolytic cleavage sites in the transcribed spacer regions of pre-rRNAs in rice. We further found that two pre-rRNA processing pathways, distinguished by the order of 5' ETS removal and ITS1 cleavage, coexist in vivo. Moreover, exposing rice to chilling stress resulted in the inhibition of rRNA biogenesis mainly at the pre-rRNA processing level, suggesting that these energy-intensive processes may be reduced to increase acclimation and survival at lower temperatures. Overall, our study identified the pre-rRNA processing pathway in rice and showed that ribosome biogenesis is quickly inhibited by low temperatures, which may shed light on the link between ribosome biogenesis and environmental acclimation in crop plants.
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MESH Headings
- Cold Temperature
- Models, Biological
- Oryza/genetics
- Oryza/physiology
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal, 18S/metabolism
- Ribosome Subunits, Large/metabolism
- Ribosome Subunits, Small/metabolism
- Stress, Physiological
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Affiliation(s)
- Runlai Hang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong Province, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong Province, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
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28
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Liu Y, Imai R. Function of Plant DExD/H-Box RNA Helicases Associated with Ribosomal RNA Biogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:125. [PMID: 29472942 PMCID: PMC5809497 DOI: 10.3389/fpls.2018.00125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
Ribosome biogenesis is a highly complex process that requires several cofactors, including DExD/H-box RNA helicases (RHs). RHs are a family of ATPases that rearrange the secondary structures of RNA and thus remodel ribonucleoprotein complexes. DExD/H-box RHs are found in most organisms and play critical roles in a variety of RNA-involved cellular events. In human and yeast cells, many DExD/H box RHs participate in multiple steps of ribosome biogenesis and regulate cellular proliferation and stress responses. In plants, several DExD/H-box RHs have been demonstrated to be associated with plant development and abiotic stress tolerance through their functions in modulating pre-rRNA processing. In this review, we summarize the pleiotropic roles of DExD/H-box RHs in rRNA biogenesis and other biological functions. We also describe the overall function of the DExD/H-box RH family in ribosome biogenesis based on data from human and yeast.
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29
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Matsumura Y, Ohbayashi I, Takahashi H, Kojima S, Ishibashi N, Keta S, Nakagawa A, Hayashi R, Saéz-Vásquez J, Echeverria M, Sugiyama M, Nakamura K, Machida C, Machida Y. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open 2016; 5:942-54. [PMID: 27334696 PMCID: PMC4958277 DOI: 10.1242/bio.019109] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1) and AS2 (AS1-AS2) is critical to repress abaxial (ventral) genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal) development in leaf primordia at shoot apices. Double mutations of rh10-1 and as2 (or as1) synergistically up-regulated the abaxial genes, which generated abaxialized filamentous leaves with loss of the adaxial domain. DDX47 is part of the small subunit processome (SSUP) that mediates rRNA biogenesis. In rh10-1 we found various defects in SSUP-related events, such as: accumulation of 35S/33S rRNA precursors; reduction in the 18S/25S ratio; and nucleolar hypertrophy. Double mutants of as2 with mutations of genes that encode other candidate SSUP-related components such as nucleolin and putative rRNA methyltransferase exhibited similar synergistic defects caused by up-regulation of ETT/ARF3 and ARF4. These results suggest a tight link between putative SSUP and AS1-AS2 in repression of the abaxial-determining genes for cell fate decisions for adaxial development. Summary: This paper reports the importance of cooperative action between the nucleus-localized epigenetic repressor and the nucleolus-localized proteins involved in ribosomal RNA processing for polarity establishment of Arabidopsis leaves.
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Affiliation(s)
- Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Iwai Ohbayashi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba 271-8510, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Rika Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Julio Saéz-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Manuel Echeverria
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Kenzo Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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30
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Wang D, Qin B, Li X, Tang D, Zhang Y, Cheng Z, Xue Y. Nucleolar DEAD-Box RNA Helicase TOGR1 Regulates Thermotolerant Growth as a Pre-rRNA Chaperone in Rice. PLoS Genet 2016; 12:e1005844. [PMID: 26848586 PMCID: PMC4743921 DOI: 10.1371/journal.pgen.1005844] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/13/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have evolved a considerable number of intrinsic tolerance strategies to acclimate to ambient temperature increase. However, their molecular mechanisms remain largely obscure. Here we report a DEAD-box RNA helicase, TOGR1 (Thermotolerant Growth Required1), prerequisite for rice growth themotolerance. Regulated by both temperature and the circadian clock, its expression is tightly coupled to daily temperature fluctuations and its helicase activities directly promoted by temperature increase. Located in the nucleolus and associated with the small subunit (SSU) pre-rRNA processome, TOGR1 maintains a normal rRNA homeostasis at high temperature. Natural variation in its transcript level is positively correlated with plant height and its overexpression significantly improves rice growth under hot conditions. Our findings reveal a novel molecular mechanism of RNA helicase as a key chaperone for rRNA homeostasis required for rice thermotolerant growth and provide a potential strategy to breed heat-tolerant crops by modulating the expression of TOGR1 and its orthologs. Global warming is increasingly posing negative impacts on crop productivity. In this study, we report a nucleolar-located RNA helicase TOGR1 for thermotolerant growth in rice. TOGR1 maintains pre-rRNA homeostasis under high temperature by securing a proper pre-rRNA structure via elevating its helicase activity. Its expression is high temperature inducible with an afternoon peak expression, consistent with a high temperature anticipation of the circadian clock. Transcriptome analysis revealed that TOGR1 is essential in coordinating primary metabolisms to support thermotolerant growth. Importantly, an enhanced expression of TOGR1 significantly increased biomass of rice. Our findings reveal a novel role of a RNA helicase in thermotolerance and provide a potential strategy to breed heat-tolerant rice cultivars and possibly other heat-tolerant crops.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Baoxiang Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Xiang Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Yu’e Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yongbiao Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Suthar MK, Purva M, Maherchandani S, Kashyap SK. Identification and in silico analysis of cattle DExH/D box RNA helicases. SPRINGERPLUS 2016; 5:25. [PMID: 26783509 PMCID: PMC4705078 DOI: 10.1186/s40064-015-1640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/20/2015] [Indexed: 12/16/2022]
Abstract
The helicases are motor proteins participating
in a range of nucleic acid metabolisms. RNA helicase families are characterized by the presence of conserved motifs. This article reports a comprehensive in silico analysis of Bos taurus DExH/D helicase members. Bovine helicases were identified using the helicase domain sequences including 38 DDX (DEAD box) and 16 DHX (DEAH box) members. Signature motifs were used for the validation of these proteins. Putative sub cellular localization and phylogenetic relationship for these RNA helicases were established. Comparative analysis of these proteins with human DDX and DHX members was carried out. These bovine helicase have been assigned putative physiological functions. Present study of cattle DExH/D helicase will provides an invaluable source for the detailed biochemical and physiological research on these members.
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Affiliation(s)
- Manish Kumar Suthar
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Mukul Purva
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Sunil Maherchandani
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
| | - Sudhir Kumar Kashyap
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan 334001 India
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Wang Z, Murigneux V, Le Hir H. Transcriptome-wide modulation of splicing by the exon junction complex. Genome Biol 2015; 15:551. [PMID: 25476502 PMCID: PMC4268817 DOI: 10.1186/s13059-014-0551-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/23/2022] Open
Abstract
Background The exon junction complex (EJC) is a dynamic multi-protein complex deposited onto nuclear spliced mRNAs upstream of exon-exon junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells. Results Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates. Conclusion Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0551-7) contains supplementary material, which is available to authorized users.
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Sun L, Hartson SD, Matts RL. Identification of proteins associated with Aha1 in HeLa cells by quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:365-80. [PMID: 25614414 DOI: 10.1016/j.bbapap.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/20/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023]
Abstract
The identification of the activator of heat shock protein 90 (Hsp90) ATPase's (Aha1) protein-protein interaction (PPI) network will provide critical insights into the relationship of Aha1 with multi-molecular complexes and shed light onto Aha1's interconnections with Hsp90-regulated biological functions. Flag-tagged Aha1 was over-expressed in HeLa cells and isolated by anti-Flag affinity pull downs, followed by trypsin digestion and identification co-adsorbing proteins by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). A probability-based identification of Aha1 PPIs was generated from the LC-MS/MS analysis by using a relative quantification strategy, spectral counting (SC). By comparing the SC-based protein levels between Aha1 pull-down samples and negative controls, 164 Aha1-interacting proteins were identified that were quantitatively enriched in the pull-down samples over the controls. The identified Aha1-interacting proteins are involved in a wide number of intracellular bioprocesses, including DNA maintenance, chromatin structure, RNA processing, translation, nucleocytoplasmic and vesicle transport, among others. The interactions of 33 of the identified proteins with Aha1 were further confirmed by Western blotting, demonstrating the reliability of our affinity-purification-coupled quantitative SC-MS strategy. Our proteomic data suggests that Aha1 may participate in diverse biological pathways to facilitate Hsp90 chaperone functions in response to stress.
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Affiliation(s)
- Liang Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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Miyazawa N, Yoshikawa H, Magae S, Ishikawa H, Izumikawa K, Terukina G, Suzuki A, Nakamura-Fujiyama S, Miura Y, Hayano T, Komatsu W, Isobe T, Takahashi N. Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA. Genes Cells 2014; 19:273-86. [DOI: 10.1111/gtc.12129] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/05/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Miyazawa
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Harunori Yoshikawa
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Satomi Magae
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Hideaki Ishikawa
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Keiichi Izumikawa
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Goro Terukina
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
| | - Ai Suzuki
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Sally Nakamura-Fujiyama
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
| | - Yutaka Miura
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Toshiya Hayano
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Wataru Komatsu
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
| | - Toshiaki Isobe
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Chemistry; Graduate School of Sciences and Engineering; Tokyo Metropolitan University; 1-1 Minamiosawa Hachiouji-shi Tokyo 192-0397 Japan
| | - Nobuhiro Takahashi
- Department of Applied Life Science; United Graduate School of Agriculture; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho Fuchu-shi Tokyo 183-8509 Japan
- Core Research for Evolutional Science and Technology; Japan Science and Technology Agency; Sanbancho 5 Chiyoda-ku Tokyo 102-0075 Japan
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu-shi Tokyo 183-8509 Japan
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Rodríguez-Galán O, García-Gómez JJ, de la Cruz J. Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:775-90. [PMID: 23357782 DOI: 10.1016/j.bbagrm.2013.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/15/2013] [Accepted: 01/16/2013] [Indexed: 11/17/2022]
Abstract
Ribosome biogenesis is a fundamental process that is conserved in eukaryotes. Although spectacular progress has been made in understanding mammalian ribosome synthesis in recent years, by far, this process has still been best characterised in the yeast Saccharomyces cerevisiae. In yeast, besides the rRNAs, the ribosomal proteins and the 75 small nucleolar RNAs, more than 250 non-ribosomal proteins, generally referred to as trans-acting factors, are involved in ribosome biogenesis. These factors include nucleases, RNA modifying enzymes, ATPases, GTPases, kinases and RNA helicases. Altogether, they likely confer speed, accuracy and directionality to the ribosome synthesis process, however, the precise functions for most of them are still largely unknown. This review summarises our current knowledge on eukaryotic RNA helicases involved in ribosome biogenesis, particularly focusing on the most recent advances with respect to the molecular roles of these enzymes and their co-factors in yeast and human cells. This article is part of a Special Issue entitled: The Biology of RNA helicases-Modulation for life.
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Martin R, Straub AU, Doebele C, Bohnsack MT. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol 2012; 10:4-18. [PMID: 22922795 DOI: 10.4161/rna.21879] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Ribosome synthesis requires a multitude of cofactors, among them DExD/H-box RNA helicases. Bacterial RNA helicases involved in ribosome assembly are not essential, while eukaryotes strictly require multiple DExD/H-box proteins that are involved in the much more complex ribosome biogenesis pathway. Here, RNA helicases are thought to act in structural remodeling of the RNPs including the modulation of protein binding, and they are required for allowing access or the release of specific snoRNPs from pre-ribosomes. Interestingly, helicase action is modulated by specific cofactors that can regulate recruitment and enzymatic activity. This review summarizes the current knowledge and focuses on recent findings and open questions on RNA helicase function and regulation in ribosome synthesis.
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Affiliation(s)
- Roman Martin
- Centre for Biochemistry and Molecular Cell Biology, Göttingen University, Göttingen, Germany
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37
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Santos MCT, Goldfeder MB, Zanchin NIT, Oliveira CC. The essential nucleolar yeast protein Nop8p controls the exosome function during 60S ribosomal subunit maturation. PLoS One 2011; 6:e21686. [PMID: 21747919 PMCID: PMC3126838 DOI: 10.1371/journal.pone.0021686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 06/08/2011] [Indexed: 11/19/2022] Open
Abstract
The yeast nucleolar protein Nop8p has previously been shown to interact with Nip7p and to be required for 60S ribosomal subunit formation. Although depletion of Nop8p in yeast cells leads to premature degradation of rRNAs, the biochemical mechanism responsible for this phenotype is still not known. In this work, we show that the Nop8p amino-terminal region mediates interaction with the 5.8S rRNA, while its carboxyl-terminal portion interacts with Nip7p and can partially complement the growth defect of the conditional mutant strain Δnop8/GAL::NOP8. Interestingly, Nop8p mediates association of Nip7p to pre-ribosomal particles. Nop8p also interacts with the exosome subunit Rrp6p and inhibits the complex activity in vitro, suggesting that the decrease in 60S ribosomal subunit levels detected upon depletion of Nop8p may result from degradation of pre-rRNAs by the exosome. These results strongly indicate that Nop8p may control the exosome function during pre-rRNA processing.
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Affiliation(s)
- Marcia C. T. Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Mauricio B. Goldfeder
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Nilson I. T. Zanchin
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, São Paulo, Brazil
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira, São Paulo, Brazil
| | - Carla C. Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- * E-mail:
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38
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Ddx18 is essential for cell-cycle progression in zebrafish hematopoietic cells and is mutated in human AML. Blood 2011; 118:903-15. [PMID: 21653321 DOI: 10.1182/blood-2010-11-318022] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In a zebrafish mutagenesis screen to identify genes essential for myelopoiesis, we identified an insertional allele hi1727, which disrupts the gene encoding RNA helicase dead-box 18 (Ddx18). Homozygous Ddx18 mutant embryos exhibit a profound loss of myeloid and erythroid cells along with cardiovascular abnormalities and reduced size. These mutants also display prominent apoptosis and a G1 cell-cycle arrest. Loss of p53, but not Bcl-xl overexpression, rescues myeloid cells to normal levels, suggesting that the hematopoietic defect is because of p53-dependent G1 cell-cycle arrest. We then sequenced primary samples from 262 patients with myeloid malignancies because genes essential for myelopoiesis are often mutated in human leukemias. We identified 4 nonsynonymous sequence variants (NSVs) of DDX18 in acute myeloid leukemia (AML) patient samples. RNA encoding wild-type DDX18 and 3 NSVs rescued the hematopoietic defect, indicating normal DDX18 activity. RNA encoding one mutation, DDX18-E76del, was unable to rescue hematopoiesis, and resulted in reduced myeloid cell numbers in ddx18(hi1727/+) embryos, indicating this NSV likely functions as a dominant-negative allele. These studies demonstrate the use of the zebrafish as a robust in vivo system for assessing the function of genes mutated in AML, which will become increasingly important as more sequence variants are identified by next-generation resequencing technologies.
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Abstract
DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.
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40
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O'Leary DA, Sharif O, Anderson P, Tu B, Welch G, Zhou Y, Caldwell JS, Engels IH, Brinker A. Identification of small molecule and genetic modulators of AON-induced dystrophin exon skipping by high-throughput screening. PLoS One 2009; 4:e8348. [PMID: 20020055 PMCID: PMC2791862 DOI: 10.1371/journal.pone.0008348] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 11/23/2009] [Indexed: 11/28/2022] Open
Abstract
One therapeutic approach to Duchenne Muscular Dystrophy (DMD) recently entering clinical trials aims to convert DMD phenotypes to that of a milder disease variant, Becker Muscular Dystrophy (BMD), by employing antisense oligonucleotides (AONs) targeting splice sites, to induce exon skipping and restore partial dystrophin function. In order to search for small molecule and genetic modulators of AON-dependent and independent exon skipping, we screened ∼10,000 known small molecule drugs, >17,000 cDNA clones, and >2,000 kinase- targeted siRNAs against a 5.6 kb luciferase minigene construct, encompassing exon 71 to exon 73 of human dystrophin. As a result, we identified several enhancers of exon skipping, acting on both the reporter construct as well as endogenous dystrophin in mdx cells. Multiple mechanisms of action were identified, including histone deacetylase inhibition, tubulin modulation and pre-mRNA processing. Among others, the nucleolar protein NOL8 and staufen RNA binding protein homolog 2 (Stau2) were found to induce endogenous exon skipping in mdx cells in an AON-dependent fashion. An unexpected but recurrent theme observed in our screening efforts was the apparent link between the inhibition of cell cycle progression and the induction of exon skipping.
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Affiliation(s)
- Debra A. O'Leary
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail: (DAO); (IHE)
| | - Orzala Sharif
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Paul Anderson
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Buu Tu
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Genevieve Welch
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jeremy S. Caldwell
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Ingo H. Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail: (DAO); (IHE)
| | - Achim Brinker
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
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Lam YW, Evans VC, Heesom KJ, Lamond AI, Matthews DA. Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol Cell Proteomics 2009; 9:117-30. [PMID: 19812395 PMCID: PMC2808258 DOI: 10.1074/mcp.m900338-mcp200] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Adenoviruses replicate primarily in the host cell nucleus, and it is well
established that adenovirus infection affects the structure and function of host
cell nucleoli in addition to coding for a number of nucleolar targeted viral
proteins. Here we used unbiased proteomics methods, including high throughput
mass spectrometry coupled with stable isotope labeling by amino acids in cell
culture (SILAC) and traditional two-dimensional gel electrophoresis, to identify
quantitative changes in the protein composition of the nucleolus during
adenovirus infection. Two-dimensional gel analysis revealed changes in six
proteins. By contrast, SILAC-based approaches identified 351 proteins with 24
proteins showing at least a 2-fold change after infection. Of those, four were
previously reported to have aberrant localization and/or functional relevance
during adenovirus infection. In total, 15 proteins identified as changing in
amount by proteomics methods were examined in infected cells using confocal
microscopy. Eleven of these proteins showed altered patterns of localization in
adenovirus-infected cells. Comparing our data with the effects of actinomycin D
on the nucleolar proteome revealed that adenovirus infection apparently
specifically targets a relatively small subset of nucleolar antigens at the time
point examined.
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Affiliation(s)
- Yun W Lam
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China
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42
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Enrichment and Differentiation of Human Germ-Like Cells Mediated by Feeder Cells and Basic Fibroblast Growth Factor Signaling. Stem Cells 2008; 26:2768-76. [DOI: 10.1634/stemcells.2008-0124] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Zou Y, Wu J, Giannone RJ, Boucher L, Du H, Huang Y, Johnson DK, Liu Y, Wang Y. Nucleophosmin/B23 negatively regulates GCN5-dependent histone acetylation and transactivation. J Biol Chem 2007; 283:5728-37. [PMID: 18165222 DOI: 10.1074/jbc.m709932200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin/B23 is a multifunctional phosphoprotein that is overexpressed in cancer cells and has been shown to be involved in both positive and negative regulation of transcription. In this study, we first identified GCN5 acetyltransferase as a B23-interacting protein by mass spectrometry, which was then confirmed by in vivo co-immunoprecipitation. An in vitro assay demonstrated that B23 bound the PCAF-N domain of GCN5 and inhibited GCN5-mediated acetylation of both free and mononucleosomal histones, probably through interfering with GCN5 and masking histones from being acetylated. Mitotic B23 exhibited higher inhibitory activity on GCN5-mediated histone acetylation than interphase B23. Immunodepletion experiments of mitotic extracts revealed that phosphorylation of B23 at Thr 199 enhanced the inhibition of GCN5-mediated histone acetylation. Moreover, luciferase reporter and microarray analyses suggested that B23 attenuated GCN5-mediated transactivation in vivo. Taken together, our studies suggest a molecular mechanism of B23 in the mitotic inhibition of GCN5-mediated histone acetylation and transactivation.
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Affiliation(s)
- Yonglong Zou
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Liu Z, Kenworthy R, Green C, Tang H. Molecular determinants of nucleolar translocation of RNA helicase A. Exp Cell Res 2007; 313:3743-54. [PMID: 17822697 DOI: 10.1016/j.yexcr.2007.07.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 07/11/2007] [Accepted: 07/27/2007] [Indexed: 11/30/2022]
Abstract
RNA helicase A (RHA) is a member of the DEAH-box family of DNA/RNA helicases involved in multiple cellular processes and the life cycles of many viruses. The subcellular localization of RHA is dynamic despite its steady-state concentration in the nucleoplasm. We have previously shown that it shuttles rapidly between the nucleus and the cytoplasm by virtue of a bidirectional nuclear transport domain (NTD) located in its carboxyl terminus. Here, we investigate the molecular determinants for its translocation within the nucleus and, more specifically, its redistribution from the nucleoplasm to nucleolus or the perinucleolar region. We found that low temperature treatment, transcription inhibition or replication of hepatitis C virus caused the intranuclear redistribution of the protein, suggesting that RHA shuttles between the nucleolus and nucleoplasm and becomes trapped in the nucleolus or the perinucleolar region upon blockade of transport to the nucleoplasm. Both the NTD and ATPase activity were essential for RHA's transport to the nucleolus or perinucleolar region. One of the double-stranded RNA binding domains (dsRBD II) was also required for this nucleolar translocation (NoT) phenotype. RNA interference studies revealed that RHA is essential for survival of cultured hepatoma cells and the ATPase activity appears to be important for this critical role.
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Affiliation(s)
- Zhe Liu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370, USA
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