1
|
Ma J, Liu L, Yang H, Wan Y, Zhang Y, Wang F. Melatonin regulates the antioxidant capacity of sheep granulosa cells through a novel uORF-Nrf2aa mediated Nrf2/KEAP1 pathway. Life Sci 2024; 349:122693. [PMID: 38710277 DOI: 10.1016/j.lfs.2024.122693] [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: 02/27/2024] [Revised: 04/13/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Ovarian dysfunction stands as a prevalent contributor to female infertility, with its etiology intertwined with genetic, autoimmune, and environmental factors. Within the ovarian follicles, granulosa cells (GCs) represent the predominant cell population. Alterations in GCs, notably oxidative stress (OS) and the consequential surge in reactive oxygen species (ROS), play pivotal roles in the orchestration of ovarian function. Nrf2aa, a newly identified upstream open reading frame (uORF), is situated within the 5' untranslated region (5'UTR) of sheep Nrf2 mRNA and is regulated by melatonin, a crucial intrafollicular antioxidant. In this study, we have noted that Nrf2aa has the capacity to encode a peptide and exerts a negative regulatory effect on the translation efficiency (TE) of the Nrf2 CDs region. Further in vitro experiments, we observed that interfering with Nrf2aa can enhance the cellular functionality of GCs under 3-np-induced oxidative stress, while overexpressing Nrf2aa has the opposite effect. Furthermore, overexpression of Nrf2aa counteracts the rescuing effect of melatonin on the cellular functions of GCs under oxidative stress conditions, including estrogen secretion, proliferation, apoptosis, and many more. Finally, we confirmed that Nrf2aa, by regulating the expression of key proteins in the Nrf2/KEAP1 signaling pathway, further modulates the antioxidant levels in GCs.
Collapse
Affiliation(s)
- Jianyu Ma
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Liang Liu
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Hua Yang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yongjie Wan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
2
|
Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome decision graphs for the representation of eukaryotic RNA translation complexity. Genome Res 2024; 34:530-538. [PMID: 38719470 PMCID: PMC11146595 DOI: 10.1101/gr.278810.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/01/2024] [Indexed: 05/21/2024]
Abstract
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, within both annotated protein-coding and noncoding regions. The biological significance of this translation is a matter of intensive investigation. However, current schematic or annotation-based representations of mRNA translation generally do not account for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable the analysis of quantitative information on translation and more accurate models for predicting the phenotypic effects of genetic variants affecting translation. To address this, we developed a conceptually novel abstraction that we term ribosome decision graphs (RDGs). RDGs represent translation as multiple ribosome paths through untranslated and translated mRNA segments. We termed the latter "translons." Nondeterministic events, such as initiation, reinitiation, selenocysteine insertion, or ribosomal frameshifting, are then represented as branching points. This representation allows for an adequate representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions and for analyzing genetic variation and quantitative genome-wide data on translation for characterization of regulatory modulators of translation.
Collapse
Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork T12 K8AF, Ireland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridge, United Kingdom
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Nicola Whiffin
- The Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland;
| |
Collapse
|
3
|
Zhang Y, Yan Z, Nan N, Qin G, Sang N. Circadian rhythm disturbances involved in ozone-induced glucose metabolism disorder in mouse liver. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167316. [PMID: 37742977 DOI: 10.1016/j.scitotenv.2023.167316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Ozone (O3) is a key environmental factor for developing diabetes. Nevertheless, the underlying mechanisms remain unclear. This study aimed to investigate alterations of glycometabolism in mice after O3 exposure and the role of circadian rhythms in this process. C57BL/6 male mice were randomly assigned to O3 (0.5 ppm) or filtered air for four weeks (4 h/day). Then, hepatic tissues of mice were collected at 4 h intervals within 24 h after O3 exposure to test. The results showed that hepatic circadian rhythm genes oscillated abnormally, mainly at zeitgeber time (ZT)8 and ZT20 after O3 exposure. Furthermore, detection of glycometabolism (metabolites, enzymes, and genes) revealed that O3 caused change in the daily oscillations of glycometabolism. The serum glucose content decreased at ZT4 and ZT20, while hepatic glucose enhanced at ZT16 and ZT24(0). Both G6pc and Pck1, which are associated with hepatic gluconeogenesis, significantly increased at ZT20. O3 exposure disrupted glycometabolism by increasing gluconeogenesis and decreasing glycolysis in mice liver. Finally, correlation analysis showed that the association between Bmal1 and O3-induced disruption of glycometabolism was the strongest. The findings emphasized the interaction between adverse outcomes of circadian rhythms and glycometabolism following O3 exposure.
Collapse
Affiliation(s)
- Yaru Zhang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Zhipeng Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Nan Nan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Guohua Qin
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| |
Collapse
|
4
|
Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566564. [PMID: 37986835 PMCID: PMC10659439 DOI: 10.1101/2023.11.10.566564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, both within annotated protein-coding and non-coding regions. The biological significance of this translation is a matter of intensive investigation. However, current schematic or annotation-based representations of mRNA translation generally do not account for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable the analysis of quantitative information on translation and more accurate models for predicting the phenotypic effects of genetic variants affecting translation. To address this, we developed a conceptually novel abstraction that we term Ribosome Decision Graphs (RDGs). RDGs represent translation as multiple ribosome paths through untranslated and translated mRNA segments. We termed the later 'translons'. Non-deterministic events, such as initiation, re-initiation, selenocysteine insertion or ribosomal frameshifting are then represented as branching points. This representation allows for an adequate representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions, analysis of genetic variation and quantitative genome-wide data on translation for characterisation of regulatory modulators of translation.
Collapse
Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicola Whiffin
- The Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| |
Collapse
|
5
|
May GE, Akirtava C, Agar-Johnson M, Micic J, Woolford J, McManus J. Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning. eLife 2023; 12:e69611. [PMID: 37227054 PMCID: PMC10259493 DOI: 10.7554/elife.69611] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/24/2023] [Indexed: 05/26/2023] Open
Abstract
Upstream open-reading frames (uORFs) are potent cis-acting regulators of mRNA translation and nonsense-mediated decay (NMD). While both AUG- and non-AUG initiated uORFs are ubiquitous in ribosome profiling studies, few uORFs have been experimentally tested. Consequently, the relative influences of sequence, structural, and positional features on uORF activity have not been determined. We quantified thousands of yeast uORFs using massively parallel reporter assays in wildtype and ∆upf1 yeast. While nearly all AUG uORFs were robust repressors, most non-AUG uORFs had relatively weak impacts on expression. Machine learning regression modeling revealed that both uORF sequences and locations within transcript leaders predict their effect on gene expression. Indeed, alternative transcription start sites highly influenced uORF activity. These results define the scope of natural uORF activity, identify features associated with translational repression and NMD, and suggest that the locations of uORFs in transcript leaders are nearly as predictive as uORF sequences.
Collapse
Affiliation(s)
- Gemma E May
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Matthew Agar-Johnson
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - John Woolford
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Joel McManus
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
- Computational Biology Department, Carnegie Mellon UniversityPittsburghUnited States
| |
Collapse
|
6
|
Zhou Z, Wang J, Yu Q, Lan H. Promoter activity and transcriptome analyses decipher functions of CgbHLH001 gene (Chenopodium glaucum L.) in response to abiotic stress. BMC PLANT BIOLOGY 2023; 23:116. [PMID: 36849913 PMCID: PMC9969703 DOI: 10.1186/s12870-023-04128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Our previous studies revealed that CgbHLH001 transcription factor (TF) played an important role in abiotic stress tolerance, suggesting that its promoter was a potential target in response to stress signals. In addition, the regulatory mechanism of CgbHLH001 TF is still limited. RESULTS In the present study, a 1512 bp of 5'-flanking sequence of CgbHLH001 gene was identified, and the sequence carried quite a few of cis-acting elements. The gene promoter displayed strong activity and was induced by multiple abiotic stress. A series of 5'-deletions of the promoter sequence resulted in a gradual decrease in its activity, especially, the 5' untranslated region (UTR) was necessary to drive promoter activity. Further, CgbHLH001 promoter drove its own gene overexpression ectopically at the transcriptional and translational levels, which in turn conferred the stress tolerance to transgenic Arabidopsis. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple biological regulatory processes. Differentially expressed genes (DEGs) that mediate phytohormone signal transduction and mitogen-activated protein kinase (MAPK) signaling pathway were widely induced and mostly upregulated under salt stress, and the transcription levels in PbHLH::bHLH-overexpressing transgenic lines were higher than that of 35S::bHLH overexpression. CONCLUSIONS The CgbHLH001 promoter exhibited a positive response to abiotic stress and its 5' UTR sequence enhanced the regulation of gene expression to stress. A few important pathways and putative key genes involved in salt tolerance were identified, which can be used to elucidate the mechanism of salt tolerance and decipher the regulatory mechanism of promoters to develop an adaptation strategy for desert halophytes.
Collapse
Affiliation(s)
- Zixin Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830017, China.
| |
Collapse
|
7
|
Vasu K, Ramachandiran I, Chechi A, Khan K, Khan D, Kaufman R, Fox PL. Translational control of murine adiponectin expression by an upstream open reading frame element. RNA Biol 2023; 20:737-749. [PMID: 37702393 PMCID: PMC10501164 DOI: 10.1080/15476286.2023.2256094] [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] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5'-leader identified an inhibitory cis-regulatory sequence. The 5'-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the Adipoq 5'-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser51 phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.
Collapse
Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Randall Kaufman
- Degenerative Diseases Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paul L. Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| |
Collapse
|
8
|
5′ Untranslated mRNA Regions Allow Bypass of Host Cell Translation Inhibition by Legionella pneumophila. Infect Immun 2022; 90:e0017922. [DOI: 10.1128/iai.00179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Legionella pneumophila
grows within membrane-bound vacuoles in alveolar macrophages during human disease. Pathogen manipulation of the host cell is driven by bacterial proteins translocated through a type IV secretion system (T4SS).
Collapse
|
9
|
Dörr D, Obermayer B, Weiner JM, Zimmermann K, Anania C, Wagner LK, Lyras EM, Sapozhnikova V, Lara-Astiaso D, Prósper F, Lang R, Lupiáñez DG, Beule D, Höpken UE, Leutz A, Mildner A. C/EBPβ regulates lipid metabolism and
Pparg
isoform 2 expression in alveolar macrophages. Sci Immunol 2022; 7:eabj0140. [DOI: 10.1126/sciimmunol.abj0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pulmonary alveolar proteinosis (PAP) is a syndrome characterized by accumulation of surfactant lipoproteins within the lung alveoli. Alveolar macrophages (AMs) are crucial for surfactant clearance, and their differentiation depends on colony-stimulating factor 2 (CSF2), which regulates the establishment of an AM-characteristic gene regulatory network. Here, we report that the transcription factor CCAAT/enhancer binding protein β (C/EBPβ) is essential for the development of the AM identity, as demonstrated by transcriptome and chromatin accessibility analysis. Furthermore, C/EBPβ-deficient AMs showed severe defects in proliferation, phagocytosis, and lipid metabolism, collectively resulting in a PAP-like syndrome. Mechanistically, the long C/EBPβ protein variants LAP* and LAP together with CSF2 signaling induced the expression of
Pparg
isoform 2 but not
Pparg
isoform 1, a molecular regulatory mechanism that was also observed in other CSF2-primed macrophages. These results uncover C/EBPβ as a key regulator of AM cell fate and shed light on the molecular networks controlling lipid metabolism in macrophages.
Collapse
Affiliation(s)
- Dorothea Dörr
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - January Mikolaj Weiner
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karin Zimmermann
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Chiara Anania
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetics and Sex Development Group, Berlin, Germany
| | - Lisa Katharina Wagner
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Ekaterini Maria Lyras
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Valeriia Sapozhnikova
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - David Lara-Astiaso
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Roland Lang
- Institute of Clinical Microbiology, Immunology, and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Darío G. Lupiáñez
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetics and Sex Development Group, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Uta E. Höpken
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
| | - Achim Leutz
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Alexander Mildner
- Max-Delbrück-Center for Molecular Medicine in Helmholtz Association (MDC), Berlin, Germany
- Institute of Biomedicine, Medicity University of Turku, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| |
Collapse
|
10
|
Magnusson R, Rundquist O, Kim MJ, Hellberg S, Na CH, Benson M, Gomez-Cabrero D, Kockum I, Tegnér JN, Piehl F, Jagodic M, Mellergård J, Altafini C, Ernerudh J, Jenmalm MC, Nestor CE, Kim MS, Gustafsson M. RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases. Front Mol Biosci 2022; 9:916128. [PMID: 36106020 PMCID: PMC9465313 DOI: 10.3389/fmolb.2022.916128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/25/2022] [Indexed: 12/18/2022] Open
Abstract
Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between mRNA expression and protein abundance. We hypothesised that these correlations could be improved by mathematical models based on measuring splice variants and time delay in protein translation. We characterised time-series of primary human naïve CD4+ T cells during early T helper type 1 differentiation with RNA-sequencing and mass-spectrometry proteomics. We performed computational time-series analysis in this system and in two other key human and murine immune cell types. Linear mathematical mixed time delayed splice variant models were used to predict protein abundances, and the models were validated using out-of-sample predictions. Lastly, we re-analysed RNA-seq datasets to evaluate biomarker discovery in five T-cell associated diseases, further validating the findings for multiple sclerosis (MS) and asthma. The new models significantly out-performing models not including the usage of multiple splice variants and time delays, as shown in cross-validation tests. Our mathematical models provided more differentially expressed proteins between patients and controls in all five diseases. Moreover, analysis of these proteins in asthma and MS supported their relevance. One marker, sCD27, was validated in MS using two independent cohorts for evaluating response to treatment and disease prognosis. In summary, our splice variant and time delay models substantially improved the prediction of protein abundance from mRNA expression in three different immune cell types. The models provided valuable biomarker candidates, which were further validated in MS and asthma.
Collapse
Affiliation(s)
- Rasmus Magnusson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Olof Rundquist
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Min Jung Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in, South Korea
| | - Sandra Hellberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - David Gomez-Cabrero
- Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra, IdiSNA, Pamplona, Spain
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jesper N. Tegnér
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Johan Mellergård
- Department of Neurology, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudio Altafini
- Department of Automatic Control, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Linköping University, Linköping, Sweden
| | - Maria C. Jenmalm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Maria C. Jenmalm, ; Mika Gustafsson,
| | - Colm E. Nestor
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- *Correspondence: Maria C. Jenmalm, ; Mika Gustafsson,
| |
Collapse
|
11
|
Causier B, Hopes T, McKay M, Paling Z, Davies B. Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation. PLANT, CELL & ENVIRONMENT 2022; 45:1229-1241. [PMID: 35128674 PMCID: PMC9305500 DOI: 10.1111/pce.14277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 05/08/2023]
Abstract
The regulation of protein synthesis plays an important role in the growth and development of all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic messenger RNA transcripts and typically attenuate the translation of associated downstream main ORFs (mORFs). Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which have been shown to conditionally regulate translation by ribosome stalling. Here, we show that Arabidopsis CPuORF19, CPuORF46 and CPuORF47, which are ancient in origin, regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat stress and water limitation. Consequently, these CPuORFs represent a versatile toolkit for inducible gene expression with broad applications. Finally, we note that different classes of CPuORFs may operate during distinct phases of translation, which has implications for the bioengineering of these regulatory factors.
Collapse
Affiliation(s)
- Barry Causier
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Mary McKay
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Zachary Paling
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| | - Brendan Davies
- Faculty of Biological Sciences, Centre for Plant SciencesUniversity of LeedsLeedsUK
| |
Collapse
|
12
|
Wei S, Guo W, Qian Y, Xiang J, Liu K, Gao XJ, Gao X, Chen Y. Ribosome profiling reveals translatome remodeling in cancer cells in response to zinc oxide nanoparticles. Aging (Albany NY) 2021; 13:23119-23132. [PMID: 34620733 PMCID: PMC8544296 DOI: 10.18632/aging.203606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
The anticancer effect of zinc oxide nanoparticles (ZnO NPs) largely relies on cellular responses such as alteration of gene expression. Although ZnO NPs have been reported to induce transcriptional changes, the potential of ZnO NPs to affect cellular translatome remains largely unknown. Using ribosome profiling, we demonstrated that the transcription of 78 genes and the translation of 1,448 genes are affected during one hour of ZnO NPs exposure in A549 human lung cancer cells. The mitogen-activated protein kinase (MAPK) pathway is up-regulated upon ZnO NP treatment. The upstream open reading frame (uORF) plays a pervasive role in the induction of up-regulated genes, including TLNRD1 and CCNB1IP1. Knockdown of TLNRD1 or CCNB1IP1 reduces ZnO NP-induced cytotoxicity. Together, our study characterizes the landscape of translational alteration under ZnO NPs treatment and provides potential targets to augment the anticancer effect of ZnO NPs.
Collapse
Affiliation(s)
- Saisai Wei
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Endoscopic Technique Research of Zhejiang Province, Sir Run-Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China
| | - Wenhao Guo
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Urology, Shaoxing Branch of Sir Run-Run Shaw Hospital, College of Medicine, Zhejiang University, Shaoxing 312000, China
| | - Yu Qian
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jie Xiang
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Kangli Liu
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiang-Jing Gao
- Department of Occupational Health and Radiation Protection, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, Zhejiang, China
| | - Xiangwei Gao
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yicheng Chen
- Sir Run-Run Shaw Hospital, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Urology, Sir Run-Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
| |
Collapse
|
13
|
Silva J, Nina P, Romão L. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells. Biomedicines 2021; 9:biomedicines9080911. [PMID: 34440115 PMCID: PMC8389594 DOI: 10.3390/biomedicines9080911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
Collapse
Affiliation(s)
- Joana Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro Nina
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; (J.S.); (P.N.)
- Instituto de Biossistemas e Ciências Integrativas (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-750-8155
| |
Collapse
|
14
|
Al Madhoun A, Haddad D, Al Tarrah M, Jacob S, Al-Ali W, Nizam R, Miranda L, Al-Rashed F, Sindhu S, Ahmad R, Bitar MS, Al-Mulla F. Microarray analysis reveals ONC201 mediated differential mechanisms of CHOP gene regulation in metastatic and nonmetastatic colorectal cancer cells. Sci Rep 2021; 11:11893. [PMID: 34088951 PMCID: PMC8178367 DOI: 10.1038/s41598-021-91092-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/20/2021] [Indexed: 01/03/2023] Open
Abstract
The imipramine ONC201 has antiproliferative effects in several cancer cell types and activates integrated stress response pathway associated with the induction of Damage Inducible Transcript 3 (DDIT3, also known as C/EBP homologous protein or CHOP). We investigated the signaling pathways through which ONC201/CHOP crosstalk is regulated in ONC201-treated nonmetastatic and metastatic cancer cell lines (Dukes' type B colorectal adenocarcinoma nonmetastatic SW480 and metastatic LS-174T cells, respectively). Cell proliferation and apoptosis were evaluated by MTT assays and flow cytometry, gene expression was assessed by Affymetrix microarray, signaling pathway perturbations were assessed in silico, and key regulatory proteins were validated by Western blotting. Unlike LS-174T cells, SW480 cells were resistant to ONC201 treatment; Gene Ontology analysis of differentially expressed genes showed that cellular responsiveness to ONC201 treatment also differed substantially. In both ONC201-treated cell lines, CHOP expression was upregulated; however, its upstream regulatory mechanisms were perturbed. Although, PERK, ATF6 and IRE1 ER-stress pathways upregulated CHOP in both cell types, the Bak/Bax pathway regulated CHOP only LS-174T cells. Additionally, CHOP RNA splicing profiles varied between cell lines; these were further modified by ONC201 treatment. In conclusion, we delineated the signaling mechanisms by which CHOP expression is regulated in ONC201-treated non-metastatic and metastatic colorectal cell lines. The observed differences could be related to cellular plasticity and metabolic reprogramming, nevertheless, detailed mechanistic studies are required for further validations.
Collapse
Affiliation(s)
- Ashraf Al Madhoun
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait. .,Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute, 15462, Dasman, Kuwait.
| | - Dania Haddad
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Mustafa Al Tarrah
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Sindhu Jacob
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Waleed Al-Ali
- Department of Pharmacology and Toxicology, Faculty of Medicine, Kuwait University, 046302, Jabriya, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Lavina Miranda
- Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Fatema Al-Rashed
- Department of Immunology and Microbiology, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Sardar Sindhu
- Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute, 15462, Dasman, Kuwait.,Department of Immunology and Microbiology, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Rasheed Ahmad
- Department of Immunology and Microbiology, Dasman Diabetes Institute, 15462, Dasman, Kuwait
| | - Milad S Bitar
- Department of Pharmacology and Toxicology, Faculty of Medicine, Kuwait University, 046302, Jabriya, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, 15462, Dasman, Kuwait.
| |
Collapse
|
15
|
uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast. Methods Mol Biol 2021. [PMID: 33765283 DOI: 10.1007/978-1-0716-1150-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The identification of upstream open reading frames (uORFs) using ribosome profiling data is complicated by several factors such as the noise inherent to the procedure, the substantial increase in potential translation initiation sites (and false positives) when one includes non-canonical start codons, and the paucity of molecularly validated uORFs. Here we present uORF-seqr, a novel machine learning algorithm that uses ribosome profiling data, in conjunction with RNA-seq data, as well as transcript aware genome annotation files to identify statistically significant AUG and near-cognate codon uORFs.
Collapse
|
16
|
Reprogramming translation for gene therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:439-476. [PMID: 34175050 DOI: 10.1016/bs.pmbts.2021.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Translational control plays a fundamental role in the regulation of gene expression in eukaryotes. Modulating translational efficiency allows the cell to fine-tune the expression of genes, spatially control protein localization, and trigger fast responses to environmental stresses. Translational regulation involves mechanisms acting on multiple steps of the protein synthesis pathway: initiation, elongation, and termination. Many cis-acting elements present in the 5' UTR of transcripts can influence translation at the initiation step. Among them, the Kozak sequence impacts translational efficiency by regulating the recognition of the start codon; upstream open reading frames (uORFs) are associated with inhibition of translation of the downstream protein; internal ribosomal entry sites (IRESs) can promote cap-independent translation. CRISPR-Cas technology is a revolutionary gene-editing tool that has also been applied to the regulation of gene expression. In this chapter, we focus on the genome editing approaches developed to modulate the translational efficiency with the aim to find novel therapeutic approaches, in particular acting on the cis-elements, that regulate the initiation of protein synthesis.
Collapse
|
17
|
Miyoshi M, Imakado Y, Otani L, Kaji M, Aanzai Y, Sugimoto N, Murakami T, Fukuoka M, Hohjoh H, Jia H, Kato H. Maternal protein restriction induces renal AT2R promoter hypomethylation in salt-sensitive, hypertensive rats. Food Sci Nutr 2021; 9:1452-1459. [PMID: 33747459 PMCID: PMC7958563 DOI: 10.1002/fsn3.2113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/08/2020] [Accepted: 12/28/2020] [Indexed: 11/06/2022] Open
Abstract
SCOPE We previously demonstrated that protein restriction in utero induced salt-sensitive hypertension and changed renal levels of angiotensin type 2 receptor (AT2R) in Stroke-Prone Spontaneously Hypertensive Rat (SHRSP). Here, we investigated if this characteristic alteration of AT2R is related to AT2R DNA methylation profiles. METHODS AND RESULTS First, we examined the relation between AT2R DNA methylation and its promoter activity in vitro. Luciferase assays revealed a negative correlation between these two variables. Next, we fed SHRSP dams and grand-dams a control 20% casein diet or a 9% casein diet during pregnancy. Adult offspring and grand-offspring were supplied either water or 1% saline solution for 2 weeks. Renal AT2R promoter DNA near the TATA-box was hypomethylated, mRNA expression was suppressed, and protein expression tended to be higher, in adult offspring of mothers fed a low casein diet. Moreover, adult grand-offspring exhibited high blood pressure after salt loading, along with suppressed transcription of AT2R mRNA and elevated translated protein. CONCLUSIONS Under a fetal environment of protein restriction, the increase in protein expression due to hypomethylation of the AT2R promoter region occurs as a response to increased salt sensitivity, and controlling this mechanism may be important for the prevention of hypertension.
Collapse
Affiliation(s)
- Moe Miyoshi
- Health NutritionGraduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
| | - Yasuhisa Imakado
- Health NutritionGraduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
| | - Lila Otani
- Health NutritionGraduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
- Department of Food Science and NutritionFaculty of AgricultureKinki UniversityNaraJapan
| | - Misa Kaji
- Department of Food Science and NutritionFaculty of AgricultureKinki UniversityNaraJapan
| | - Yuki Aanzai
- Department of Food Science and NutritionFaculty of AgricultureKinki UniversityNaraJapan
| | - Naoya Sugimoto
- Department of Food Science and NutritionFaculty of AgricultureKinki UniversityNaraJapan
| | - Tetsuo Murakami
- Department of Food Science and NutritionFaculty of AgricultureKinki UniversityNaraJapan
| | | | | | - Huijuan Jia
- Health NutritionGraduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
| | - Hisanori Kato
- Health NutritionGraduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
| |
Collapse
|
18
|
Zhang H, Wang Y, Wu X, Tang X, Wu C, Lu J. Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. Nat Commun 2021; 12:1076. [PMID: 33597535 PMCID: PMC7889888 DOI: 10.1038/s41467-021-21394-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/20/2021] [Indexed: 01/02/2023] Open
Abstract
Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.
Collapse
Affiliation(s)
- Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Yirong Wang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- College of Biology, Hunan University, Changsha, China
| | - Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
19
|
Liu X, Xiao M, Zhang L, Li L, Zhu G, Shen E, Lv M, Lu X, Sun Z. The m6A methyltransferase METTL14 inhibits the proliferation, migration, and invasion of gastric cancer by regulating the PI3K/AKT/mTOR signaling pathway. J Clin Lab Anal 2020; 35:e23655. [PMID: 33314339 PMCID: PMC7957981 DOI: 10.1002/jcla.23655] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/17/2020] [Indexed: 12/28/2022] Open
Abstract
Background N6‐methyladenosine (m6A) modification may participate in the regulation of occurrence and development of tumors. However, the m6A level and the potential regulatory mechanism of m6A in gastric cancer (GC) remain uncertain. Methods RNA m6A quantification assay was conducted to detect the m6A level in GC tissues and cell lines. Methyltransferase‐like 14 (METTL14) expression in GC tissues was explored by bioinformatics and immunohistochemistry. Then, the function of METTL14 in GC cells was examined by CCK‐8, colony formation assay, wound healing assay, and Transwell assay. Besides, Western blotting was conducted to probe the PI3K/AKT/mTOR pathway and the epithelial‐mesenchymal transformation (EMT) pathway‐related gene expression. Results The m6A modification level was decreased in GC and METTL14 was a key regulator resulting in m6A disorder in GC. METTL14 was downregulated in GC by analyzing both clinical samples and bioinformatics. METTL14 overexpression suppressed GC cell proliferation and aggression by deactivating the PI3K/AKT/mTOR pathway and the EMT pathway, respectively. Conclusions Our findings indicate that METTL14 partakes in the biological process of GC as a tumor suppressor and may be an emerging biomarker in GC.
Collapse
Affiliation(s)
- Xin Liu
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Department of Surgical Oncology and General Surgery, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Mingyang Xiao
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Liang Zhang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Liuli Li
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Guolian Zhu
- Department of Oncology, Shenyang Fifth People Hospital, Shenyang, China
| | - Erdong Shen
- Department of Oncology, Yueyang First People Hospital, Yueyang, China
| | - Mingyue Lv
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Department of Surgical Oncology and General Surgery, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaobo Lu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Zhe Sun
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Department of Surgical Oncology and General Surgery, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| |
Collapse
|
20
|
Mantini G, Vallés AM, Le Large TYS, Capula M, Funel N, Pham TV, Piersma SR, Kazemier G, Bijlsma MF, Giovannetti E, Jimenez CR. Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers. Cell Oncol (Dordr) 2020; 43:1147-1159. [PMID: 32860207 PMCID: PMC7716908 DOI: 10.1007/s13402-020-00548-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 01/02/2023] Open
Abstract
Purpose Despite extensive biological and clinical studies, including comprehensive genomic and transcriptomic profiling efforts, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with a poor survival and limited therapeutic options. The goal of this study was to assess co-expressed PDAC proteins and their associations with biological pathways and clinical parameters. Methods Correlation network analysis is emerging as a powerful approach to infer tumor biology from omics data and to prioritize candidate genes as biomarkers or drug targets. In this study, we applied a weighted gene co-expression network analysis (WGCNA) to the proteome of 20 surgically resected PDAC specimens (PXD015744) and confirmed its clinical value in 82 independent primary cases. Results Using WGCNA, we obtained twelve co-expressed clusters with a distinct biology. Notably, we found that one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p = 0.01) and disease-free survival (p = 0.03). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 independent resected patients. Risk score evaluation of the prognostic signature confirmed its association with overall survival in multivariate analyses. Finally, immunofluorescence analysis confirmed co-expression of SPTBN1 and KHSRP in Hs766t PDAC cells. Conclusions Our WGCNA analysis revealed a PDAC module enriched for metabolic and EMT-associated processes. In addition, we found that three of the proteins involved were associated with PDAC survival. Electronic supplementary material The online version of this article (10.1007/s13402-020-00548-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- G Mantini
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Fondazione Pisana Per La Scienza, Pisa, Italy
| | - A M Vallés
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - T Y S Le Large
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, Univ of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands.,Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Amsterdam, The Netherlands
| | - M Capula
- Fondazione Pisana Per La Scienza, Pisa, Italy
| | - N Funel
- U.O. Anatomia ed Istologia Patologica II Azienda Ospedaliero Universitaria Pisana , Pisa, Italy
| | - T V Pham
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - S R Piersma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - G Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Surgery, Amsterdam, The Netherlands
| | - M F Bijlsma
- U.O. Anatomia ed Istologia Patologica II Azienda Ospedaliero Universitaria Pisana , Pisa, Italy.,Oncode Institute, Amsterdam, The Netherlands
| | - E Giovannetti
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands. .,Fondazione Pisana Per La Scienza, Pisa, Italy.
| | - C R Jimenez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
21
|
Bond S, Lopez-Lloreda C, Gannon PJ, Akay-Espinoza C, Jordan-Sciutto KL. The Integrated Stress Response and Phosphorylated Eukaryotic Initiation Factor 2α in Neurodegeneration. J Neuropathol Exp Neurol 2020; 79:123-143. [PMID: 31913484 DOI: 10.1093/jnen/nlz129] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
The proposed molecular mechanisms underlying neurodegenerative pathogenesis are varied, precluding the development of effective therapies for these increasingly prevalent disorders. One of the most consistent observations across neurodegenerative diseases is the phosphorylation of eukaryotic initiation factor 2α (eIF2α). eIF2α is a translation initiation factor, involved in cap-dependent protein translation, which when phosphorylated causes global translation attenuation. eIF2α phosphorylation is mediated by 4 kinases, which, together with their downstream signaling cascades, constitute the integrated stress response (ISR). While the ISR is activated by stresses commonly observed in neurodegeneration, such as oxidative stress, endoplasmic reticulum stress, and inflammation, it is a canonically adaptive signaling cascade. However, chronic activation of the ISR can contribute to neurodegenerative phenotypes such as neuronal death, memory impairments, and protein aggregation via apoptotic induction and other maladaptive outcomes downstream of phospho-eIF2α-mediated translation inhibition, including neuroinflammation and altered amyloidogenic processing, plausibly in a feed-forward manner. This review examines evidence that dysregulated eIF2a phosphorylation acts as a driver of neurodegeneration, including a survey of observations of ISR signaling in human disease, inspection of the overlap between ISR signaling and neurodegenerative phenomenon, and assessment of recent encouraging findings ameliorating neurodegeneration using developing pharmacological agents which target the ISR. In doing so, gaps in the field, including crosstalk of the ISR kinases and consideration of ISR signaling in nonneuronal central nervous system cell types, are highlighted.
Collapse
Affiliation(s)
- Sarah Bond
- From the Department of Biochemistry and Biophysics (SB); Department of Neuroscience (CL-L); Department of Pharmacology (PG), Perelman School of Medicine; Department of Basic and Translational Sciences (CA-E); and Department of Basic and Translational Sciences (KLJ-S), School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Claudia Lopez-Lloreda
- From the Department of Biochemistry and Biophysics (SB); Department of Neuroscience (CL-L); Department of Pharmacology (PG), Perelman School of Medicine; Department of Basic and Translational Sciences (CA-E); and Department of Basic and Translational Sciences (KLJ-S), School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Patrick J Gannon
- From the Department of Biochemistry and Biophysics (SB); Department of Neuroscience (CL-L); Department of Pharmacology (PG), Perelman School of Medicine; Department of Basic and Translational Sciences (CA-E); and Department of Basic and Translational Sciences (KLJ-S), School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cagla Akay-Espinoza
- From the Department of Biochemistry and Biophysics (SB); Department of Neuroscience (CL-L); Department of Pharmacology (PG), Perelman School of Medicine; Department of Basic and Translational Sciences (CA-E); and Department of Basic and Translational Sciences (KLJ-S), School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kelly L Jordan-Sciutto
- From the Department of Biochemistry and Biophysics (SB); Department of Neuroscience (CL-L); Department of Pharmacology (PG), Perelman School of Medicine; Department of Basic and Translational Sciences (CA-E); and Department of Basic and Translational Sciences (KLJ-S), School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
22
|
Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa. Appl Environ Microbiol 2020; 86:AEM.00653-20. [PMID: 32471912 DOI: 10.1128/aem.00653-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R 2 = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.IMPORTANCE Lignocellulases are important industrial enzymes for sustainable production of biofuels and bio-products. Insoluble cellulose has been commonly used to induce the production of lignocellulases in filamentous fungi, which causes a difficult fermentation operation and enzyme loss due to adsorption to cellulose. The disadvantages can be overcome by using soluble inducers, such as the disaccharide cellobiose. Quantitative proteome profiling of the model filamentous fungus Neurospora crassa revealed cellobiose-dependent pathways for cellulase production, including protein processing and export. A protein (CWH43) potentially involved in protein processing was found to be a positive regulator of lignocellulase production. The cellobiose-dependent mechanisms provide new opportunities to improve the production of lignocellulases in filamentous fungi.
Collapse
|
23
|
Gu M, Cosenza G, Gaspa G, Iannaccone M, Macciotta NPP, Chemello G, Di Stasio L, Pauciullo A. Sequencing of lipoprotein lipase gene in the Mediterranean river buffalo identified novel variants affecting gene expression. J Dairy Sci 2020; 103:6374-6382. [PMID: 32418698 DOI: 10.3168/jds.2019-17968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/13/2020] [Indexed: 01/23/2023]
Abstract
Lipoprotein lipase (LPL) is a key enzyme for lipid metabolism, playing a fundamental role in the composition of fat in adipose tissue and milk. The LPL gene has been seldom investigated in dairy ruminants and barely studied in river buffalo (Bubalus bubalis). The aim of this work was to explore the genetic diversity of LPL and its promoter and to identify functional mutations, using a combined approach based on sequencing, dual-color electrophoretic mobility shift assay, and quantitative PCR. Thirteen consensus sequences for transcription factors were found in the promoter. Eleven SNP were detected, and the attention was focused on the SNP with potential functional effects: g.-446A>G, because the presence of G created a consensus motif for the transcription factor Sp1, and g.107A>G, which was the only exonic SNP. We developed PCR-RFLP methods for genotyping the 2 SNP and calculated the allele frequencies. A strong linkage disequilibrium (D' = 1; r2 = 0.903) was found between the 2 SNP. The dual-color electrophoretic mobility shift assay demonstrated that only genotype g.-446GG allowed the binding of the Sp1 transcription factor, resulting in overexpression of the gene (~2.5 fold), as confirmed by the quantitative PCR results. Haploinsufficiency is proposed as a regulation mechanism. This study adds further knowledge on the structure of the LPL gene and its expression in river buffalo, with potential effects on milk qualitative and quantitative production.
Collapse
Affiliation(s)
- M Gu
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy; School of Life Science, Peking University, 100871 Beijing, China
| | - G Cosenza
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
| | - G Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - M Iannaccone
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy
| | - N P P Macciotta
- Department of Agricultural Sciences, University of Sassari, 07100, Sassari, Italy
| | - G Chemello
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - L Di Stasio
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - A Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy; National Research Council of Italy, Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Laboratory of Animal Cytogenetic and Gene Mapping, 80147 Naples, Italy.
| |
Collapse
|
24
|
Palavecino CE, Carrasco-Véliz N, Quest AFG, Garrido MP, Valenzuela-Valderrama M. The 5' untranslated region of the anti-apoptotic protein Survivin contains an inhibitory upstream AUG codon. Biochem Biophys Res Commun 2020; 526:898-905. [PMID: 32279998 DOI: 10.1016/j.bbrc.2020.03.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 03/28/2020] [Indexed: 12/20/2022]
Abstract
Survivin (BIRC5) is an anti-apoptotic protein that is important in cancer. Mechanisms responsible for controlling Survivin levels in cells include transcriptional regulation and modulation of protein stability via post-translational modifications; however to date, translational control has been poorly studied. Here, we focused particularly on the primary control elements present in the Survivin 5' untranslated region (5'UTR). Bioinformatic analysis of ribosome occupancy on the Survivin 5'UTR revealed the presence of elongating ribosomes upstream of the canonical initiator AUG, suggesting an alternative upstream initiator AUG (uAUG) might exist. This uAUG was found out-of-frame at position -71 and appeared as a conserved element in mammals. RACE analysis revealed different transcriptional start sites for BIRC5, which indicated that translational control by this uAUG is restricted to longer 5'UTR variants. We studied the activity of the uAUG in different cell types by cloning the Survivin 5'UTR DNA sequence (wild-type and mutated variants) upstream of renilla luciferase (RLuc) into a pcDNA3 plasmid. Changes in RLuc activity were determined by luminescence assays and Western blotting. Results showed that when this uAUG was mutated to AUU or AGG in the cloned Survivin 5'UTR, RLuc activity was significantly increased. Similar results were obtained when uAUG was positioned inframe with the RLuc initiator AUG. Immunodetection of Renilla (35 kDa) by Western blotting revealed the presence of a second band (37 kDa approximately) in cells transfected with the Inframe reporter constructs, indicating that the uAUG was functional in our experimental conditions. In conclusion, our experimental data demonstrate the presence of an alternative and inhibitory initiator uAUG in the Survivin 5' UTR. This inhibitory uAUG may help understanding how Survivin expression is downregulated under physiological or pathological conditions.
Collapse
Affiliation(s)
- Christian E Palavecino
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Nicolás Carrasco-Véliz
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile
| | - Andrew F G Quest
- Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile; Laboratorio de Comunicaciones Celulares, Centro de Estudios en Ejercicio, Metabolismo y Cáncer (CEMC), Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Avenida Independencia 1027, Independencia, 8380453, Chile
| | - Maritza P Garrido
- Laboratorio de Endocrinología y Biología de la Reproducción, Departamento de Obstetricia y Ginecología, Hospital Clínico Universidad de Chile, Avenida Santos Dumont 999, Independencia, 8380456, Chile
| | - Manuel Valenzuela-Valderrama
- Laboratorio de Microbiología Celular, Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Lord Cochrane 418, Santiago, 8320000, Chile; Centro de Estudios Avanzados en Enfermedades Crónicas (ACCDiS), Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile.
| |
Collapse
|
25
|
TBX5 R264K acts as a modifier to develop dilated cardiomyopathy in mice independently of T-box pathway. PLoS One 2020; 15:e0227393. [PMID: 32236096 PMCID: PMC7112173 DOI: 10.1371/journal.pone.0227393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/05/2020] [Indexed: 11/28/2022] Open
Abstract
Background TBX5 is a transcription factor that has an important role in development of heart. TBX5 variants in the region encoding the T-box domain have been shown to cause cardiac defects, such as atrial septal defect or ventricular septal defect, while TBX5 variants have also been identified in a few cardiomyopathy patients and considered causative. We identified a TBX5 variant (c.791G>A, p.Arg264Lys), that is over-represented in cardiomyopathy patients. This variant is located outside of the T-box domain, and its pathogenicity has not been confirmed by functional analyses. Objective To investigate whether the TBX5 R264K is deleterious and could contribute to the pathogenesis of cardiomyopathy. Methods and results We developed mice expressing Tbx5 R264K. Mice homozygous for this variant displayed compensated dilated cardiomyopathy; mild decreased fractional shortening, dilatation of the left ventricle, left ventricular wall thinning and increased heart weight without major heart structural disorders. There was no difference in activation of the ANF promotor, a transcriptional target of Tbx5, compared to wild-type. However, analysis of RNA isolated from left ventricular samples showed significant increases in the expression of Acta1 in left ventricle with concomitant increases in the protein level of ACTA1. Conclusions Mice homozygous for Tbx5 R264K showed compensated dilated cardiomyopathy. Thus, TBX5 R264K may have a significant pathogenic role in some cardiomyopathy patients independently of T-box domain pathway.
Collapse
|
26
|
Zhu YP, Zheng Z, Hu S, Ru X, Fan Z, Qiu L, Zhang Y. Unification of Opposites between Two Antioxidant Transcription Factors Nrf1 and Nrf2 in Mediating Distinct Cellular Responses to the Endoplasmic Reticulum Stressor Tunicamycin. Antioxidants (Basel) 2019; 9:antiox9010004. [PMID: 31861550 PMCID: PMC7022656 DOI: 10.3390/antiox9010004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/07/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
The water-soluble Nrf2 (nuclear factor, erythroid 2-like 2, also called Nfe2l2) is accepted as a master regulator of antioxidant responses to cellular stress, and it was also identified as a direct target of the endoplasmic reticulum (ER)-anchored PERK (protein kinase RNA-like endoplasmic reticulum kinase). However, the membrane-bound Nrf1 (nuclear factor, erythroid 2-like 1, also called Nfe2l1) response to ER stress remains elusive. Herein, we report a unity of opposites between these two antioxidant transcription factors, Nrf1 and Nrf2, in coordinating distinct cellular responses to the ER stressor tunicamycin (TU). The TU-inducible transcription of Nrf1 and Nrf2, as well as GCLM (glutamate cysteine ligase modifier subunit) and HO-1 (heme oxygenase 1), was accompanied by activation of ER stress signaling networks. Notably, the unfolded protein response (UPR) mediated by ATF6 (activating transcription factor 6), IRE1 (inositol requiring enzyme 1) and PERK was significantly suppressed by Nrf1α-specific knockout, but hyper-expression of Nrf2 and its target genes GCLM and HO-1 has retained in Nrf1α−/− cells. By contrast, Nrf2−/−ΔTA cells with genomic deletion of its transactivation (TA) domain resulted in significant decreases of GCLM, HO-1 and Nrf1; this was accompanied by partial decreases of IRE1 and ATF6, rather than PERK, but with an increase of ATF4 (activating transcription factor 4). Interestingly, Nrf1 glycosylation and its trans-activity to mediate the transcriptional expression of the 26S proteasomal subunits, were repressed by TU. This inhibitory effect was enhanced by Nrf1α−/− and Nrf2−/−ΔTA, but not by a constitutive activator caNrf2ΔN (that increased abundances of the non-glycosylated and processed Nrf1). Furthermore, caNrf2ΔN also enhanced induction of PERK and IRE1 by TU, but reduced expression of ATF4 and HO-1. Thus, it is inferred that such distinct roles of Nrf1 and Nrf2 are unified to maintain cell homeostasis by a series of coordinated ER-to-nuclear signaling responses to TU. Nrf1α (i.e., a full-length form) acts in a cell-autonomous manner to determine the transcription of most of UPR-target genes, albeit Nrf2 is also partially involved in this process. Consistently, transactivation of ARE (antioxidant response element)-driven BIP (binding immunoglobulin protein)-, PERK- and XBP1 (X-box binding protein 1)-Luc reporter genes was mediated directly by Nrf1 and/or Nrf2. Interestingly, Nrf1α is more potent than Nrf2 at mediating the cytoprotective responses against the cytotoxicity of TU alone or plus tBHQ (tert-butylhydroquinone). This is also further supported by the evidence that the intracellular reactive oxygen species (ROS) levels are increased in Nrf1α−/− cells, but rather are, to our surprise, decreased in Nrf2−/−ΔTA cells.
Collapse
Affiliation(s)
- Yu-ping Zhu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
| | - Ze Zheng
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
| | - Shaofan Hu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
| | - Xufang Ru
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
| | - Zhuo Fan
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
| | - Lu Qiu
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
- School of Life Sciences, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou 450001, China
| | - Yiguo Zhang
- The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China (Z.Z.); (S.H.); (X.R.); (Z.F.); (L.Q.)
- Correspondence: or
| |
Collapse
|
27
|
Anokhina IP, Anokhin PK, Kokhan VS. Combined Irradiation by Gamma Rays and Carbon Nuclei Increases the C/EBP-β LIP Isoform Content in the Pituitary Gland of Rats. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2019; 488:133-135. [PMID: 31732897 DOI: 10.1134/s0012496619050016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 11/23/2022]
Abstract
C/EBP-β, a basic leucine zipper transcription factor, has important roles in the regulation of the body immune and inflammatory responses. Wistar rats subjected to combined irradiation were characterized by an increase in the content of the C/EBP-β LIP isoform in the pituitary gland. The obtained data indicate that moderate doses of ionizing radiation to initiate the endoplasmic reticulum stress response and are likely to initiate C/EBP-β-mediated cell death according to the apoptotic scenario. This study also confirms the earlier hypothesis about the alterations of the hypothalamic-pituitary-adrenocortical axis in response to moderate doses of ionizing radiation.
Collapse
Affiliation(s)
- I P Anokhina
- Serbsky Federal Medical Research Centre for Psychiatry and Narcology, Moscow, Russia
| | - P K Anokhin
- Serbsky Federal Medical Research Centre for Psychiatry and Narcology, Moscow, Russia
| | - V S Kokhan
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
28
|
Ribeiro DE, Müller HK, Elfving B, Eskelund A, Joca SR, Wegener G. Antidepressant-like effect induced by P2X7 receptor blockade in FSL rats is associated with BDNF signalling activation. J Psychopharmacol 2019; 33:1436-1446. [PMID: 31526216 DOI: 10.1177/0269881119872173] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND P2X7 receptors (P2X7R) are ligand-gated ion channels activated by adenosine 5'-triphosphate (ATP), which are involved in processes that are dysfunctional in stress response and depression, such as neurotransmitter release, and neuroimmune response. Genetic and pharmacological inhibition of the P2X7R induce antidepressant-like effects in animals exposed to stress. However, the effect of P2X7R antagonism in an animal model of depression based on selective breeding has not previously been studied, and the mechanism underling the antidepressant-like effect induced by the P2X7R blockade remains unknown. AIMS The present study aimed to: (1) determine whether P2X7R blockade induces antidepressant-like effects in the Flinders Sensitive Line (FSL) rats and, (2) investigate whether brain-derived neurotrophic factor (BDNF) signalling in the frontal cortex and hippocampus is involved in this effect. METHODS FSL and the control Flinders Resistant Line (FRL) rats were treated with vehicle or the P2X7R antagonist A-804598 (3, 10 or 30 mg/Kg/day) for 1 or 7 days before being exposed to the forced swim test (FST). After the behavioural test, animals were decapitated, their brains were removed and the frontal cortex, ventral and dorsal hippocampus were dissected for BDNF signalling analysis. RESULTS We found that repeated treatment with A-804598 (30 mg/Kg) reduced the immobility time in the FST and activated the BDNF signalling in the ventral hippocampus of FSL rats. CONCLUSIONS P2X7R blockade induces an antidepressant-like effect associated with increased levels of BDNF-AKT-p70 S6 kinase in the ventral hippocampus, which may be mediated by tropomyosin-related kinase B (TRKB) receptor activation supporting the notion of P2X7R antagonism as a potential new antidepressant strategy.
Collapse
Affiliation(s)
- Deidiane E Ribeiro
- Department of Pharmacology, School of Medicine of Ribeirão Preto - University of São Paulo, São Paulo, Brazil.,Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - University of São Paulo, Ribeirão Preto, Brazil.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, Brazil
| | - Heidi K Müller
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Betina Elfving
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amanda Eskelund
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Samia Rl Joca
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - University of São Paulo, Ribeirão Preto, Brazil.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Gregers Wegener
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,AUGUST Centre, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| |
Collapse
|
29
|
Dumesic PA, Egan DF, Gut P, Tran MT, Parisi A, Chatterjee N, Jedrychowski M, Paschini M, Kazak L, Wilensky SE, Dou F, Bogoslavski D, Cartier JA, Perrimon N, Kajimura S, Parikh SM, Spiegelman BM. An Evolutionarily Conserved uORF Regulates PGC1α and Oxidative Metabolism in Mice, Flies, and Bluefin Tuna. Cell Metab 2019; 30:190-200.e6. [PMID: 31105043 PMCID: PMC6620024 DOI: 10.1016/j.cmet.2019.04.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/25/2019] [Accepted: 04/21/2019] [Indexed: 12/29/2022]
Abstract
Mitochondrial abundance and function are tightly controlled during metabolic adaptation but dysregulated in pathological states such as diabetes, neurodegeneration, cancer, and kidney disease. We show here that translation of PGC1α, a key governor of mitochondrial biogenesis and oxidative metabolism, is negatively regulated by an upstream open reading frame (uORF) in the 5' untranslated region of its gene (PPARGC1A). We find that uORF-mediated translational repression is a feature of PPARGC1A orthologs from human to fly. Strikingly, whereas multiple inhibitory uORFs are broadly present in fish PPARGC1A orthologs, they are completely absent in the Atlantic bluefin tuna, an animal with exceptionally high mitochondrial content. In mice, an engineered mutation disrupting the PPARGC1A uORF increases PGC1α protein levels and oxidative metabolism and confers protection from acute kidney injury. These studies identify a translational regulatory element governing oxidative metabolism and highlight its potential contribution to the evolution of organismal mitochondrial function.
Collapse
Affiliation(s)
- Phillip A Dumesic
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Daniel F Egan
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Philipp Gut
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Mei T Tran
- Division of Nephrology and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Alice Parisi
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Nirmalya Chatterjee
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mark Jedrychowski
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | | | - Lawrence Kazak
- Goodman Cancer Research Centre, Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Florence Dou
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | | | - Norbert Perrimon
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Shingo Kajimura
- Diabetes Center and Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | - Samir M Parikh
- Division of Nephrology and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Bruce M Spiegelman
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA.
| |
Collapse
|
30
|
Chen HH, Tarn WY. uORF-mediated translational control: recently elucidated mechanisms and implications in cancer. RNA Biol 2019; 16:1327-1338. [PMID: 31234713 DOI: 10.1080/15476286.2019.1632634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is tightly regulated, and its dysregulation can contribute to the pathology of various diseases, including cancer. Increased or selective translation of mRNAs can promote cancer cell proliferation, metastasis and tumor expansion. Translational control is one of the most important means for cells to quickly adapt to environmental stresses. Adaptive translation involves various alternative mechanisms of translation initiation. Upstream open reading frames (uORFs) serve as a major regulator of stress-responsive translational control. Since recent advances in omics technologies including ribo-seq have expanded our knowledge of translation, we discuss emerging mechanisms for uORF-mediated translation regulation and its impact on cancer cell biology. A better understanding of dysregulated translational control of uORFs in cancer would facilitate the development of new strategies for cancer therapy.
Collapse
Affiliation(s)
- Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
| |
Collapse
|
31
|
Dvorak P, Leupen S, Soucek P. Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. Cells 2019; 8:cells8060623. [PMID: 31234415 PMCID: PMC6627321 DOI: 10.3390/cells8060623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.
Collapse
Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
| | - Sarah Leupen
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300 Pilsen, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42 Prague 10, Czech Republic.
| |
Collapse
|
32
|
Liang XH, Shen W, Crooke ST. Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639196 DOI: 10.1007/978-981-10-4310-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.
Collapse
Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| |
Collapse
|
33
|
Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA. Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. G3 (BETHESDA, MD.) 2019; 9:1045-1053. [PMID: 30723103 PMCID: PMC6469420 DOI: 10.1534/g3.118.200802] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/25/2019] [Indexed: 11/18/2022]
Abstract
We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that prevented translation of the main ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown. Here we find that, indeed, a similar type of regulation occurs at the locus for the human oncogene MDM2 We observe evidence of transcriptional interference between the two MDM2 promoters, which produce a poorly translated distal promoter-derived uORF-containing mRNA isoform and a well-translated proximal promoter-derived transcript. Down-regulation of distal promoter activity markedly up-regulates proximal promoter-driven expression and results in local reduction of histone H3K36 trimethylation. Moreover, we observe that this transcript toggling between the two MDM2 isoforms naturally occurs during human embryonic stem cell differentiation programs.
Collapse
Affiliation(s)
- Ina Hollerer
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Juliet C Barker
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Amy Tresenrider
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Leon Y Chan
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley, CA 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| | - Gloria A Brar
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA 94720
| |
Collapse
|
34
|
Dittmar G, Hernandez DP, Kowenz-Leutz E, Kirchner M, Kahlert G, Wesolowski R, Baum K, Knoblich M, Hofstätter M, Muller A, Wolf J, Reimer U, Leutz A. PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. iScience 2019; 13:351-370. [PMID: 30884312 PMCID: PMC6424098 DOI: 10.1016/j.isci.2019.02.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/20/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
CCAAT enhancer-binding protein beta (C/EBPβ) is a pioneer transcription factor that specifies cell differentiation. C/EBPβ is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPβ differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPβ alters protein interactions and cell differentiation, suggesting that a C/EBPβ PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPβ using an array technique based on spot-synthesized C/EBPβ-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions. We identified interaction footprints of ∼1,300 proteins in nuclear extracts, many with chromatin modifying, chromatin remodeling, and RNA processing functions. The results suggest that C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.
Collapse
Affiliation(s)
- Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany.
| | - Daniel Perez Hernandez
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Günther Kahlert
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Radoslaw Wesolowski
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Katharina Baum
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Knoblich
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Hofstätter
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Arnaud Muller
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Jana Wolf
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; Humboldt-University of Berlin, Institute of Biology, 10115 Berlin, Germany.
| |
Collapse
|
35
|
Silva J, Fernandes R, Romão L. Translational Regulation by Upstream Open Reading Frames and Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:99-116. [DOI: 10.1007/978-3-030-19966-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
36
|
Control of mRNA Translation by Versatile ATP-Driven Machines. Trends Biochem Sci 2018; 44:167-180. [PMID: 30527974 DOI: 10.1016/j.tibs.2018.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 12/13/2022]
Abstract
Translation is organized in a cycle that requires ribosomal subunits, mRNA, aminoacylated transfer RNAs, and myriad regulatory factors. As soon as translation reaches a stop codon or stall, a termination or surveillance process is launched via the release factors eRF1 or Pelota, respectively. The ATP-binding cassette (ABC) protein ABCE1 interacts with release factors and coordinates the recycling process in Eukarya and Archaea. After splitting, ABCE1 stays with the small ribosomal subunit and emerges as an integral part of translation initiation complexes. In addition, eEF3 and ABCF proteins control translation by binding at the E-site. In this review, we highlight advances in the fundamental role of ABC systems in mRNA translation in view of their collective inner mechanics.
Collapse
|
37
|
Fan Z, Zheng J, Xue Y, Liu X, Wang D, Yang C, Ma J, Liu L, Ruan X, Wang Z, Liu Y. NR2C2-uORF targeting UCA1-miR-627-5p-NR2C2 feedback loop to regulate the malignant behaviors of glioma cells. Cell Death Dis 2018; 9:1165. [PMID: 30518750 PMCID: PMC6281640 DOI: 10.1038/s41419-018-1149-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022]
Abstract
Accumulating evidence has highlighted the potential role of non-coding RNAs (ncRNAs) and upstream open-reading frames (uORFs) in the biological behaviors of glioblastoma. Here, we elucidated the function and possible molecular mechanisms of the effect of some ncRNAs and NR2C2-uORF on the biological behaviors of gliomas. Quantitative real-time PCR was conducted to profile the cell expression of lnc-UCA1 and microRNA-627-5p (miR-627-5p) in glioma tissues and cells. Western blot assay was used to determine the expression levels of NR2C2, SPOCK1, and NR2C2-uORF in glioma tissues and cells. Stable knockdown of lnc-UCA1 or overexpression of miR-627-5p in glioma cell lines (U87 and U251) were established to explore the function of lnc-UCA1 and miR-627-5p in glioma cells. Further, Dual luciferase report assay was used to investigate the correlation between lnc-UCA1 and miR-627-5p. Cell Counting Kit-8, transwell assays, and flow cytometry were used to investigate lnc-UCA1 and miR-627-5p function including cell proliferation, migration and invasion, and apoptosis, respectively. ChIP assays were used to ascertain the correlations between NR2C2 and SPOCK1 as well as NR2C2 between lnc-UCA1. This study confirmed that lnc-UCA1 was up-regulated in glioma tissues and cells. UCA1 knockdown inhibited the malignancies of glioma cells by reducing proliferation, migration, and invasion, but inducing apoptosis. We found that lnc-UCA1 acted as miR-627-5p sponge in a sequence-specific manner. Meanwhile, upregulated lnc-UCA1 inhibited miR-627-5p expression. In addition, miR-627-5p targeted 3'UTR of NR2C2 and down-regulated its expression. Moreover, UCA1 knockdown impaired NR2C2 expression by upregulating miR-627-5p. An uORF was identified in mRNA 5'UTR of NR2C2 and overexpression of whom negatively regulated NR2C2 expression. Remarkably, lnc-UCA1 knockdown combined with uORF overepression and NR2C2 knockdown led to severe tumor suppression in vivo. This study demonstrated that the NR2C2-uORF impaired the pivotal roles that UCA1-miR-627-5p-NR2C2 feedback loop had in regulating the malignancies of glioma cells by targeting NR2C2 directly. And this may provide a potential therapeutic strategy for treating glioma.
Collapse
MESH Headings
- Animals
- Apoptosis/genetics
- Brain Neoplasms/genetics
- Brain Neoplasms/metabolism
- Brain Neoplasms/mortality
- Brain Neoplasms/pathology
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Feedback, Physiological
- Gene Expression Regulation, Neoplastic
- Glioblastoma/genetics
- Glioblastoma/metabolism
- Glioblastoma/mortality
- Glioblastoma/pathology
- Humans
- Mice
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Open Reading Frames
- Promoter Regions, Genetic
- Proteoglycans/genetics
- Proteoglycans/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Signal Transduction
- Survival Analysis
- Tumor Burden
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Zirong Fan
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, College of Basic Medicine, China Medical University, 110122, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, 110122, Shenyang, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, 110122, Shenyang, China
| | - Zhenhua Wang
- Department of Physiology, College of Basic Medicine, China Medical University, 110122, Shenyang, Liaoning, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, 110004, Shenyang, China.
- Liaoning Clinical Medical Research Center in Nervous System Disease, 110004, Shenyang, China.
- Key Laboratory of Neuro-oncology in Liaoning Province, 110004, Shenyang, China.
| |
Collapse
|
38
|
Xiang Y, Wang M, Hu S, Qiu L, Yang F, Zhang Z, Yu S, Pi J, Zhang Y. Mechanisms controlling the multistage post-translational processing of endogenous Nrf1α/TCF11 proteins to yield distinct isoforms within the coupled positive and negative feedback circuits. Toxicol Appl Pharmacol 2018; 360:212-235. [DOI: 10.1016/j.taap.2018.09.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/23/2018] [Accepted: 09/23/2018] [Indexed: 01/20/2023]
|
39
|
Rouzeau C, Dagkesamanskaya A, Langer K, Bibette J, Baudry J, Pompon D, Anton-Leberre V. Adaptive response of yeast cells to triggered toxicity of phosphoribulokinase. Res Microbiol 2018; 169:335-342. [PMID: 29964131 DOI: 10.1016/j.resmic.2018.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/26/2022]
Abstract
Adjustment of plasmid copy number resulting from the balance between positive and negative impacts of borne synthetic genes, plays a critical role in the global efficiency of multistep metabolic engineering. Differential expression of co-expressed engineered genes is frequently observed depending on growth phases, metabolic status and triggered adjustments of plasmid copy numbers, constituting a dynamic process contributing to minimize global engineering burden. A yeast model involving plasmid based expression of phosphoribulokinase (PRKp), a key enzyme for the reconstruction of synthetic Calvin cycle, was designed to gain further insights into such a mechanism. A conditional PRK expression cassette was cloned either onto a low (ARS-CEN based) or a high (2-micron origin based) copy number plasmid using complementation of a trp1 genomic mutation as constant positive selection. Evolution of plasmid copy numbers, PRKp expressions, and cell growth rates were dynamically monitored following gene de-repression through external doxycycline concentration shifts. In the absence of RubisCO encoding gene permitting metabolic recycling, PRKp expression that led to depletion of ribulose phosphate, a critical metabolite for aromatic amino-acids biosynthesis, and accumulation of the dead-end diphosphate product contribute to toxicity. Triggered copy number adjustment was found to be a dynamic process depending both on plasmid types and levels of PRK induction. With the ARS-CEN plasmid, cell growth was abruptly affected only when level PRKp expression exceeded a threshold value. In contrast, a proportional relationship was observed with the 2-micron plasmid consistent with large copy number adjustments. Micro-compartment partitioning of bulk cultures by embedding individual cells into inverse culture medium/oil droplets, revealed the presence of slow and fast growing subpopulations that differ in relative proportions for low and high copy number plasmids.
Collapse
Affiliation(s)
| | | | - Krzysztof Langer
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Jérôme Bibette
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Denis Pompon
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | |
Collapse
|
40
|
LNX1/LNX2 proteins: functions in neuronal signalling and beyond. Neuronal Signal 2018; 2:NS20170191. [PMID: 32714586 PMCID: PMC7373230 DOI: 10.1042/ns20170191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022] Open
Abstract
Ligand of NUMB Protein X1 and X2 (LNX1 and LNX2) are E3 ubiquitin ligases, named for their ability to interact with and promote the degradation of the cell fate determinant protein NUMB. On this basis they are thought to play a role in modulating NUMB/NOTCH signalling during processes such as cortical neurogenesis. However, LNX1/2 proteins can bind, via their four PDZ (PSD95, DLGA, ZO-1) domains, to an extraordinarily large number of other proteins besides NUMB. Many of these interactions suggest additional roles for LNX1/2 proteins in the nervous system in areas such as synapse formation, neurotransmission and regulating neuroglial function. Twenty years on from their initial discovery, I discuss here the putative neuronal functions of LNX1/2 proteins in light of the anxiety-related phenotype of double knockout mice lacking LNX1 and LNX2 in the central nervous system (CNS). I also review what is known about non-neuronal roles of LNX1/2 proteins, including their roles in embryonic patterning and pancreas development in zebrafish and their possible involvement in colorectal cancer (CRC), osteoclast differentiation and immune function in mammals. The emerging picture places LNX1/2 proteins as potential regulators of multiple cellular signalling processes, but in many cases the physiological significance of such roles remains only partly validated and needs to be considered in the context of the tight control of LNX1/2 protein levels in vivo.
Collapse
|
41
|
Sim TY, Harith HH, Tham CL, Md Hashim NF, Shaari K, Sulaiman MR, Israf DA. The Protective Effects of a Synthetic Geranyl Acetophenone in a Cellular Model of TNF-α-Induced Pulmonary Epithelial Barrier Dysfunction. Molecules 2018; 23:molecules23061355. [PMID: 29874809 PMCID: PMC6100020 DOI: 10.3390/molecules23061355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 01/19/2023] Open
Abstract
Alveolar epithelial barrier dysfunction contributes to lung edema and can lead to acute lung injury (ALI). The features include increased epithelial permeability, upregulation of inflammatory mediators and downregulation of junctional complex molecules; these changes are often induced by inflammation. tHGA is an acetophenone analogue with therapeutic potential in asthma. Its therapeutic potential in ALI is presently unknown. Herein, the effects of tHGA on epithelial barrier dysfunction were determined in TNF-α-induced human alveolar epithelial cells. The anti-inflammatory properties of tHGA were assessed by monocyte adhesion assay and analysis of MCP-1 and ICAM-1 expression. The epithelial barrier function was assessed by paracellular permeability and transepithelial electrical resistance (TEER) assays, and analysis of junctional complex molecules expression. To elucidate the mechanism of action, the effects of tHGA on the NF-κB and MAPK pathways were determined. Gene and protein expression were analyzed by RT-PCR and Western blotting or ELISA, respectively. tHGA suppressed leukocyte adhesion to TNF-α-induced epithelium and reduced MCP-1 and ICAM-1 gene expression and secretion. tHGA also increased TEER readings, reduced epithelial permeability and enhanced expression of junctional complex molecules (zona occludens-1, occludin and E-cadherin) in TNF-α-induced cells. Correspondingly, the NF-κB, ERK and p38 MAPK pathways were also inhibited by tHGA. These findings suggest that tHGA is able to preserve alveolar epithelial barrier function in response to acute inflammation, via its anti-inflammatory activity and stabilization of epithelial barrier integrity, mediated by NF-κB, ERK and p38 MAPK signaling.
Collapse
Affiliation(s)
- Tee Yee Sim
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Hanis Hazeera Harith
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nur Fariesha Md Hashim
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Khozirah Shaari
- Natural Products Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Roslan Sulaiman
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Daud Ahmad Israf
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| |
Collapse
|
42
|
Steri M, Idda ML, Whalen MB, Orrù V. Genetic variants in mRNA untranslated regions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1474. [PMID: 29582564 DOI: 10.1002/wrna.1474] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/05/2018] [Accepted: 02/11/2018] [Indexed: 12/24/2022]
Abstract
Genome Wide Association Studies (GWAS) have mapped thousands of genetic variants associated with complex disease risk and regulating quantitative traits, thus exploiting an unprecedented high-resolution genetic characterization of the human genome. A small fraction (3.7%) of the identified associations is located in untranslated regions (UTRs), and the molecular mechanism has been elucidated for few of them. Genetic variations at UTRs may modify regulatory elements affecting the interaction of the UTRs with proteins and microRNAs. The overall functional consequences include modulation of messenger RNA (mRNA) transcription, secondary structure, stability, localization, translation, and access to regulators like microRNAs (miRNAs) and RNA-binding proteins (RBPs). Alterations of these regulatory mechanisms are known to modify molecular pathways and cellular processes, potentially leading to disease processes. Here, we analyze some examples of genetic risk variants mapping in the UTR regulatory elements. We describe a recently identified genetic variant localized in the 3'UTR of the TNFSF13B gene, associated with autoimmunity risk and responsible of an increased stability and translation of TNFSF13B mRNA. We discuss how the correct use and interpretation of public GWAS repositories could lead to a better understanding of etiopathogenetic mechanisms and the generation of robust biological hypothesis as starting point for further functional studies. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institute of Health, Baltimore, Maryland
| | - Michael B Whalen
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Trento, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| |
Collapse
|
43
|
Pomerantz DJ, Ferdinandusse S, Cogan J, Cooper DN, Reimschisel T, Robertson A, Bican A, McGregor T, Gauthier J, Millington DS, Andrae JLW, Tschannen MR, Helbling DC, Demos WM, Denis S, Wanders RJA, Newman JN, Hamid R, Phillips JA. Clinical heterogeneity of mitochondrial NAD kinase deficiency caused by a NADK2 start loss variant. Am J Med Genet A 2018; 176:692-698. [PMID: 29388319 PMCID: PMC6185736 DOI: 10.1002/ajmg.a.38602] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/12/2022]
Abstract
Mitochondrial NAD kinase deficiency (NADK2D, OMIM #615787) is a rare autosomal recessive disorder of NADPH biosynthesis that can cause hyperlysinemia and dienoyl-CoA reductase deficiency (DECRD, OMIM #616034). NADK2 deficiency has been reported in only three unrelated patients. Two had severe, unremitting disease; one died at 4 months and the other at 5 years of age. The third was a 10 year old female with CNS anomalies, ataxia, and incoordination. In two cases mutations in NADK2 have been demonstrated. Here, we report the fourth known case, a 15 year old female with normal intelligence and a mild clinical and biochemical phenotype presumably without DECRD. Her clinical symptoms, which are now stable, became evident at the age of 9 with the onset of decreased visual acuity, bilateral optic atrophy, nystagmus, episodic lower extremity weakness, peripheral neuropathy, and gait abnormalities. Plasma amino acid levels were within normal limits except for mean lysine and proline levels that were 3.7 and 2.5 times the upper limits of normal. Whole exome sequencing (WES) revealed homozygosity for a g.36241900 A>G p. Met1Val start loss mutation in the primary NADK2 transcript (NM_001085411.1) encoding the 442 amino acid isoform. This presumed hypomorphic mutation has not been previously reported and is absent from the v1000GP, EVS, and ExAC databases. Our patient's normal intelligence and stable disease expands the clinical heterogeneity and the prognosis associated with NADK2 deficiency. Our findings also clarify the mechanism underlying NADK2 deficiency and suggest that this disease should be ruled out in cases of hyperlysinemia, especially those with visual loss, and neurological phenotypes.
Collapse
Affiliation(s)
- Daniel J. Pomerantz
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - Joy Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Heath Park, Cardiff University, Cardiff, United Kingdom
| | - Tyler Reimschisel
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Amy Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tracy McGregor
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jackie Gauthier
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David S. Millington
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina
| | | | | | | | | | - Simone Denis
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - Ronald J. A. Wanders
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - John N. Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John A. Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | | |
Collapse
|
44
|
Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, Castaños-Vélez E, Fichtner I, Tunn PU, Denkert C, Klaas O, Berdel WE, von Kries JP, Makalowski W, Andrade-Navarro MA, Leutz A, Wethmar K. Loss-of-function uORF mutations in human malignancies. Sci Rep 2018; 8:2395. [PMID: 29402903 PMCID: PMC5799362 DOI: 10.1038/s41598-018-19201-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 12/27/2017] [Indexed: 11/09/2022] Open
Abstract
Ribosome profiling revealed widespread translational activity at upstream open reading frames (uORFs) and validated uORF-mediated translational control as a commonly repressive mechanism of gene expression. Translational activation of proto-oncogenes through loss-of-uORF mutations has been demonstrated, yet a systematic search for cancer-associated genetic alterations in uORFs is lacking. Here, we applied a PCR-based, multiplex identifier-tagged deep sequencing approach to screen 404 uORF translation initiation sites of 83 human tyrosine kinases and 49 other proto-oncogenes in 308 human malignancies. We identified loss-of-function uORF mutations in EPHB1 in two samples derived from breast and colon cancer, and in MAP2K6 in a sample of colon adenocarcinoma. Both mutations were associated with enhanced translation, suggesting that loss-of-uORF-mediated translational induction of the downstream main protein coding sequence may have contributed to carcinogenesis. Computational analysis of whole exome sequencing datasets of 464 colon adenocarcinomas subsequently revealed another 53 non-recurrent somatic mutations functionally deleting 22 uORF initiation and 31 uORF termination codons, respectively. These data provide evidence for somatic mutations affecting uORF initiation and termination codons in human cancer. The insufficient coverage of uORF regions in current whole exome sequencing datasets demands for future genome-wide analyses to ultimately define the contribution of uORF-mediated translational deregulation in oncogenesis.
Collapse
Affiliation(s)
- Julia Schulz
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Nancy Mah
- Charité University Medicine Berlin, Campus Virchow-Klinikum, Berlin-Brandenburg Center for Regenerative Therapies, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Martin Neuenschwander
- Leibniz Institute fuer Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Tabea Kischka
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Straße 14, 48149, Muenster, Germany
| | - Richard Ratei
- Carl-Thiem-Klinikum, 2. Medizinische Klinik, Thiemstr. 111, 03048, Cottbus, Germany.,Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125, Berlin, Germany
| | - Peter M Schlag
- Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Iduna Fichtner
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Per-Ulf Tunn
- Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125, Berlin, Germany
| | - Carsten Denkert
- Charité University Medicine Berlin, Institute of Pathology, Chariteplatz 1, 10117, Berlin, Germany
| | - Oliver Klaas
- University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany
| | - Wolfgang E Berdel
- University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany
| | - Jens P von Kries
- Leibniz Institute fuer Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Wojciech Makalowski
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Straße 14, 48149, Muenster, Germany
| | - Miguel A Andrade-Navarro
- Johannes-Gutenberg University of Mainz, Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Achim Leutz
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany. .,Humboldt-University, Department of Biology, Invalidenstr. 43, 10115, Berlin, Germany.
| | - Klaus Wethmar
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany. .,University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany.
| |
Collapse
|
45
|
Gazon H, Barbeau B, Mesnard JM, Peloponese JM. Hijacking of the AP-1 Signaling Pathway during Development of ATL. Front Microbiol 2018; 8:2686. [PMID: 29379481 PMCID: PMC5775265 DOI: 10.3389/fmicb.2017.02686] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of a fatal malignancy known as adult T-cell leukemia (ATL). One way to address the pathology of the disease lies on conducting research with a molecular approach. In addition to the analysis of ATL-relevant signaling pathways, understanding the regulation of important and relevant transcription factors allows researchers to reach this fundamental objective. HTLV-1 encodes for two oncoproteins, Tax and HTLV-1 basic leucine-zipper factor, which play significant roles in the cellular transformation and the activation of the host's immune responses. Activating protein-1 (AP-1) transcription factor has been linked to cancer and neoplastic transformation ever since the first representative members of the Jun and Fos gene family were cloned and shown to be cellular homologs of viral oncogenes. AP-1 is a dimeric transcription factor composed of proteins belonging to the Jun (c-Jun, JunB, and JunD), Fos (c-Fos, FosB, Fra1, and Fra2), and activating transcription factor protein families. Activation of AP-1 transcription factor family by different stimuli, such as inflammatory cytokines, stress inducers, or pathogens, results in innate and adaptive immunity. AP-1 is also involved in various cellular events including differentiation, proliferation, survival, and apoptosis. Deregulated expression of AP-1 transcription factors is implicated in various lymphomas such as classical Hodgkin lymphomas, anaplastic large cell lymphomas, diffuse large B-cell lymphomas, and adult T-cell leukemia. Here, we review the current thinking behind deregulation of the AP-1 pathway and its contribution to HTLV-induced cellular transformation.
Collapse
Affiliation(s)
- Hélène Gazon
- Belgium Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, Liège, Belgium
| | - Benoit Barbeau
- Département des Sciences Biologiques and Centre de Recherche BioMed, Université du Québec à Montréal, Montréal, QC, Canada
| | - Jean-Michel Mesnard
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Jean-Marie Peloponese
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| |
Collapse
|
46
|
Abstract
Themospermine is a structural isomer of spermine and is present in some bacteria and most of plants. An Arabidopsis mutant, acaulis5 (acl5), that is defective in the biosynthesis of thermospermine displays excessive proliferation of xylem vessels with dwarfed growth. Recent studies using acl5 and its suppressor mutants that recover the growth without thermospermine have revealed that thermospermine plays a key role in the negative control of the proliferation of xylem vessels through enhancing translation of specific mRNAs that contain a conserved upstream open-reading-frame (uORF) in the 5' leader region.
Collapse
Affiliation(s)
- Taku Takahashi
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, kita-ku, 700-8530, Okayama, Japan.
| |
Collapse
|
47
|
Tang L, Morris J, Wan J, Moore C, Fujita Y, Gillaspie S, Aube E, Nanda J, Marques M, Jangal M, Anderson A, Cox C, Hiraishi H, Dong L, Saito H, Singh CR, Witcher M, Topisirovic I, Qian SB, Asano K. Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide. Nucleic Acids Res 2017; 45:11941-11953. [PMID: 28981728 PMCID: PMC5714202 DOI: 10.1093/nar/gkx808] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/31/2017] [Indexed: 12/27/2022] Open
Abstract
In the human genome, translation initiation from non-AUG codons plays an important role in various gene regulation programs. However, mechanisms regulating the non-AUG initiation rate remain poorly understood. Here, we show that the non-AUG initiation rate is nearly consistent under a fixed nucleotide context in various human and insect cells. Yet, it ranges from <1% to nearly 100% compared to AUG translation, depending on surrounding sequences, including Kozak, and possibly additional nucleotide contexts. Mechanistically, this range of non-AUG initiation is controlled in part, by the eIF5-mimic protein (5MP). 5MP represses non-AUG translation by competing with eIF5 for the Met-tRNAi-binding factor eIF2. Consistently, eIF5 increases, whereas 5MP decreases translation of NAT1/EIF4G2/DAP5, whose sole start codon is GUG. By modulating eIF5 and 5MP1 expression in combination with ribosome profiling we identified a handful of previously unknown non-AUG initiation sites, some of which serve as the exclusive start codons. If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUG-initiated isoforms. We propose that the homeostasis of the non-AUG translatome is maintained through balanced expression of eIF5 and 5MP.
Collapse
Affiliation(s)
- Leiming Tang
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jacob Morris
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Chelsea Moore
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Yoshihiko Fujita
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Sarah Gillaspie
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Eric Aube
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | | | - Maud Marques
- Lady Davis Institute, and the Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Maika Jangal
- Lady Davis Institute, and the Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Abbey Anderson
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Christian Cox
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Hiroyuki Hiraishi
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Chingakham Ranjit Singh
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael Witcher
- Lady Davis Institute, and the Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Ivan Topisirovic
- Lady Davis Institute, and the Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
48
|
Balbinot C, Vanier M, Armant O, Nair A, Penichon J, Soret C, Martin E, Saandi T, Reimund JM, Deschamps J, Beck F, Domon-Dell C, Gross I, Duluc I, Freund JN. Fine-tuning and autoregulation of the intestinal determinant and tumor suppressor homeobox gene CDX2 by alternative splicing. Cell Death Differ 2017; 24:2173-2186. [PMID: 28862703 DOI: 10.1038/cdd.2017.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
On the basis of phylogenetic analyses, we uncovered a variant of the CDX2 homeobox gene, a major regulator of the development and homeostasis of the gut epithelium, also involved in cancer. This variant, miniCDX2, is generated by alternative splicing coupled to alternative translation initiation, and contains the DNA-binding homeodomain but is devoid of transactivation domain. It is predominantly expressed in crypt cells, whereas the CDX2 protein is present in crypt cells but also in differentiated villous cells. Functional studies revealed a dominant-negative effect exerted by miniCDX2 on the transcriptional activity of CDX2, and conversely similar effects regarding several transcription-independent functions of CDX2. In addition, a regulatory role played by the CDX2 and miniCDX2 homeoproteins on their pre-mRNA splicing is displayed, through interactions with splicing factors. Overexpression of miniCDX2 in the duodenal Brunner glands leads to the expansion of the territory of these glands and ultimately to brunneroma. As a whole, this study characterized a new and original variant of the CDX2 homeobox gene. The production of this variant represents not only a novel level of regulation of this gene, but also a novel way to fine-tune its biological activity through the versatile functions exerted by the truncated variant compared to the full-length homeoprotein. This study highlights the relevance of generating protein diversity through alternative splicing in the gut and its diseases.
Collapse
Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Marie Vanier
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Postfach 3640, Karlsruhe 76021, Germany
| | - Asmaa Nair
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Julien Penichon
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Christine Soret
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Thoueiba Saandi
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Marie Reimund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jacqueline Deschamps
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London E1 2ES, UK
| | - Claire Domon-Dell
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Gross
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Duluc
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| |
Collapse
|
49
|
Álvarez A, Toledo H. The histone-like protein HU has a role in gene expression during the acid adaptation response in Helicobacter pylori. Helicobacter 2017; 22. [PMID: 28244177 DOI: 10.1111/hel.12381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Gastritis, ulcers, and gastric malignancy have been linked to human gastric epithelial colonization by Helicobacter pylori. Characterization of the mechanisms by which H. pylori adapts to the human stomach environment is of crucial importance to understand H. pylori pathogenesis. MATERIAL AND METHODS In an effort to extend our knowledge of these mechanisms, we used proteomic analysis and qRT-PCR to characterize the role of the histone-like protein HU in the response of H. pylori to low pH. RESULTS Proteomic analysis revealed that genes involved in chemotaxis, oxidative stress, or metabolism are under control of the HU protein. Also, expression of the virulence factors Ggt and NapA is affected by the null mutation of hup gene both at neutral and acid pH, as evidenced by qRT-PCR analysis. CONCLUSIONS Those results showed that H. pylori gene expression is altered by shift to low pH, thus confirming that acid exposure leads to profound changes in genomic expression, and suggest that the HU protein is a regulator that may help the bacterium adapt to the acid stress. In accordance with previous reports, we found that the HU protein participates in gene expression regulation when the microorganism is exposed to acid stress. Such transcriptional regulation underlies protein accumulation in the H. pylori cell.
Collapse
Affiliation(s)
- Alhejandra Álvarez
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
| | - Héctor Toledo
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
| |
Collapse
|
50
|
Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
Collapse
Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
| |
Collapse
|