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Millward DJ. Post-natal muscle growth and protein turnover: a narrative review of current understanding. Nutr Res Rev 2024; 37:141-168. [PMID: 37395180 DOI: 10.1017/s0954422423000124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
A model explaining the dietary-protein-driven post-natal skeletal muscle growth and protein turnover in the rat is updated, and the mechanisms involved are described, in this narrative review. Dietary protein controls both bone length and muscle growth, which are interrelated through mechanotransduction mechanisms with muscle growth induced both from stretching subsequent to bone length growth and from internal work against gravity. This induces satellite cell activation, myogenesis and remodelling of the extracellular matrix, establishing a growth capacity for myofibre length and cross-sectional area. Protein deposition within this capacity is enabled by adequate dietary protein and other key nutrients. After briefly reviewing the experimental animal origins of the growth model, key concepts and processes important for growth are reviewed. These include the growth in number and size of the myonuclear domain, satellite cell activity during post-natal development and the autocrine/paracrine action of IGF-1. Regulatory and signalling pathways reviewed include developmental mechanotransduction, signalling through the insulin/IGF-1-PI3K-Akt and the Ras-MAPK pathways in the myofibre and during mechanotransduction of satellite cells. Likely pathways activated by maximal-intensity muscle contractions are highlighted and the regulation of the capacity for protein synthesis in terms of ribosome assembly and the translational regulation of 5-TOPmRNA classes by mTORC1 and LARP1 are discussed. Evidence for and potential mechanisms by which volume limitation of muscle growth can occur which would limit protein deposition within the myofibre are reviewed. An understanding of how muscle growth is achieved allows better nutritional management of its growth in health and disease.
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Affiliation(s)
- D Joe Millward
- Department of Nutritional Sciences, School of Biosciences & Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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2
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Smith BC, Silvers R. 1H, 13C, and 15N resonance assignments of the La Motif of the human La-related protein 1. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:111-118. [PMID: 38691336 DOI: 10.1007/s12104-024-10176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
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Affiliation(s)
- Benjamin C Smith
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA
| | - Robert Silvers
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
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3
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Priyanka P, Gopalakrishnan AP, Nisar M, Shivamurthy PB, George M, John L, Sanjeev D, Yandigeri T, Thomas SD, Rafi A, Dagamajalu S, Velikkakath AKG, Abhinand CS, Kanekar S, Prasad TSK, Balaya RDA, Raju R. A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1). Int J Biochem Cell Biol 2024; 170:106558. [PMID: 38479581 DOI: 10.1016/j.biocel.2024.106558] [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: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
Thousand and one amino acid kinase 1 (TAOK1) is a sterile 20 family Serine/Threonine kinase linked to microtubule dynamics, checkpoint signaling, DNA damage response, and neurological functions. Molecular-level alterations of TAOK1 have been associated with neurodevelopment disorders and cancers. Despite their known involvement in physiological and pathophysiological processes, and as a core member of the hippo signaling pathway, the phosphoregulatory network of TAOK1 has not been visualized. Aimed to explore this network, we first analyzed the predominantly detected and differentially regulated TAOK1 phosphosites in global phosphoproteome datasets across diverse experimental conditions. Based on 709 qualitative and 210 quantitative differential cellular phosphoproteome datasets that were systematically assembled, we identified that phosphorylation at Ser421, Ser9, Ser965, and Ser445 predominantly represented TAOK1 in almost 75% of these datasets. Surprisingly, the functional role of all these phosphosites in TAOK1 remains unexplored. Hence, we employed a robust strategy to extract the phosphosites in proteins that significantly correlated in expression with predominant TAOK1 phosphosites. This led to the first categorization of the phosphosites including those in the currently known and predicted interactors, kinases, and substrates, that positively/negatively correlated with the expression status of each predominant TAOK1 phosphosites. Subsequently, we also analyzed the phosphosites in core proteins of the hippo signaling pathway. Based on the TAOK1 phosphoregulatory network analysis, we inferred the potential role of the predominant TAOK1 phosphosites. Especially, we propose pSer9 as an autophosphorylation and TAOK1 kinase activity-associated phosphosite and pS421, the most frequently detected phosphosite in TAOK1, as a significant regulatory phosphosite involved in the maintenance of genome integrity. Considering that the impact of all phosphosites that predominantly represent each kinase is essential for the efficient interpretation of global phosphoproteome datasets, we believe that the approach undertaken in this study is suitable to be extended to other kinases for accelerated research.
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Affiliation(s)
- Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Athira Perunelly Gopalakrishnan
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sonet D Thomas
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Ahmad Rafi
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Anoop Kumar G Velikkakath
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
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4
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Romeo-Cardeillac C, Trovero MF, Radío S, Smircich P, Rodríguez-Casuriaga R, Geisinger A, Sotelo-Silveira J. Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis. BMC Genomics 2024; 25:295. [PMID: 38509455 PMCID: PMC10953240 DOI: 10.1186/s12864-024-10170-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Mammalian testis is a highly complex and heterogeneous tissue. This complexity, which mostly derives from spermatogenic cells, is reflected at the transcriptional level, with the largest number of tissue-specific genes and long noncoding RNAs (lncRNAs) compared to other tissues, and one of the highest rates of alternative splicing. Although it is known that adequate alternative-splicing patterns and stage-specific isoforms are critical for successful spermatogenesis, so far only a very limited number of reports have addressed a detailed study of alternative splicing and isoforms along the different spermatogenic stages. RESULTS In the present work, using highly purified stage-specific testicular cell populations, we detected 33,002 transcripts expressed throughout mouse spermatogenesis not annotated so far. These include both splice variants of already annotated genes, and of hitherto unannotated genes. Using conservative criteria, we uncovered 13,471 spermatogenic lncRNAs, which reflects the still incomplete annotation of lncRNAs. A distinctive feature of lncRNAs was their lower number of splice variants compared to protein-coding ones, adding to the conclusion that lncRNAs are, in general, less complex than mRNAs. Besides, we identified 2,794 unannotated transcripts with high coding potential (including some arising from yet unannotated genes), many of which encode unnoticed putative testis-specific proteins. Some of the most interesting coding splice variants were chosen, and validated through RT-PCR. Remarkably, the largest number of stage-specific unannotated transcripts are expressed during early meiotic prophase stages, whose study has been scarcely addressed in former transcriptomic analyses. CONCLUSIONS We detected a high number of yet unannotated genes and alternatively spliced transcripts along mouse spermatogenesis, hence showing that the transcriptomic diversity of the testis is considerably higher than previously reported. This is especially prominent for specific, underrepresented stages such as those of early meiotic prophase, and its unveiling may constitute a step towards the understanding of their key events.
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Affiliation(s)
- Carlos Romeo-Cardeillac
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - María Fernanda Trovero
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santiago Radío
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
| | - Adriana Geisinger
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay.
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), 11,400, Montevideo, Uruguay.
| | - José Sotelo-Silveira
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay.
- Department of Cell and Molecular Biology, Facultad de Ciencias, UdelaR, 11,400, Montevideo, Uruguay.
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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Hochstoeger T, Papasaikas P, Piskadlo E, Chao JA. Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs. SCIENCE ADVANCES 2024; 10:eadi7830. [PMID: 38363833 PMCID: PMC10871529 DOI: 10.1126/sciadv.adi7830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
A central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation of ribosomal protein and translation factor mRNAs mediated by the 5'-terminal oligopyrimidine motif (5'TOP). Recently, La-related protein 1 (LARP1) was proposed to be the specific regulator of 5'TOP mRNA translation downstream of mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested to have a general role in translational repression of all transcripts. Here, we use single-molecule translation site imaging of 5'TOP and canonical mRNAs to study the translation of single mRNAs in living cells. Our data reveal that 4EBP1/2 has a dominant role in repression of translation of both 5'TOP and canonical mRNAs during pharmacological inhibition of mTOR. In contrast, we find that LARP1 selectively protects 5'TOP mRNAs from degradation in a transcriptome-wide analysis of mRNA half-lives. Our results clarify the roles of 4EBP1/2 and LARP1 in regulating 5'TOP mRNAs and provide a framework to further study how these factors control cell growth during development and disease.
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Affiliation(s)
- Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | | | - Ewa Piskadlo
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jeffrey A. Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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Liu X, Zhang WM, Meng N, Lin LJ, Tang GD. LARP1 knockdown inhibits cultured gastric carcinoma cell cycle progression and metastatic behavior. Open Life Sci 2024; 19:20220806. [PMID: 38283117 PMCID: PMC10811526 DOI: 10.1515/biol-2022-0806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 01/30/2024] Open
Abstract
This study aimed to clarify the role of la-related protein 1 (LARP1) in cell cycle progression and metastatic behavior of cultured gastric carcinoma (GC) cells. To do that, LARP1 expression was detected in clinical GC tissues and cell lines using quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. The cell viability, apoptosis, cell cycle, migration, invasion, and cell growth were examined using a Cell Counting Kit-8, Annexin V-FITC staining, propidium iodide staining, Transwell migration and invasion assays, and colony formation assays after LARP1 knockdown. Phosphatidyl inositol 3-kinase (PI3K) and AKT1 mRNA and protein expression levels of PI3K, p-AKT1, AKT1, p-BAD, p-mTOR, and p21 in si-LARP1 transfected GC cells were determined using qRT-PCR and western blotting. Here, we've shown that LARP1 expression was upregulated in human GC tissues and KATO III cells. LARP1 knockdown inhibited GC cell proliferation, cell cycle progression, migration, invasion, and colony formation and promoted apoptosis. In si-LARP1-transfected KATO III cells, the mRNA expression levels of PI3K and AKT1, PI3K protein expression, and the p-AKT1/AKT1 ratio were significantly suppressed. p-mTOR and p-BAD were significantly decreased, whereas p21 was significantly increased in si-LARP1-transfected KATO III cells. In conclusion LARP1 knockdown induces apoptosis and inhibits cell cycle progression and metastatic behavior via PI3K/AKT1 signaling in GC cells.
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Affiliation(s)
- Xin Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
- Department of Gastroenterology, Wuming Hospital Affiliated to Guangxi Medical University, Nanning, Guangxi, 530199, P. R. China
| | - Wei-Ming Zhang
- Department of Radiotherapy, Wuming Hospital Affiliated to Guangxi Medical University, Nanning, Guangxi, 530199, P. R. China
| | - Nuo Meng
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
| | - Lian-Jie Lin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
| | - Guo-Du Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, Guangxi 530021, P. R. China
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8
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Knop K, Gomez-Moreira C, Galloway A, Ditsova D, Cowling VH. RAM is upregulated during T cell activation and is required for RNA cap formation and gene expression. DISCOVERY IMMUNOLOGY 2023; 3:kyad021. [PMID: 38572449 PMCID: PMC10989996 DOI: 10.1093/discim/kyad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 10/29/2023] [Indexed: 04/05/2024]
Abstract
On T cell activation, upregulation of gene expression produces the protein required for the differentiation and proliferation of effector cell populations. RAM (RNMT-Activating Mini protein/RAMAC/Fam103a1), the cofactor of the RNA cap methyltransferase RNMT (RNA guanosine N-7 cap methyltransferase), is upregulated following activation. Formation of the RNA cap protects RNA during synthesis and guides RNA processing and translation. Using conditional gene deletion, we found that Ram expression stabilizes RNMT protein in T cells and is required for its upregulation on activation. When the Ram gene is deleted in naïve T cells, there are major impacts on activation-induced RNA cap formation and gene expression. Activated T cell proliferation is dependent on increased ribosome production; in Ram knockout T cells, activation-induced expression of ribosomal protein genes and snoRNAs is most severely reduced. Consistent with these changes, Ram deletion resulted in reduced protein synthesis, and reduced growth and proliferation of CD4 T cells. Deletion of Ram results in a similar but milder phenotype to Rnmt deletion, supporting the role of RAM as a RNMT cofactor.
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Affiliation(s)
- Katarzyna Knop
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | | | - Alison Galloway
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Dimitrinka Ditsova
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Victoria H Cowling
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
- School of Cancer Sciences, University of Glasgow, G61 1QH, Glasgow, UK
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9
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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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10
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Gahurova L, Tomankova J, Cerna P, Bora P, Kubickova M, Virnicchi G, Kovacovicova K, Potesil D, Hruska P, Zdrahal Z, Anger M, Susor A, Bruce AW. Spatial positioning of preimplantation mouse embryo cells is regulated by mTORC1 and m 7G-cap-dependent translation at the 8- to 16-cell transition. Open Biol 2023; 13:230081. [PMID: 37553074 PMCID: PMC10409569 DOI: 10.1098/rsob.230081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Preimplantation mouse embryo development involves temporal-spatial specification and segregation of three blastocyst cell lineages: trophectoderm, primitive endoderm and epiblast. Spatial separation of the outer-trophectoderm lineage from the two other inner-cell-mass (ICM) lineages starts with the 8- to 16-cell transition and concludes at the 32-cell stages. Accordingly, the ICM is derived from primary and secondary contributed cells; with debated relative EPI versus PrE potencies. We report generation of primary but not secondary ICM populations is highly dependent on temporal activation of mammalian target of Rapamycin (mTOR) during 8-cell stage M-phase entry, mediated via regulation of the 7-methylguanosine-cap (m7G-cap)-binding initiation complex (EIF4F) and linked to translation of mRNAs containing 5' UTR terminal oligopyrimidine (TOP-) sequence motifs, as knockdown of identified TOP-like motif transcripts impairs generation of primary ICM founders. However, mTOR inhibition-induced ICM cell number deficits in early blastocysts can be compensated by the late blastocyst stage, after inhibitor withdrawal; compensation likely initiated at the 32-cell stage when supernumerary outer cells exhibit molecular characteristics of inner cells. These data identify a novel mechanism specifically governing initial spatial segregation of mouse embryo blastomeres, that is distinct from those directing subsequent inner cell formation, contributing to germane segregation of late blastocyst lineages.
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Affiliation(s)
- Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Jana Tomankova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Pavlina Cerna
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Michaela Kubickova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Giorgio Virnicchi
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Kristina Kovacovicova
- Laboratory of Cell Division Control, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
- Department of Genetics and Reproduction, Central European Institute of Technology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - David Potesil
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Pavel Hruska
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Martin Anger
- Laboratory of Cell Division Control, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
- Department of Genetics and Reproduction, Central European Institute of Technology, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Alexander W. Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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11
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Ma J, Sun L, Gao W, Li Y, Dong D. RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors. J Transl Med 2023; 21:512. [PMID: 37507746 PMCID: PMC10386658 DOI: 10.1186/s12967-023-04373-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Mitochondria are the only organelles regulated by two genomes. The coordinated translation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), which together co-encode the subunits of the oxidative phosphorylation (OXPHOS) complex, is critical for determining the metabolic plasticity of tumor cells. RNA-binding protein (RBP) is a post-transcriptional regulatory factor that plays a pivotal role in determining the fate of mRNA. RBP rapidly and effectively reshapes the mitochondrial proteome in response to intracellular and extracellular stressors, mediating the cytoplasmic and mitochondrial translation balance to adjust mitochondrial respiratory capacity and provide energy for tumor cells to adapt to different environmental pressures and growth needs. This review highlights the ability of RBPs to use liquid-liquid phase separation (LLPS) as a platform for translation regulation, integrating nuclear-mitochondrial positive and retrograde signals to coordinate cross-department translation, reshape mitochondrial energy metabolism, and promote the development and survival of tumor cells.
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Affiliation(s)
- Jiaoyan Ma
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Weinan Gao
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yang Li
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Delu Dong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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12
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Jennings MD, Srivastava P, Kershaw CJ, Talavera D, Grant C, Pavitt G. Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs. Nucleic Acids Res 2023; 51:5755-5773. [PMID: 37070186 PMCID: PMC10287931 DOI: 10.1093/nar/gkad272] [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: 07/22/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
In response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress responses, we determined LARP mRNA binding positions in stressed and unstressed cells. Both proteins bind within coding regions of stress-regulated antioxidant enzyme and other highly translated mRNAs in both optimal and stressed conditions. LARP interaction sites are framed and enriched with ribosome footprints suggesting ribosome-LARP-mRNA complexes are identified. Although stress-induced translation of antioxidant enzyme mRNAs is attenuated in slf1Δ, these mRNAs remain on polysomes. Focusing further on Slf1, we find it binds to both monosomes and disomes following RNase treatment. slf1Δ reduces disome enrichment during stress and alters programmed ribosome frameshifting rates. We propose that Slf1 is a ribosome-associated translational modulator that stabilises stalled/collided ribosomes, prevents ribosome frameshifting and so promotes translation of a set of highly-translated mRNAs that together facilitate cell survival and adaptation to stress.
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Affiliation(s)
- Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Priya Srivastava
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
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13
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Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M. SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543769. [PMID: 37333139 PMCID: PMC10274648 DOI: 10.1101/2023.06.05.543769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
RNA binding proteins (RBPs) play crucial roles in regulating every stage of the mRNA life cycle and mediating non-coding RNA functions. Despite their importance, the specific roles of most RBPs remain unexplored because we do not know what specific RNAs most RBPs bind. Current methods, such as crosslinking and immunoprecipitation followed by sequencing (CLIP-seq), have expanded our knowledge of RBP-RNA interactions but are generally limited by their ability to map only one RBP at a time. To address this limitation, we developed SPIDR (Split and Pool Identification of RBP targets), a massively multiplexed method to simultaneously profile global RNA binding sites of dozens to hundreds of RBPs in a single experiment. SPIDR employs split-pool barcoding coupled with antibody-bead barcoding to increase the throughput of current CLIP methods by two orders of magnitude. SPIDR reliably identifies precise, single-nucleotide RNA binding sites for diverse classes of RBPs simultaneously. Using SPIDR, we explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 acts as a dynamic RBP that selectively binds to 5'-untranslated regions of specific translationally repressed mRNAs only upon mTOR inhibition. This observation provides a potential mechanism to explain the specificity of translational regulation controlled by mTOR signaling. SPIDR has the potential to revolutionize our understanding of RNA biology and both transcriptional and post-transcriptional gene regulation by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.
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Affiliation(s)
- Erica Wolin
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Jimmy K. Guo
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R. Blanco
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Andrew A. Perez
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Isabel N. Goronzy
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Ahmed A. Abdou
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Darvesh Gorhe
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
| | - Mitchell Guttman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York City, New York 10027, USA
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14
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Smith BC, Silvers R. NMR Resonance Assignment of the LA Motif of Human LA-Related Protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539749. [PMID: 37214987 PMCID: PMC10197598 DOI: 10.1101/2023.05.09.539749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5' s terminal oligopyrimidine (5'TOP) mRNAs as well as other mRNAs and binds to both the 5'TOP motif and the 3'-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
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15
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Turner M. Regulation and function of poised mRNAs in lymphocytes. Bioessays 2023; 45:e2200236. [PMID: 37009769 DOI: 10.1002/bies.202200236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 04/04/2023]
Abstract
Pre-existing but untranslated or 'poised' mRNA exists as a means to rapidly induce the production of specific proteins in response to stimuli and as a safeguard to limit the actions of these proteins. The translation of poised mRNA enables immune cells to express quickly genes that enhance immune responses. The molecular mechanisms that repress the translation of poised mRNA and, upon stimulation, enable translation have yet to be elucidated. They likely reflect intrinsic properties of the mRNAs and their interactions with trans-acting factors that direct poised mRNAs away from or into the ribosome. Here, I discuss mechanisms by which this might be regulated.
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Affiliation(s)
- Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge, UK
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16
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Balaskas P, Goljanek-Whysall K, Clegg PD, Fang Y, Cremers A, Smagul A, Welting TJM, Peffers MJ. MicroRNA Signatures in Cartilage Ageing and Osteoarthritis. Biomedicines 2023; 11:biomedicines11041189. [PMID: 37189806 DOI: 10.3390/biomedicines11041189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Osteoarthritis is the most common degenerative joint disorder. MicroRNAs are gene expression regulators that act post-transcriptionally to control tissue homeostasis. Microarray analysis was undertaken in osteoarthritic intact, lesioned and young intact cartilage. Principal component analysis showed that young intact cartilage samples were clustered together; osteoarthritic samples had a wider distribution; and osteoarthritic intact samples were separated into two subgroups, osteoarthritic-Intact-1 and osteoarthritic-Intact-2. We identified 318 differentially expressed microRNAs between young intact and osteoarthritic lesioned cartilage, 477 between young intact and osteoarthritic-Intact-1 cartilage and 332 between young intact and osteoarthritic-Intact-2 cartilage samples. For a selected list of differentially expressed microRNAs, results were verified in additional cartilage samples using qPCR. Of the validated DE microRNAs, four-miR-107, miR-143-3p, miR-361-5p and miR-379-5p-were selected for further experiments in human primary chondrocytes treated with IL-1β. Expression of these microRNAs decreased in human primary chondrocytes treated with IL-1β. For miR-107 and miR-143-3p, gain- and loss-of-function approaches were undertaken and associated target genes and molecular pathways were investigated using qPCR and mass spectrometry proteomics. Analyses showed that WNT4 and IHH, predicted targets of miR-107, had increased expression in osteoarthritic cartilage compared to young intact cartilage and in primary chondrocytes treated with miR-107 inhibitor, and decreased expression in primary chondrocytes treated with miR-107 mimic, suggesting a role of miR-107 in chondrocyte survival and proliferation. In addition, we identified an association between miR-143-3p and EIF2 signalling and cell survival. Our work supports the role of miR-107 and miR-143-3p in important chondrocyte mechanisms regulating proliferation, hypertrophy and protein translation.
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Affiliation(s)
- Panagiotis Balaskas
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Katarzyna Goljanek-Whysall
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
- Department of Physiology, College of Medicine, Nursing and Health Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Peter D Clegg
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Andy Cremers
- Department of Orthopaedic Surgery, Medical Centre, Maastricht University, 6202 AZ Maastricht, The Netherlands
| | - Aibek Smagul
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Tim J M Welting
- Department of Orthopaedic Surgery, Medical Centre, Maastricht University, 6202 AZ Maastricht, The Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
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17
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Goering R, Arora A, Pockalny MC, Taliaferro JM. RNA localization mechanisms transcend cell morphology. eLife 2023; 12:e80040. [PMID: 36867563 PMCID: PMC9984196 DOI: 10.7554/elife.80040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/24/2023] [Indexed: 03/04/2023] Open
Abstract
RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins (RBPs). Generally, our knowledge of the mechanistic details behind the localization of a given RNA is restricted to a particular cell type. Here, we show that RNA/RBP interactions that regulate RNA localization in one cell type predictably regulate localization in other cell types with vastly different morphologies. To determine transcriptome-wide RNA spatial distributions across the apicobasal axis of human intestinal epithelial cells, we used our recently developed RNA proximity labeling technique, Halo-seq. We found that mRNAs encoding ribosomal proteins (RP mRNAs) were strongly localized to the basal pole of these cells. Using reporter transcripts and single-molecule RNA FISH, we found that pyrimidine-rich motifs in the 5' UTRs of RP mRNAs were sufficient to drive basal RNA localization. Interestingly, the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells. In both cell types, the regulatory activity of this motif was dependent on it being in the 5' UTR of the transcript, was abolished upon perturbation of the RNA-binding protein LARP1, and was reduced upon inhibition of kinesin-1. To extend these findings, we compared subcellular RNAseq data from neuronal and epithelial cells. We found that the basal compartment of epithelial cells and the projections of neuronal cells were enriched for highly similar sets of RNAs, indicating that broadly similar mechanisms may be transporting RNAs to these morphologically distinct locations. These findings identify the first RNA element known to regulate RNA localization across the apicobasal axis of epithelial cells, establish LARP1 as an RNA localization regulator, and demonstrate that RNA localization mechanisms cut across cell morphologies.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Megan C Pockalny
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
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18
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Anreiter I, Tian YW, Soller M. The cap epitranscriptome: Early directions to a complex life as mRNA. Bioessays 2023; 45:e2200198. [PMID: 36529693 DOI: 10.1002/bies.202200198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Animal, protist and viral messenger RNAs (mRNAs) are most prominently modified at the beginning by methylation of cap-adjacent nucleotides at the 2'-O-position of the ribose (cOMe) by dedicated cap methyltransferases (CMTrs). If the first nucleotide of an mRNA is an adenosine, PCIF1 can methylate at the N6 -position (m6 A), while internally the Mettl3/14 writer complex can methylate. These modifications are introduced co-transcriptionally to affect many aspects of gene expression including localisation to synapses and local translation. Of particular interest, transcription start sites of many genes are heterogeneous leading to sequence diversity at the beginning of mRNAs, which together with cOMe and m6 Am could constitute an extensive novel layer of gene expression control. Given the role of cOMe and m6 A in local gene expression at synapses and higher brain functions including learning and memory, such code could be implemented at the transcriptional level for lasting memories through local gene expression at synapses.
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Affiliation(s)
- Ina Anreiter
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
| | - Yuan W Tian
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Matthias Soller
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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19
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Breznak SM, Kotb NM, Rangan P. Dynamic regulation of ribosome levels and translation during development. Semin Cell Dev Biol 2023; 136:27-37. [PMID: 35725716 DOI: 10.1016/j.semcdb.2022.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 06/12/2022] [Indexed: 01/11/2023]
Abstract
The ability of ribosomes to translate mRNAs into proteins is the basis of all life. While ribosomes are essential for cell viability, reduction in levels of ribosomes can affect cell fate and developmental transitions in a tissue specific manner and can cause a plethora of related diseases called ribosomopathies. How dysregulated ribosomes homeostasis influences cell fate and developmental transitions is not fully understood. Model systems such as Drosophila and C. elegans oogenesis have been used to address these questions since defects in conserved steps in ribosome biogenesis result in stem cell differentiation and developmental defects. In this review, we first explore how ribosome levels affect stem cell differentiation. Second, we describe how ribosomal modifications and incorporation of ribosomal protein paralogs contribute to development. Third, we summarize how cells with perturbed ribosome biogenesis are sensed and eliminated during organismal growth.
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Affiliation(s)
- Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, 12222, USA
| | - Noor M Kotb
- Department of Biomedical Sciences, The School of Public Health, University at Albany SUNY, 11 Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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20
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Dave P, Roth G, Griesbach E, Mateju D, Hochstoeger T, Chao JA. Single-molecule imaging reveals translation-dependent destabilization of mRNAs. Mol Cell 2023; 83:589-606.e6. [PMID: 36731471 PMCID: PMC9957601 DOI: 10.1016/j.molcel.2023.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
The relationship between mRNA translation and decay is incompletely understood, with conflicting reports suggesting that translation can either promote decay or stabilize mRNAs. The effect of translation on mRNA decay has mainly been studied using ensemble measurements and global transcription and translation inhibitors, which can have pleiotropic effects. We developed a single-molecule imaging approach to control the translation of a specific transcript that enabled simultaneous measurement of translation and mRNA decay. Our results demonstrate that mRNA translation reduces mRNA stability, and mathematical modeling suggests that this process is dependent on ribosome flux. Furthermore, our results indicate that miRNAs mediate efficient degradation of both translating and non-translating target mRNAs and reveal a predominant role for mRNA degradation in miRNA-mediated regulation. Simultaneous observation of translation and decay of single mRNAs provides a framework to directly study how these processes are interconnected in cells.
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Affiliation(s)
- Pratik Dave
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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21
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Wada R, Fujinuma S, Nakatsumi H, Matsumoto M, Nakayama KI. Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP1. J Biochem 2023; 173:129-138. [PMID: 36477205 DOI: 10.1093/jb/mvac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a serine-threonine kinase that is activated by extracellular signals, such as nutrients and growth factors. It plays a key role in the control of various biological processes, such as protein synthesis and energy metabolism by mediating or regulating the phosphorylation of multiple target molecules, some of which remain to be identified. We have here reanalysed a large-scale phosphoproteomics data set for mTORC1 target molecules and identified pre-B cell leukemia transcription factor 2 (PBX2) as such a novel target that is dephosphorylated downstream of mTORC1. We confirmed that PBX2, but not other members of the PBX family, is dephosphorylated in an mTORC1 activity-dependent manner. Furthermore, pharmacological and gene knockdown experiments revealed that glycogen synthase kinase 3 (GSK3) and protein phosphatase 1 (PP1) are responsible for the phosphorylation and dephosphorylation of PBX2, respectively. Our results thus suggest that the balance between the antagonistic actions of GSK3 and PP1 determines the phosphorylation status of PBX2 and its regulation by mTORC1.
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Key Words
- glycogen synthase kinase 3 (GSK3)
Abbreviations: DAPI, 4′,6-diamidino-2-phenylindole; DMSO, dimethyl sulfoxide; ERK, extracellular signal–regulated kinase; FOXK1, forkhead box K1;
GSK3, glycogen synthase kinase 3; HA, hemagglutinin; LARP1, La-related protein 1; MEK, ERK kinase; mTORC1, mechanistic target of rapamycin complex 1; PBS, phosphate-buffered saline; PBX2, pre–B cell leukemia transcription factor 2; PI3K, phosphoinositide 3-kinase; PDK1, phosphoinositide-dependent protein kinase 1; PP1, protein phosphatase 1;
PP2A, protein phosphatase 2A; RAG, RAS-related GTP-binding protein; RHEB, Ras homolog enriched in Brain; shRNA, short hairpin RNA; siRNA, small interfering RNA; TBC1D7, TBC1 (TRE2-BUB2-CDC16) domain family member 7; TSC2, tuberous sclerosis complex 2; WT, wild-type
- mechanistic target of rapamycin complex 1 (mTORC1)
- phosphorylation
- pre–B cell leukemia transcription factor 2 (PBX2)
- protein phosphatase 1 (PP1)
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Affiliation(s)
- Reona Wada
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Shun Fujinuma
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hirokazu Nakatsumi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.,Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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22
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Bakshi A, Moin M, Gayatri MB, Reddy ABM, Datla R, Madhav MS, Kirti PB. Involvement of Target of Rapamycin (TOR) Signaling in the Regulation of Crosstalk between Ribosomal Protein Small Subunit 6 Kinase-1 (RPS6K-1) and Ribosomal Proteins. PLANTS (BASEL, SWITZERLAND) 2023; 12:176. [PMID: 36616305 PMCID: PMC9824793 DOI: 10.3390/plants12010176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The target of rapamycin (TOR) protein phosphorylates its downstream effector p70kDa ribosomal protein S6 kinases (S6K1) for ribosome biogenesis and translation initiation in eukaryotes. However, the molecular mechanism of TOR-S6K1-ribosomal protein (RP) signaling is not well understood in plants. In the present study, we report the transcriptional upregulation of ribosomal protein large and small subunit (RPL and RPS) genes in the previously established TOR overexpressing transgenic lines of rice (in Oryza sativa ssp. indica, variety BPT-5204, TR-2.24 and TR-15.1) and of Arabidopsis thaliana (in Col 0 ecotype, ATR-1.4.27 and ATR-3.7.32). The mRNA levels of RP genes from this study were compared with those previously available in transcriptomic datasets on the expression of RPs in relation to TOR inhibitor and in the TOR-RNAi lines of Arabidopsis thaliana. We further analyzed TOR activity, i.e., S6K1 phosphorylation in SALK lines of Arabidopsis with mutation in rpl6, rpl18, rpl23, rpl24 and rps28C, where the rpl18 mutant showed inactivation of S6K1 phosphorylation. We also predicted similar putative Ser/Thr phosphorylation sites for ribosomal S6 kinases (RSKs) in the RPs of Oryza sativa ssp. indica and Arabidopsis thaliana. The findings of this study indicate that the TOR pathway is possibly interlinked in a cyclic manner via the phosphorylation of S6K1 as a modulatory step for the regulation of RP function to switch 'on'/'off' the translational regulation for balanced plant growth.
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Affiliation(s)
- Achala Bakshi
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Global Institute for Food Security, Saskatoon, SK S7N 0W9, Canada
| | - Mazahar Moin
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India
| | - Meher B. Gayatri
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Aramati B. M. Reddy
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Raju Datla
- Global Institute for Food Security, Saskatoon, SK S7N 0W9, Canada
| | - Maganti S. Madhav
- Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, Telangana, India
- Central Tobacco Research Institute, Rajahmundry 533105, Andhra Pradesh, India
| | - Pulugurtha B. Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Rajendranagar, Hyderabad 500030, Telangana, India
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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23
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Caruso M, Meurant S, Detraux D, Mathieu A, Gilson M, Dieu M, Fattaccioli A, Demazy C, Najimi M, Sokal E, Arnould T, Verfaillie C, Lafontaine DLJ, Renard P. The global downregulation of protein synthesis observed during hepatogenic maturation is associated with a decrease in TOP mRNA translation. Stem Cell Reports 2022; 18:254-268. [PMID: 36563686 PMCID: PMC9860114 DOI: 10.1016/j.stemcr.2022.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Translational regulation is of paramount importance for proteome remodeling during stem cell differentiation at both the global and the transcript-specific levels. In this study, we characterized translational remodeling during hepatogenic differentiation of induced pluripotent stem cells (iPSCs) by polysome profiling. We demonstrate that protein synthesis increases during exit from pluripotency and is then globally repressed during later steps of hepatogenic maturation. This global downregulation of translation is accompanied by a decrease in the abundance of protein components of the translation machinery, which involves a global reduction in translational efficiency of terminal oligopyrimidine tract (TOP) mRNA encoding translation-related factors. Despite global translational repression during hepatogenic differentiation, key hepatogenic genes remain efficiently translated, and the translation of several transcripts involved in hepatospecific functions and metabolic maturation is even induced. We conclude that, during hepatogenic differentiation, a global decrease in protein synthesis is accompanied by a specific translational rewiring of hepatospecific transcripts.
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Affiliation(s)
- Marino Caruso
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Sébastien Meurant
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Damien Detraux
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Amandine Mathieu
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Manon Gilson
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Catherine Demazy
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Etienne Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Thierry Arnould
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), Biopark Campus, Gosselies, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium.
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24
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van den Elzen AMG, Watson MJ, Thoreen CC. mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay. PLoS Genet 2022; 18:e1010532. [PMID: 36441824 PMCID: PMC9731452 DOI: 10.1371/journal.pgen.1010532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/08/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022] Open
Abstract
mRNA regulatory sequences control gene expression at multiple levels including translation initiation and mRNA decay. The 5' terminal sequences of mRNAs have unique regulatory potential because of their proximity to key post-transcriptional regulators. Here we have systematically probed the function of 5' terminal sequences in gene expression in human cells. Using a library of reporter mRNAs initiating with all possible 7-mer sequences at their 5' ends, we find an unexpected impact on transcription that underlies 200-fold differences in mRNA expression. Library sequences that promote high levels of transcription mirrored those found in native mRNAs and define two basic classes with similarities to classic Initiator (Inr) and TCT core promoter motifs. By comparing transcription, translation and decay rates, we identify sequences that are optimized for both efficient transcription and growth-regulated translation and stability, including variants of terminal oligopyrimidine (TOP) motifs. We further show that 5' sequences of endogenous mRNAs are enriched for multi-functional TCT/TOP hybrid sequences. Together, our results reveal how 5' sequences define two general classes of mRNAs with distinct growth-responsive profiles of expression across synthesis, translation and decay.
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Affiliation(s)
- Antonia M. G. van den Elzen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Maegan J. Watson
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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25
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Scarpin MR, Simmons CH, Brunkard JO. Translating across kingdoms: target of rapamycin promotes protein synthesis through conserved and divergent pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7016-7025. [PMID: 35770874 PMCID: PMC9664230 DOI: 10.1093/jxb/erac267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
mRNA translation is the growth rate-limiting step in genome expression. Target of rapamycin (TOR) evolved a central regulatory role in eukaryotes as a signaling hub that monitors nutrient availability to maintain homeostasis and promote growth, largely by increasing the rate of translation initiation and protein synthesis. The dynamic pathways engaged by TOR to regulate translation remain debated even in well-studied yeast and mammalian models, however, despite decades of intense investigation. Recent studies have firmly established that TOR also regulates mRNA translation in plants through conserved mechanisms, such as the TOR-LARP1-5'TOP signaling axis, and through pathways specific to plants. Here, we review recent advances in our understanding of the regulation of mRNA translation in plants by TOR.
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Affiliation(s)
- M Regina Scarpin
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
- Department of Plant and Microbial Biology, University of California, Berkeley,CA, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA, USA
| | - Carl H Simmons
- Laboratory of Genetics, University of Wisconsin, Madison, WI, USA
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26
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Suzuki Y, Murakawa T. Restriction of Flaviviruses by an Interferon-Stimulated Gene SHFL/C19orf66. Int J Mol Sci 2022; 23:ijms232012619. [PMID: 36293480 PMCID: PMC9604422 DOI: 10.3390/ijms232012619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Flaviviruses (the genus Flavivirus of the Flaviviridae family) include many arthropod-borne viruses, often causing life-threatening diseases in humans, such as hemorrhaging and encephalitis. Although the flaviviruses have a significant clinical impact, it has become apparent that flavivirus replication is restricted by cellular factors induced by the interferon (IFN) response, which are called IFN-stimulated genes (ISGs). SHFL (shiftless antiviral inhibitor of ribosomal frameshifting) is a novel ISG that inhibits dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) infections. Interestingly, SHFL functions as a broad-spectrum antiviral factor exhibiting suppressive activity against various types of RNA and DNA viruses. In this review, we summarize the current understanding of the molecular mechanisms by which SHFL inhibits flavivirus infection and discuss the molecular basis of the inhibitory mechanism using a predicted tertiary structure of SHFL generated by the program AlphaFold2.
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Affiliation(s)
- Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
- Correspondence: ; Tel.: +81-72-684-7367
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
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27
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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28
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Kozlov G, Mattijssen S, Jiang J, Nyandwi S, Sprules T, Iben J, Coon S, Gaidamakov S, Noronha AM, Wilds C, Maraia R, Gehring K. Structural basis of 3'-end poly(A) RNA recognition by LARP1. Nucleic Acids Res 2022; 50:9534-9547. [PMID: 35979957 PMCID: PMC9458460 DOI: 10.1093/nar/gkac696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
La-related proteins (LARPs) comprise a family of RNA-binding proteins involved in a wide range of posttranscriptional regulatory activities. LARPs share a unique tandem of two RNA-binding domains, La motif (LaM) and RNA recognition motif (RRM), together referred to as a La-module, but vary in member-specific regions. Prior structural studies of La-modules reveal they are pliable platforms for RNA recognition in diverse contexts. Here, we characterize the La-module of LARP1, which plays an important role in regulating synthesis of ribosomal proteins in response to mTOR signaling and mRNA stabilization. LARP1 has been well characterized functionally but no structural information exists for its La-module. We show that unlike other LARPs, the La-module in LARP1 does not contain an RRM domain. The LaM alone is sufficient for binding poly(A) RNA with submicromolar affinity and specificity. Multiple high-resolution crystal structures of the LARP1 LaM domain in complex with poly(A) show that it is highly specific for the RNA 3'-end, and identify LaM residues Q333, Y336 and F348 as the most critical for binding. Use of a quantitative mRNA stabilization assay and poly(A) tail-sequencing demonstrate functional relevance of LARP1 RNA binding in cells and provide novel insight into its poly(A) 3' protection activity.
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Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jianning Jiang
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Samuel Nyandwi
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Tara Sprules
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada,Quebec/Eastern Canada NMR Centre, McGill University, Montréal, Canada
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Anne M Noronha
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Canada
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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29
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Yang M, Lu Y, Piao W, Jin H. The Translational Regulation in mTOR Pathway. Biomolecules 2022; 12:biom12060802. [PMID: 35740927 PMCID: PMC9221026 DOI: 10.3390/biom12060802] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanistic/mammalian target of rapamycin (mTOR) plays a master role in cell proliferation and growth in response to insulin, amino acids, energy levels, and oxygen. mTOR can coordinate upstream signals with downstream effectors, including transcriptional and translational apparatuses to regulate fundamental cellular processes such as energy utilization, protein synthesis, autophagy, cell growth, and proliferation. Of the above, protein synthesis is highly energy-consuming; thus, mRNA translation is under the tight and immediate control of mTOR signaling. The translational regulation driven by mTOR signaling mainly relies on eukaryotic translation initiation factor 4E (eIF4E)-binding protein (4E-BP), ribosomal protein S6 kinase (S6K), and its downstream players, which are significant in rapid cellular response to environmental change. mTOR signaling not only controls the general mRNA translation, but preferential mRNA translation as well. This means that mTOR signaling shows the stronger selectivity to particular target mRNAs. Some evidence has supported the contribution of 4E-BP and La-related proteins 1 (LARP1) to such translational regulation. In this review, we summarize the mTOR pathway and mainly focus on mTOR-mediated mRNA translational regulation. We introduce the major components of mTOR signaling and their functions in translational control in a general or particular manner, and describe how the specificity of regulation is coordinated. Furthermore, we summarize recent research progress and propose additional ideas for reference. Because the mTOR pathway is on the center of cell growth and metabolism, comprehensively understanding this pathway will contribute to the therapy of related diseases, including cancers, type 2 diabetes, obesity, and neurodegeneration.
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Affiliation(s)
| | | | | | - Hua Jin
- Correspondence: (W.P.); (H.J.)
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30
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Martin ET, Blatt P, Nguyen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani S, Siekhaus DE, Berman A, Fuchs G, Rangan P. A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis. Dev Cell 2022; 57:883-900.e10. [PMID: 35413237 PMCID: PMC9011129 DOI: 10.1016/j.devcel.2022.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/11/2022] [Accepted: 03/10/2022] [Indexed: 01/26/2023]
Abstract
Ribosomal defects perturb stem cell differentiation, and this is the cause of ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discover that three DExD/H-box proteins govern ribosome biogenesis (RiBi) and Drosophila oogenesis. Loss of these DExD/H-box proteins, which we name Aramis, Athos, and Porthos, aberrantly stabilizes p53, arrests the cell cycle, and stalls germline stem cell (GSC) differentiation. Aramis controls cell-cycle progression by regulating translation of mRNAs that contain a terminal oligo pyrimidine (TOP) motif in their 5' UTRs. We find that TOP motifs confer sensitivity to ribosome levels that are mediated by La-related protein (Larp). One such TOP-containing mRNA codes for novel nucleolar protein 1 (Non1), a conserved p53 destabilizing protein. Upon a sufficient ribosome concentration, Non1 is expressed, and it promotes GSC cell-cycle progression via p53 degradation. Thus, a previously unappreciated TOP motif in Drosophila responds to reduced RiBi to co-regulate the translation of ribosomal proteins and a p53 repressor, coupling RiBi to GSC differentiation.
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Affiliation(s)
- Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Elaine Nguyen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roni Lahr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sangeetha Selvam
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA
| | - Hyun Ah M Yoon
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; Albany Medical College, Albany, NY 12208, USA
| | - Tyler Pocchiari
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA; SUNY Upstate Medical University, Syracuse, NY 13210-2375, USA
| | - Shamsi Emtenani
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daria E Siekhaus
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Andrea Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany, SUNY, Albany, NY 12202, USA.
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31
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Desi N, Tong QY, Teh V, Chan JJ, Zhang B, Tabatabaeian H, Tan HQ, Kapeli K, Jin W, Lim CY, Kwok ZH, Tan HT, Wang S, Siew BE, Lee KC, Chong CS, Tan KK, Yang H, Kappei D, Yeo GW, Chung MCM, Tay Y. Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis. Cell Mol Life Sci 2022; 79:147. [PMID: 35195778 PMCID: PMC11072786 DOI: 10.1007/s00018-021-04093-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
In addition to genomic alterations, aberrant changes in post-transcriptional regulation can modify gene function and drive cancer development. RNA-binding proteins (RBPs) are a large class of post-transcriptional regulators that have been increasingly implicated in carcinogenesis. By integrating multi-omics data, we identify LARP1 as one of the most upregulated RBPs in colorectal cancer (CRC) and demonstrate its oncogenic properties. We perform LARP1:RNA interactome profiling and unveil a previously unexplored role for LARP1 in targeting the 3'UTR of oncogenes in CRC. Notably, we identify the proto-oncogenic transcription factor MYC as a key LARP1-regulated target. Our data show that LARP1 positively modulates MYC expression by associating with its 3'UTR. In addition, antisense oligonucleotide-mediated blocking of the interaction between LARP1 and the MYC 3'UTR reduces MYC expression and in vitro CRC growth. Furthermore, a systematic analysis of LARP1:protein interactions reveals IGF2BP3 and YBX1 as LARP1-interacting proteins that also regulate MYC expression and CRC development. Finally, we demonstrate that MYC reciprocally modulates LARP1 expression by targeting its enhancer. In summary, our data reveal a critical, previously uncharacterized role of LARP1 in promoting CRC tumorigenesis, validate its direct regulation of the proto-oncogene MYC and delineate a model of the positive feedback loop between MYC and LARP1 that promotes CRC growth and development.
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Affiliation(s)
- Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Qing Yun Tong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Velda Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Division of Pulmonary and Critical Care, Boston University, Boston, MA, 02118, USA
| | - Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei-En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok-Chung Lee
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon-Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, San Diego, USA
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
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32
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Nishimura T, Fujii K, Nakamura H, Naruki S, Sakai H, Kimura H, Miyazawa T, Takagi M, Furuya N, Marko-Varga G, Kato H, Saji H. Protein co-expression network-based profiles revealed from laser-microdissected cancerous cells of lung squamous-cell carcinomas. Sci Rep 2021; 11:20209. [PMID: 34642392 PMCID: PMC8511190 DOI: 10.1038/s41598-021-99695-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/30/2021] [Indexed: 01/06/2023] Open
Abstract
No therapeutic targets have been identified for lung squamous cell cancer (SqCC) which is the second most prevalent lung cancer because its molecular profiles remain unclear. This study aimed to unveil disease-related protein networks by proteomic and bioinformatic assessment of laser-microdissected cancerous cells from seven SqCCs compared with eight representative lung adenocarcinomas. We identified three network modules significant to lung SqCC using weighted gene co-expression network analysis. One module was intrinsically annotated to keratinization and cell proliferation of SqCC, accompanied by hypoxia-induced aerobic glycolysis, in which key regulators were activated (HIF1A, ROCK2, EFNA1-5) and highly suppressed (KMT2D). The other two modules were significant for translational initiation, nonsense-mediated mRNA decay, inhibited cell death, and interestingly, eIF2 signaling, in which key regulators, MYC and MLXIPL, were highly activated. Another key regulator LARP1, the master regulator in cap-dependent translation, was highly suppressed although upregulations were observed for hub proteins including EIF3F and LARP1 targeted ribosomal proteins, among which PS25 is the key ribosomal protein in IRES-dependent translation. Our results suggest an underlying progression mechanism largely caused by switching to the cap-independent, IRES-dependent translation of mRNA subsets encoding oncogenic proteins. Our findings may help to develop therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan. .,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.
| | - Kiyonaga Fujii
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Laboratory of Analytical Chemistry, Daiichi University of Pharmacy, Fukuoka, Fukuoka, 815-8511, Japan
| | - Haruhiko Nakamura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Saeko Naruki
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hiroki Sakai
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hiroyuki Kimura
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Tomoyuki Miyazawa
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Masayuki Takagi
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Gyorgy Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Harubumi Kato
- Tokyo Medical University, Tokyo, 160-0023, Japan.,International University of Health and Welfare, Tokyo, 107-8402, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
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Morita E, Suzuki Y. Membrane-Associated Flavivirus Replication Complex-Its Organization and Regulation. Viruses 2021; 13:v13061060. [PMID: 34205058 PMCID: PMC8228428 DOI: 10.3390/v13061060] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Flavivirus consists of a large number of arthropod-borne viruses, many of which cause life-threatening diseases in humans. A characteristic feature of flavivirus infection is to induce the rearrangement of intracellular membrane structure in the cytoplasm. This unique membranous structure called replication organelle is considered as a microenvironment that provides factors required for the activity of the flaviviral replication complex. The replication organelle serves as a place to coordinate viral RNA amplification, protein translation, and virion assembly and also to protect the viral replication complex from the cellular immune defense system. In this review, we summarize the current understanding of how the formation and function of membrane-associated flaviviral replication organelle are regulated by cellular factors.
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Affiliation(s)
- Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki-shi 036-8561, Japan
- Correspondence: (E.M.); (Y.S.); Tel.: +81-172-39-3586 (E.M.); +81-72-684-7367 (Y.S.)
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki 569-8686, Japan
- Correspondence: (E.M.); (Y.S.); Tel.: +81-172-39-3586 (E.M.); +81-72-684-7367 (Y.S.)
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Solsona R, Pavlin L, Bernardi H, Sanchez AMJ. Molecular Regulation of Skeletal Muscle Growth and Organelle Biosynthesis: Practical Recommendations for Exercise Training. Int J Mol Sci 2021; 22:2741. [PMID: 33800501 PMCID: PMC7962973 DOI: 10.3390/ijms22052741] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022] Open
Abstract
The regulation of skeletal muscle mass and organelle homeostasis is dependent on the capacity of cells to produce proteins and to recycle cytosolic portions. In this investigation, the mechanisms involved in skeletal muscle mass regulation-especially those associated with proteosynthesis and with the production of new organelles-are presented. Thus, the critical roles of mammalian/mechanistic target of rapamycin complex 1 (mTORC1) pathway and its regulators are reviewed. In addition, the importance of ribosome biogenesis, satellite cells involvement, myonuclear accretion, and some major epigenetic modifications related to protein synthesis are discussed. Furthermore, several studies conducted on the topic of exercise training have recognized the central role of both endurance and resistance exercise to reorganize sarcomeric proteins and to improve the capacity of cells to build efficient organelles. The molecular mechanisms underlying these adaptations to exercise training are presented throughout this review and practical recommendations for exercise prescription are provided. A better understanding of the aforementioned cellular pathways is essential for both healthy and sick people to avoid inefficient prescriptions and to improve muscle function with emergent strategies (e.g., hypoxic training). Finally, current limitations in the literature and further perspectives, notably on epigenetic mechanisms, are provided to encourage additional investigations on this topic.
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Affiliation(s)
- Robert Solsona
- Laboratoire Interdisciplinaire Performance Santé Environnement de Montagne (LIPSEM), Faculty of Sports Sciences, University of Perpignan Via Domitia, UR 4640, 7 Avenue Pierre de Coubertin, 66120 Font-Romeu, France;
| | - Laura Pavlin
- DMEM, University of Montpellier, INRAE UMR866, 2 Place Pierre Viala, 34060 Montpellier, France; (L.P.); (H.B.)
| | - Henri Bernardi
- DMEM, University of Montpellier, INRAE UMR866, 2 Place Pierre Viala, 34060 Montpellier, France; (L.P.); (H.B.)
| | - Anthony MJ Sanchez
- Laboratoire Interdisciplinaire Performance Santé Environnement de Montagne (LIPSEM), Faculty of Sports Sciences, University of Perpignan Via Domitia, UR 4640, 7 Avenue Pierre de Coubertin, 66120 Font-Romeu, France;
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Li M, Yin B, Chen M, Peng J, Mu X, Deng Z, Xiao J, Li W, Fan J. Downregulation of the lncRNA ASB16-AS1 Decreases LARP1 Expression and Promotes Clear Cell Renal Cell Carcinoma Progression via miR-185-5p/miR-214-3p. Front Oncol 2021; 10:617105. [PMID: 33680937 PMCID: PMC7933513 DOI: 10.3389/fonc.2020.617105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) comprises approximately 75% of renal cell carcinomas, which is one of the most common and lethal urologic cancers, with poor quality of life for patients and is a huge economic burden to health care systems. It is imperative we find novel prognostic and therapeutic targets for ccRCC clinical intervention. In this study, we found that the expression of the long noncoding RNA (lncRNA) ASB16-AS1 was downregulated in ccRCC tissues compared with non-diseased tissues and was also associated with advanced tumor stage and larger tumors. By constructing cell and mouse models, it was found that downregulated lncRNA ASB16-AS1 enhanced cell proliferation, migration, invasion, and promoted tumor growth and metastasis. Furthermore, by performing bioinformatics analysis, biotinylated RNA pull-downs, AGO2-RIP, and luciferase reporter assays, our findings showed that downregulated ASB16-AS1 decreased La-related protein 1 (LARP1) expression by inhibiting miR-185-5p and miR-214-3p. Furthermore, it was found that overexpression of LARP1 reversed the promotive effects of downregulated ASB16-AS1 on ccRCC cellular progression. Our results revealed that downregulated ASB16-AS1 promotes ccRCC progression via a miR-185-5p-miR-214-3p-LARP1 pathway. We suggest that this pathway could be used to monitor prognosis and presents therapeutic targets for ccRCC clinical management.
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Affiliation(s)
- Mingzi Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Bingde Yin
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, China
| | - Mulin Chen
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jingtao Peng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyu Mu
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhen Deng
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiantao Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Weiguo Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jie Fan
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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36
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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37
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Mattijssen S, Kozlov G, Gaidamakov S, Ranjan A, Fonseca BD, Gehring K, Maraia RJ. The isolated La-module of LARP1 mediates 3' poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1. RNA Biol 2021; 18:275-289. [PMID: 33292040 PMCID: PMC7928023 DOI: 10.1080/15476286.2020.1860376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the LARPs in linker length and RRM subtype. The La-modules of La protein and LARP7 bind and protect nuclear RNAs with UUU-3' tails from degradation by 3' exonucleases. LARP4 is an mRNA poly(A) stabilization factor that binds poly(A) and the cytoplasmic poly(A)-binding protein PABPC1 (also known as PABP). LARP1 exhibits poly(A) length protection and mRNA stabilization similar to LARP4. Here, we show that these LARP1 activities are mediated by its La-module and dependent on a PAM2 motif that binds PABP. The isolated La-module of LARP1 is sufficient for PABP-dependent poly(A) length protection and mRNA stabilization in HEK293 cells. A point mutation in the PAM2 motif in the La-module impairs mRNA stabilization and PABP binding in vivo but does not impair oligo(A) RNA binding by the purified recombinant La-module in vitro. We characterize the unusual PAM2 sequence of LARP1 and show it may differentially affect stable and unstable mRNAs. The unique LARP1 La-module can function as an autonomous factor to confer poly(A) protection and stabilization to heterologous mRNAs.
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Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Amitabh Ranjan
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA
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38
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Werneck-de-Castro JP, Peçanha FLM, Silvestre DH, Bernal-Mizrachi E. The RNA-binding protein LARP1 is dispensable for pancreatic β-cell function and mass. Sci Rep 2021; 11:2079. [PMID: 33483593 PMCID: PMC7822907 DOI: 10.1038/s41598-021-81457-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) deficiency or chronic hyperactivation in pancreatic β-cells leads to diabetes. mTORC1 complexes with La-related protein 1 (LARP1) to specifically regulate the expression of 5' terminal oligopyrimidine tract (5'TOP) mRNAs which encode proteins of the translation machinery and ribosome biogenesis. Here we show that LARP1 is the most expressed LARP in mouse islets and human β-cells, being 2-4-fold more abundant than LARP1B, a member of the family that also interacts with mTORC1. Interestingly, β-cells from diabetic patients have higher LARP1 and LARP1B expression. However, specific deletion of Larp1 gene in β-cells (β-Larp1KO mice) did not impair insulin secretion and glucose metabolism in male and female mice. High fat or high branched-chain amino acid (BCAA) diets did not disturb glucose homeostasis compared to control littermates up to 8 weeks; BCAA diet slightly impaired glucose tolerance in the β-Larp1KO mice at 16 weeks. However, no differences in plasma insulin levels, non-fasting glycemia and β-cell mass were observed in the β-Larp1KO mice. In conclusion, LARP1 is the most abundant LARP in mouse islets and human β-cells, and it is upregulated in diabetic subjects. However, genetically disruption of Larp1 gene did not impact glucose homeostasis in basal and diabetogenic conditions, suggesting no major role for LARP1 in β-cells.
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Affiliation(s)
- Joao Pedro Werneck-de-Castro
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Miami VA Health Care System, Miami, FL, 33136, USA
| | - Flavia Leticia Martins Peçanha
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Diego Henrique Silvestre
- Institute of Nutrition Josué de Castro, Federal University of Rio de Janeiro, Rio de Janeiro, 21941090, Brazil
| | - Ernesto Bernal-Mizrachi
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Miami VA Health Care System, Miami, FL, 33136, USA.
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Mariano G, Farthing RJ, Lale-Farjat SLM, Bergeron JRC. Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be. Front Mol Biosci 2020; 7:605236. [PMID: 33392262 PMCID: PMC7773825 DOI: 10.3389/fmolb.2020.605236] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread in humans in almost every country, causing the disease COVID-19. Since the start of the COVID-19 pandemic, research efforts have been strongly directed towards obtaining a full understanding of the biology of the viral infection, in order to develop a vaccine and therapeutic approaches. In particular, structural studies have allowed to comprehend the molecular basis underlying the role of many of the SARS-CoV-2 proteins, and to make rapid progress towards treatment and preventive therapeutics. Despite the great advances that have been provided by these studies, many knowledge gaps on the biology and molecular basis of SARS-CoV-2 infection still remain. Filling these gaps will be the key to tackle this pandemic, through development of effective treatments and specific vaccination strategies.
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Affiliation(s)
- Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rebecca J. Farthing
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | | | - Julien R. C. Bergeron
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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40
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Scarpin MR, Leiboff S, Brunkard JO. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. eLife 2020; 9:e58795. [PMID: 33054972 PMCID: PMC7584452 DOI: 10.7554/elife.58795] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
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Affiliation(s)
- M Regina Scarpin
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
| | - Samuel Leiboff
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California at BerkeleyBerkeleyUnited States
- Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research ServiceAlbanyUnited States
- Laboratory of Genetics, University of Wisconsin—MadisonMadisonUnited States
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Kalous J, Jansová D, Šušor A. Role of Cyclin-Dependent Kinase 1 in Translational Regulation in the M-Phase. Cells 2020; 9:cells9071568. [PMID: 32605021 PMCID: PMC7408968 DOI: 10.3390/cells9071568] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Cyclin dependent kinase 1 (CDK1) has been primarily identified as a key cell cycle regulator in both mitosis and meiosis. Recently, an extramitotic function of CDK1 emerged when evidence was found that CDK1 is involved in many cellular events that are essential for cell proliferation and survival. In this review we summarize the involvement of CDK1 in the initiation and elongation steps of protein synthesis in the cell. During its activation, CDK1 influences the initiation of protein synthesis, promotes the activity of specific translational initiation factors and affects the functioning of a subset of elongation factors. Our review provides insights into gene expression regulation during the transcriptionally silent M-phase and describes quantitative and qualitative translational changes based on the extramitotic role of the cell cycle master regulator CDK1 to optimize temporal synthesis of proteins to sustain the division-related processes: mitosis and cytokinesis.
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