1
|
Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00712-2. [PMID: 38637632 DOI: 10.1038/s41576-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
Collapse
Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
2
|
Staněk D. Coilin and Cajal bodies. Nucleus 2023; 14:2256036. [PMID: 37682044 PMCID: PMC10494742 DOI: 10.1080/19491034.2023.2256036] [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: 07/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
The nucleus of higher eukaryotes contains a number of structures that concentrate specific biomolecules and play distinct roles in nuclear metabolism. In recent years, the molecular mechanisms controlling their formation have been intensively studied. In this brief review, I focus on coilin and Cajal bodies. Coilin is a key scaffolding protein of Cajal bodies that is evolutionarily conserved in metazoans. Cajal bodies are thought to be one of the archetypal nuclear structures involved in the metabolism of several short non-coding nuclear RNAs. Yet surprisingly little is known about the structure and function of coilin, and a comprehensive model to explain the origin of Cajal bodies is also lacking. Here, I summarize recent results on Cajal bodies and coilin and discuss them in the context of the last three decades of research in this field.
Collapse
Affiliation(s)
- David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
3
|
Taliansky ME, Love AJ, Kołowerzo-Lubnau A, Smoliński DJ. Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants. THE PLANT CELL 2023; 35:3214-3235. [PMID: 37202374 PMCID: PMC10473218 DOI: 10.1093/plcell/koad140] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/20/2023]
Abstract
Proper orchestration of the thousands of biochemical processes that are essential to the life of every cell requires highly organized cellular compartmentalization of dedicated microenvironments. There are 2 ways to create this intracellular segregation to optimize cellular function. One way is to create specific organelles, enclosed spaces bounded by lipid membranes that regulate macromolecular flux in and out of the compartment. A second way is via membraneless biomolecular condensates that form due to to liquid-liquid phase separation. Although research on these membraneless condensates has historically been performed using animal and fungal systems, recent studies have explored basic principles governing the assembly, properties, and functions of membraneless compartments in plants. In this review, we discuss how phase separation is involved in a variety of key processes occurring in Cajal bodies (CBs), a type of biomolecular condensate found in nuclei. These processes include RNA metabolism, formation of ribonucleoproteins involved in transcription, RNA splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles of CBs, we discuss unique plant-specific functions of CBs in RNA-based regulatory pathways such as nonsense-mediated mRNA decay, mRNA retention, and RNA silencing. Finally, we summarize recent progress and discuss the functions of CBs in responses to pathogen attacks and abiotic stresses, responses that may be regulated via mechanisms governed by polyADP-ribosylation. Thus, plant CBs are emerging as highly complex and multifunctional biomolecular condensates that are involved in a surprisingly diverse range of molecular mechanisms that we are just beginning to appreciate.
Collapse
Affiliation(s)
| | - Andrew J Love
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Agnieszka Kołowerzo-Lubnau
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| |
Collapse
|
4
|
Nie Y, Li Y, Liu M, Ma B, Sui X, Chen J, Yu Y, Dong CH. The nucleoporin NUP160 and NUP96 regulate nucleocytoplasmic export of mRNAs and participate in ethylene signaling and response in Arabidopsis. PLANT CELL REPORTS 2023; 42:549-559. [PMID: 36598573 DOI: 10.1007/s00299-022-02976-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis nucleoporin involved in the regulation of ethylene signaling via controlling of nucleocytoplasmic transport of mRNAs. The two-way transport of mRNAs between the nucleus and cytoplasm are controlled by the nuclear pore complex (NPC). In higher plants, the NPC contains at least 30 nucleoporins. The Arabidopsis nucleoporins are involved in various biological processes such as pathogen interaction, nodulation, cold response, flowering, and hormone signaling. However, little is known about the regulatory functions of the nucleoporin NUP160 and NUP96 in ethylene signaling pathway. In the present study, we provided data showing that the Arabidopsis nucleoporin NUP160 and NUP96 participate in ethylene signaling-related mRNAs nucleocytoplasmic transport. The Arabidopsis nucleoporin mutants (nup160, nup96-1, nup96-2) exhibited enhanced ethylene sensitivity. Nuclear qRT-PCR analysis and poly(A)-mRNA in situ hybridization showed that the nucleoporin mutants affected the nucleocytoplasmic transport of all the examined mRNAs, including the ethylene signaling-related mRNAs such as ETR2, ERS1, ERS2, EIN4, CTR1, EIN2, and EIN3. Transcriptome analysis of the nucleoporin mutants provided clues suggesting that the nucleoporin NUP160 and NUP96 may participate in ethylene signaling via various molecular mechanisms. These observations significantly advance our understanding of the regulatory mechanisms of nucleoporin proteins in ethylene signaling and ethylene response.
Collapse
Affiliation(s)
- Yuanyuan Nie
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Menghui Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Binran Ma
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinying Sui
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiacai Chen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanchong Yu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chun-Hai Dong
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
5
|
Górka S, Kubiak D, Ciesińska M, Niedojadło K, Tyburski J, Niedojadło J. Function of Cajal Bodies in Nuclear RNA Retention in A. thaliana Leaves Subjected to Hypoxia. Int J Mol Sci 2022; 23:ijms23147568. [PMID: 35886915 PMCID: PMC9321658 DOI: 10.3390/ijms23147568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Retention of RNA in the nucleus precisely regulates the time and rate of translation and controls transcriptional bursts that can generate profound variability in mRNA levels among identical cells in tissues. In this study, we investigated the function of Cajal bodies (CBs) in RNA retention in A. thaliana leaf nuclei during hypoxia stress was investigated. It was observed that in ncb-1 mutants with a complete absence of CBs, the accumulation of poly(A+) RNA in the leaf nuclei was lower than that in wt under stress. Moreover, unlike in root cells, CBs store less RNA, and RNA retention in the nuclei is much less intense. Our results reveal that the function of CBs in the accumulation of RNA in nuclei under stress depends on the plant organ. Additionally, in ncb-1, retention of introns of mRNA RPB1 (largest subunit of RNA polymerase II) mRNA was observed. However, this isoform is highly accumulated in the nucleus. It thus follows that intron retention in transcripts is more important than CBs for the accumulation of RNA in nuclei. Accumulated mRNAs with introns in the nucleus could escape transcript degradation by NMD (nonsense-mediated mRNA decay). From non-fully spliced mRNAs in ncb-1 nuclei, whose levels increase during hypoxia, introns are removed during reoxygenation. Then, the mRNA is transferred to the cytoplasm, and the RPB1 protein is translated. Despite the accumulation of isoforms in nuclei with retention of introns in reoxygenation, ncb-1 coped much worse with long hypoxia, and manifested faster yellowing and shrinkage of leaves.
Collapse
Affiliation(s)
- Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Małgorzata Ciesińska
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Jarosław Tyburski
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland;
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Correspondence:
| |
Collapse
|