1
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Lu L, Zhang J, Zheng X, Xia N, Diao Z, Wang X, Chen Z, Tang D, Li S. OsMPK12 positively regulates rice blast resistance via OsEDC4-mediated transcriptional regulation of immune-related genes. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38770581 DOI: 10.1111/pce.14955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Mitogen-activated protein kinase (MAPK) signalling cascades are functionally important signalling modules in eukaryotes. Transcriptome reprogramming of immune-related genes is a key process in plant immunity. Emerging evidence shows that plant MAPK cascade is associated with processing (P)-body components and contributes to transcriptome reprogramming of immune-related genes. However, it remains largely unknown how this process is regulated. Here, we show that OsMPK12, which is induced by Magnaporthe oryzae infection, positively regulates rice blast resistance. Further analysis revealed that OsMPK12 directly interacts with enhancer of mRNA decapping protein 4 (OsEDC4), a P-body-located protein, and recruits OsEDC4 to where OsMPK12 is enriched. Importantly, OsEDC4 directly interacts with two decapping complex members OsDCP1 and OsDCP2, indicating that OsEDC4 is a subunit of the mRNA decapping complex. Additionally, we found that OsEDC4 positively regulates rice blast resistance by regulating expression of immune-related genes and maintaining proper mRNA levels of some negatively-regulated genes. And OsMPK12 and OsEDC4 are also involved in rice growth and development regulation. Taken together, our data demonstrate that OsMPK12 positively regulates rice blast resistance via OsEDC4-mediated mRNA decay of immune-related genes, providing new insight into not only the new role of the MAPK signalling cascade, but also posttranscriptional regulation of immune-related genes.
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Affiliation(s)
- Ling Lu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Zhang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingxing Zheng
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Na Xia
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijuan Diao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xun Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Chen
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengping Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Cassani M, Seydoux G. P-body-like condensates in the germline. Semin Cell Dev Biol 2024; 157:24-32. [PMID: 37407370 PMCID: PMC10761593 DOI: 10.1016/j.semcdb.2023.06.010] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
P-bodies are cytoplasmic condensates that accumulate low-translation mRNAs for temporary storage before translation or degradation. P-bodies have been best characterized in yeast and mammalian tissue culture cells. We describe here related condensates in the germline of animal models. Germline P-bodies have been reported at all stages of germline development from primordial germ cells to gametes. The activity of the universal germ cell fate regulator, Nanos, is linked to the mRNA decay function of P-bodies, and spatially-regulated condensation of P-body like condensates in embryos is required to localize mRNA regulators to primordial germ cells. In most cases, however, it is not known whether P-bodies represent functional compartments or non-functional condensation by-products that arise when ribonucleoprotein complexes saturate the cytoplasm. We speculate that the ubiquity of P-body-like condensates in germ cells reflects the strong reliance of the germline on cytoplasmic, rather than nuclear, mechanisms of gene regulation.
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Affiliation(s)
- Madeline Cassani
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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3
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Bermudez Y, Hatfield D, Muller M. A Balancing Act: The Viral-Host Battle over RNA Binding Proteins. Viruses 2024; 16:474. [PMID: 38543839 PMCID: PMC10974049 DOI: 10.3390/v16030474] [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: 12/15/2023] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of a productive viral infection is the co-opting of host cell resources for viral replication. Despite the host repertoire of molecular functions and biological counter measures, viruses still subvert host defenses to take control of cellular factors such as RNA binding proteins (RBPs). RBPs are involved in virtually all steps of mRNA life, forming ribonucleoprotein complexes (mRNPs) in a highly ordered and regulated process to control RNA fate and stability in the cell. As such, the hallmark of the viral takeover of a cell is the reshaping of RNA fate to modulate host gene expression and evade immune responses by altering RBP interactions. Here, we provide an extensive review of work in this area, particularly on the duality of the formation of RNP complexes that can be either pro- or antiviral. Overall, in this review, we highlight the various ways viruses co-opt RBPs to regulate RNA stability and modulate the outcome of infection by gathering novel insights gained from research studies in this field.
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Affiliation(s)
| | | | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (Y.B.); (D.H.)
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4
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Wilby EL, Weil TT. Relating the Biogenesis and Function of P Bodies in Drosophila to Human Disease. Genes (Basel) 2023; 14:1675. [PMID: 37761815 PMCID: PMC10530015 DOI: 10.3390/genes14091675] [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: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Drosophila has been a premier model organism for over a century and many discoveries in flies have furthered our understanding of human disease. Flies have been successfully applied to many aspects of health-based research spanning from behavioural addiction, to dysplasia, to RNA dysregulation and protein misfolding. Recently, Drosophila tissues have been used to study biomolecular condensates and their role in multicellular systems. Identified in a wide range of plant and animal species, biomolecular condensates are dynamic, non-membrane-bound sub-compartments that have been observed and characterised in the cytoplasm and nuclei of many cell types. Condensate biology has exciting research prospects because of their diverse roles within cells, links to disease, and potential for therapeutics. In this review, we will discuss processing bodies (P bodies), a conserved biomolecular condensate, with a particular interest in how Drosophila can be applied to advance our understanding of condensate biogenesis and their role in disease.
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Affiliation(s)
| | - Timothy T. Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK;
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5
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Wippich F, Vaishali, Hennrich ML, Ephrussi A. Nutritional stress-induced regulation of microtubule organization and mRNP transport by HDAC1 controlled α-tubulin acetylation. Commun Biol 2023; 6:776. [PMID: 37491525 PMCID: PMC10368696 DOI: 10.1038/s42003-023-05138-w] [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: 10/14/2020] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
In response to nutritional stress, microtubules in cells of the Drosophila female germline are depleted from the cytoplasm and accumulate cortically. This triggers aggregation of mRNPs into large processing bodies (P-bodies) and oogenesis arrest. Here, we show that hyperacetylation of α-tubulin at lysine 40 (K40) alters microtubule dynamics and P-body formation. We found that depletion of histone deacetylase 1 (HDAC1) by RNAi phenocopies the nutritional stress response, causing α-tubulin hyperacetylation and accumulation of maternally deposited mRNPs in P-bodies. Through in vitro and in vivo studies, we identify HDAC1 as a direct regulator of α-tubulin K40 acetylation status. In well-fed flies, HDAC1 maintains low levels of α-tubulin acetylation, enabling the microtubule dynamics required for mRNP transport. Using quantitative phosphoproteomics we identify nutritional stress-induced changes in protein phosphorylation that act upstream of α-tubulin acetylation, including phosphorylation of HDAC1 at S391, which reduces its ability to deacetylate α-tubulin. These results reveal that Drosophila HDAC1 senses and relays the nutritional status, which regulates germline development through modulation of cytoskeleton dynamics.
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Affiliation(s)
- Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | - Vaishali
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marco L Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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6
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Bayer LV, Milano S, Formel SK, Kaur H, Ravichandran R, Cambeiro JA, Slinko L, Catrina IE, Bratu DP. Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis. RNA Biol 2023; 20:573-587. [PMID: 37553798 PMCID: PMC10413924 DOI: 10.1080/15476286.2023.2242650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte's posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of oskar mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup's recruitment to oskar mRNA and indispensable for oskar's translational repression. We now report that this Bruno1-Cup interaction leads to precise oskar mRNA regulation during early oogenesis and, importantly, the two proteins mutually influence each other's mRNA expression and protein distribution in the egg chamber. We show that these factors stably associate with oskar mRNA in vivo. Cup associates with oskar mRNA without Bruno1, while surprisingly Bruno1's stable association with oskar mRNA depends on Cup. We demonstrate that the essential factor for oskar mRNA repression in early oogenesis is Cup, not Bruno1. Furthermore, we find that Cup is a key P-body component that maintains functional P-body morphology during oogenesis and is necessary for oskar mRNA's association with P-bodies. Therefore, Cup drives the translational repression and stability of oskar mRNA. These experimental results point to a regulatory feedback loop between Bruno 1 and Cup in early oogenesis that appears crucial for oskar mRNA to reach the posterior pole and its expression in the egg chamber for accurate embryo development.
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Affiliation(s)
- Livia V. Bayer
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- Program in Molecular, Cellular, and Developmental Biology, the Graduate Center, City University of New York, New York, NY, USA
| | - Samantha Milano
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- Program in Molecular, Cellular, and Developmental Biology, the Graduate Center, City University of New York, New York, NY, USA
| | - Stephen K. Formel
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Harpreet Kaur
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Rishi Ravichandran
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Juan A. Cambeiro
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Lizaveta Slinko
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Irina E. Catrina
- Department of Chemistry and Biochemistry, Yeshiva University, New York, NY, USA
| | - Diana P. Bratu
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- Program in Molecular, Cellular, and Developmental Biology, the Graduate Center, City University of New York, New York, NY, USA
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7
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Buddika K, Huang YT, Ariyapala IS, Butrum-Griffith A, Norrell SA, O'Connor AM, Patel VK, Rector SA, Slovan M, Sokolowski M, Kato Y, Nakamura A, Sokol NS. Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity. Curr Biol 2022; 32:386-397.e6. [PMID: 34875230 PMCID: PMC8792327 DOI: 10.1016/j.cub.2021.11.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/17/2021] [Accepted: 11/11/2021] [Indexed: 01/26/2023]
Abstract
The role of processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4, and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a P-body-dependent repression activity that coordinates with known transcriptional repression programs to maintain a population of in vivo stem cells in a state primed for differentiation.
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Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Yi-Ting Huang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | | | - Sam A Norrell
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Alex M O'Connor
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Viraj K Patel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Samuel A Rector
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Mark Slovan
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Yasuko Kato
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
| | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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8
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Tikhomirova MA, Sheval EV. Formation of Biomolecular Condensates: Regulation of Embryogenesis at the Cellular Level. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Lee YM, Chiang PH, Cheng JH, Shen WH, Chen CH, Wu ML, Tian YL, Ni CH, Wang TF, Lin MD, Chou TB. Drosophila decapping protein 2 modulates the formation of cortical F-actin for germ plasm assembly. Dev Biol 2020; 461:96-106. [PMID: 32007453 DOI: 10.1016/j.ydbio.2020.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
In Drosophila, the deposition of the germ plasm at the posterior pole of the oocyte is essential for the abdomen and germ cell formation during embryogenesis. To assemble the germ plasm, oskar (osk) mRNA, produced by nurse cells, should be localized and anchored on the posterior cortex of the oocyte. Processing bodies (P-bodies) are cytoplasmic RNA granules responsible for the 5'-3' mRNA degradation. Evidence suggests that the components of P-bodies, such as Drosophila decapping protein 1 and Ge-1, are involved in the posterior localization of osk. However, whether the decapping core enzyme, Drosophila decapping protein 2 (dDcp2), is also involved remains unclear. Herein, we generated a dDcp2 null allele and showed that dDcp2 was required for the posterior localization of germ plasm components including osk. dDcp2 was distributed on the oocyte cortex and was localized posterior to the osk. In the posterior pole of dDcp2 mutant oocytes, osk was mislocalized and colocalized with F-actin detached from the cortex; moreover, considerably fewer F-actin projections were observed. Using the F-actin cosedimentation assay, we proved that dDcp2 interacted with F-actin through its middle region. In conclusion, our findings explored a novel function of dDcp2 in assisting osk localization by modulating the formation of F-actin projections on the posterior cortex.
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Affiliation(s)
- Yi-Mei Lee
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Po-Hsun Chiang
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Jen-Ho Cheng
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Wei-Hong Shen
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Chao-Han Chen
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Mei-Ling Wu
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Yi-Lu Tian
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Chao-Heng Ni
- Department of Life Sciences, College of Medicine, Tzu Chi University, 701 Zhongyang Rd, Sec. 3, Hualien, 97004, Taiwan
| | - Ting-Fang Wang
- Department of Life Sciences, College of Medicine, Tzu Chi University, 701 Zhongyang Rd, Sec. 3, Hualien, 97004, Taiwan
| | - Ming-Der Lin
- Department of Life Sciences, College of Medicine, Tzu Chi University, 701 Zhongyang Rd, Sec. 3, Hualien, 97004, Taiwan; Department of Molecular Biology and Human Genetics, College of Medicine, Tzu Chi University, 701 Zhongyang Rd, Sec. 3, Hualien, 97004, Taiwan; Department of Medical Research, Hualien Tzu Chi Hospital, 707 Zhongyang Rd, Sec. 3, Hualien, 97004, Taiwan.
| | - Tze-Bin Chou
- Institute of Molecular and Cellular Biology, College of Life Sciences, National Taiwan University, No.1, Sec.4, Roosevelt Rd, Taipei, 10617, Taiwan.
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10
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Flora P, Wong-Deyrup SW, Martin ET, Palumbo RJ, Nasrallah M, Oligney A, Blatt P, Patel D, Fuchs G, Rangan P. Sequential Regulation of Maternal mRNAs through a Conserved cis-Acting Element in Their 3' UTRs. Cell Rep 2019; 25:3828-3843.e9. [PMID: 30590052 PMCID: PMC6328254 DOI: 10.1016/j.celrep.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/28/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Maternal mRNAs synthesized during oogenesis initiate the development of future generations. Some maternal mRNAs are either somatic or germline determinants and must be translationally repressed until embryogenesis. However, the translational repressors themselves are temporally regulated. We used polar granule component (pgc), a Drosophila maternal mRNA, to ask how maternal transcripts are repressed while the regulatory landscape is shifting. pgc, a germline determinant, is translationally regulated throughout oogenesis. We find that different conserved RNA-binding proteins bind a 10-nt sequence in the 3′ UTR of pgc mRNA to continuously repress translation at different stages of oogenesis. Pumilio binds to this sequence in undifferentiated and early-differentiating oocytes to block Pgc translation. After differentiation, Bruno levels increase, allowing Bruno to bind the same sequence and take over translational repression of pgc mRNA. We have identified a class of maternal mRNAs that are regulated similarly, including zelda, the activator of the zygotic genome. Flora et al. show that pgc, a germline determinant, is translationally regulated throughout oogenesis. Different conserved RBPs bind a 10-nt sequence in the 3′ UTR to continuously repress translation throughout oogenesis. This mode of regulation applies to a class of maternal mRNAs, including zelda, the activator of the zygotic genome.
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Affiliation(s)
- Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Siu Wah Wong-Deyrup
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ryan J Palumbo
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Mohamad Nasrallah
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Andrew Oligney
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Dhruv Patel
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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11
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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12
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Swevers L, Liu J, Smagghe G. Defense Mechanisms against Viral Infection in Drosophila: RNAi and Non-RNAi. Viruses 2018; 10:E230. [PMID: 29723993 PMCID: PMC5977223 DOI: 10.3390/v10050230] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
RNAi is considered a major antiviral defense mechanism in insects, but its relative importance as compared to other antiviral pathways has not been evaluated comprehensively. Here, it is attempted to give an overview of the antiviral defense mechanisms in Drosophila that involve both RNAi and non-RNAi. While RNAi is considered important in most viral infections, many other pathways can exist that confer antiviral resistance. It is noted that very few direct recognition mechanisms of virus infections have been identified in Drosophila and that the activation of immune pathways may be accomplished indirectly through cell damage incurred by viral replication. In several cases, protection against viral infection can be obtained in RNAi mutants by non-RNAi mechanisms, confirming the variability of the RNAi defense mechanism according to the type of infection and the physiological status of the host. This analysis is aimed at more systematically investigating the relative contribution of RNAi in the antiviral response and more specifically, to ask whether RNAi efficiency is affected when other defense mechanisms predominate. While Drosophila can function as a useful model, this issue may be more critical for economically important insects that are either controlled (agricultural pests and vectors of diseases) or protected from parasite infection (beneficial insects as bees) by RNAi products.
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Affiliation(s)
- Luc Swevers
- Institute of Biosciences & Applications, NCSR "Demokritos", 15341 Athens, Greece.
| | - Jisheng Liu
- School of Life Sciences, Guangzhou University, 510006 Guangzhou, China.
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
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13
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Trovisco V, Belaya K, Nashchekin D, Irion U, Sirinakis G, Butler R, Lee JJ, Gavis ER, St Johnston D. bicoid mRNA localises to the Drosophila oocyte anterior by random Dynein-mediated transport and anchoring. eLife 2016; 5. [PMID: 27791980 PMCID: PMC5125753 DOI: 10.7554/elife.17537] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/25/2016] [Indexed: 01/17/2023] Open
Abstract
bicoid mRNA localises to the Drosophila oocyte anterior from stage 9 of oogenesis onwards to provide a local source for Bicoid protein for embryonic patterning. Live imaging at stage 9 reveals that bicoid mRNA particles undergo rapid Dynein-dependent movements near the oocyte anterior, but with no directional bias. Furthermore, bicoid mRNA localises normally in shot2A2, which abolishes the polarised microtubule organisation. FRAP and photo-conversion experiments demonstrate that the RNA is stably anchored at the anterior, independently of microtubules. Thus, bicoid mRNA is localised by random active transport and anterior anchoring. Super-resolution imaging reveals that bicoid mRNA forms 110-120 nm particles with variable RNA content, but constant size. These particles appear to be well-defined structures that package the RNA for transport and anchoring.
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Affiliation(s)
- Vítor Trovisco
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Katsiaryna Belaya
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Dmitry Nashchekin
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Uwe Irion
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - George Sirinakis
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Richard Butler
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jack J Lee
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Daniel St Johnston
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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14
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Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster. Sci Rep 2016; 6:21124. [PMID: 26928435 PMCID: PMC4772002 DOI: 10.1038/srep21124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/18/2016] [Indexed: 12/16/2022] Open
Abstract
We observed heteroses for body weight in Drosophila melanogaster after generating hybrids from three inbred lines. To better understand the mechanism for this phenomenon at the mRNA level, we compared the mRNA profiles of the parental and hybrid lines using high-throughput RNA-seq. A total of 5877 differentially expressed genes (DEGs) were found and about 92% of these exhibited parental expression level dominance. Genes in the dominance category were functionally characterized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene classifications offered by the Gene Ontology (GO) Consortium. The analysis identified genes associated with crucial processes such as development and growth in all three crosses. Functional assignments involving aminoglycan metabolism, starch and sucrose metabolism, and galactose metabolism are significantly overrepresented amongst the 215 common dominance DEGs. We conclude that dominance DEGs are important in heteroses in Drosophila melanogaster and contribute specifically to body weight heterosis.
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15
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Cao C, Magwire MM, Bayer F, Jiggins FM. A Polymorphism in the Processing Body Component Ge-1 Controls Resistance to a Naturally Occurring Rhabdovirus in Drosophila. PLoS Pathog 2016; 12:e1005387. [PMID: 26799957 PMCID: PMC4723093 DOI: 10.1371/journal.ppat.1005387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/17/2015] [Indexed: 12/30/2022] Open
Abstract
Hosts encounter an ever-changing array of pathogens, so there is continual selection for novel ways to resist infection. A powerful way to understand how hosts evolve resistance is to identify the genes that cause variation in susceptibility to infection. Using high-resolution genetic mapping we have identified a naturally occurring polymorphism in a gene called Ge-1 that makes Drosophila melanogaster highly resistant to its natural pathogen Drosophila melanogaster sigma virus (DMelSV). By modifying the sequence of the gene in transgenic flies, we identified a 26 amino acid deletion in the serine-rich linker region of Ge-1 that is causing the resistance. Knocking down the expression of the susceptible allele leads to a decrease in viral titre in infected flies, indicating that Ge-1 is an existing restriction factor whose antiviral effects have been increased by the deletion. Ge-1 plays a central role in RNA degradation and the formation of processing bodies (P bodies). A key effector in antiviral immunity, the RNAi induced silencing complex (RISC), localises to P bodies, but we found that Ge-1-based resistance is not dependent on the small interfering RNA (siRNA) pathway. However, we found that Decapping protein 1 (DCP1) protects flies against sigma virus. This protein interacts with Ge-1 and commits mRNA for degradation by removing the 5’ cap, suggesting that resistance may rely on this RNA degradation pathway. The serine-rich linker domain of Ge-1 has experienced strong selection during the evolution of Drosophila, suggesting that this gene may be under long-term selection by viruses. These findings demonstrate that studying naturally occurring polymorphisms that increase resistance to infections enables us to identify novel forms of antiviral defence, and support a pattern of major effect polymorphisms controlling resistance to viruses in Drosophila. Hosts and their pathogens are engaged in a never-ending arms race, and hosts must continually evolve new defences to protect themselves from infection. In the fruit fly Drosophila melanogaster we show that virus resistance can evolve through a single mutation. In flies that are highly resistant to a naturally occurring virus called sigma virus we identified a deletion in the protein-coding region of a gene called Ge-1. We experimentally confirmed that this was the cause of resistance by deleting this region in transgenic flies. Furthermore, we show that even the susceptible allele of Ge-1 helps protect flies against the virus, suggesting that this mutation has made an existing antiviral defence more effective. Ge-1 plays a central role in RNA degradation in regions of the cytoplasm called P bodies, and our results suggest that this pathway has been recruited during evolution to protect D. melanogaster against sigma virus. The protein domain that contains the deletion has experienced strong selection during its evolution, suggesting that it may be involved in an ongoing arms race with viruses.
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Affiliation(s)
- Chuan Cao
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Michael M. Magwire
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Florian Bayer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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16
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Tob1 is expressed in developing and adult gonads and is associated with the P-body marker, Dcp2. Cell Tissue Res 2015; 364:443-51. [DOI: 10.1007/s00441-015-2328-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 11/06/2015] [Indexed: 12/26/2022]
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17
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Rahman H, Qasim M, Oellerich M, Asif AR. Crosstalk between Edc4 and mammalian target of rapamycin complex 1 (mTORC1) signaling in mRNA decapping. Int J Mol Sci 2014; 15:23179-95. [PMID: 25514416 PMCID: PMC4284759 DOI: 10.3390/ijms151223179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/28/2014] [Accepted: 12/08/2014] [Indexed: 02/06/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is involved in the cellular transcription and translation processes. The undertaken study characterized the enhancer of mRNA decapping protein 4 (Edc4) as mTORC1 interacting protein. Human T lymphoblast (CCRF-CEM) cells were used for mTORC1 purification. Co-immunoprecipitation coupled with immunoblotting analysis was used to confirm the interaction of Edc4 in mTORC1 specific purifications. Further assays were incorporated to conclude the role of mTORC1 in mRNA decapping via Edc4. Edc4 was identified as a new interacting protein with mTORC1 in both the endogenous and myc-tag raptor component mTORC1 specific purifications. Quantitative co-localization using confocal microscopy demonstrated that raptor component of mTORC1 coexists with Edc4 in processing (P) bodies, a site for mRNA degradation. Incubation of cells with rapamycin, a known inhibitor of mTOR kinase activity, increased the total Edc4 protein expression but at the same time decreased the Edc4 interaction with mTORC1. Moreover, rapamycin treatment resulted in a significant decrease in total serine phosphorylated Edc4 protein signal and the total 5'-capped mRNA. These findings provide the first evidence for the pivotal role of mTORC1 in Edc4 regulation. Further in-depth studies are required to get a complete understanding of molecular crosstalk between mTORC1 signaling and mRNA decapping pathway.
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Affiliation(s)
- Hazir Rahman
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center, Robert-Koch-Str. 40, Goettingen 37075, Germany.
| | - Muhammad Qasim
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center, Robert-Koch-Str. 40, Goettingen 37075, Germany.
| | - Michael Oellerich
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center, Robert-Koch-Str. 40, Goettingen 37075, Germany.
| | - Abdul R Asif
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center, Robert-Koch-Str. 40, Goettingen 37075, Germany.
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18
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Abstract
Localization and the associated translational control of mRNA is a well established mechanism for segregating cellular protein expression. Drosophila has been instrumental in deciphering the prevailing mechanisms of mRNA localization and regulation. This review will discuss the diverse roles of mRNA localization in the Drosophila germline, the cis-elements and cellular components regulating localization and the superimposition of translational regulatory mechanisms. Despite a history of discovery, there are still many fundamental questions regarding mRNA localization that remain unanswered. Take home messages, outstanding questions and future approaches that will likely lead to resolving these unknowns in the future are summarized at the end.
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Affiliation(s)
- Timothy T Weil
- a Department of Zoology ; University of Cambridge ; Cambridge , UK
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19
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Xu L, Yang BF, Ai J. MicroRNA transport: a new way in cell communication. J Cell Physiol 2013; 228:1713-9. [PMID: 23460497 DOI: 10.1002/jcp.24344] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/04/2013] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) can efficiently regulate gene expression by targeting mRNA to cause mRNA cleavage or translational repression. Growing evidence indicates that miRNAs exist not only in cells but also in a variety of body fluids, which stimulates substantial interest in the transport mechanism and regulating process of extracellular miRNAs. This article reviews the basic biogenesis of miRNAs in detail to explore the origin of extracellular miRNAs. Different miRNA transporters have been summarized (e.g., exosomes, microvesicles, apoptosis bodies, and RNA-binding proteins). In addition, we discuss the regulators affecting miRNA transport (e.g., ATP and ceramide) and the selection mechanism for different miRNA transporters. Studies about miRNA transporters and the transport mechanism are new and developing. With the progress of the research, new functions of extracellular miRNAs may be uncovered in the future.
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Affiliation(s)
- Ling Xu
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, Heilongjiang Province, China
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20
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Carter JM, Baker SC, Pink R, Carter DRF, Collins A, Tomlin J, Gibbs M, Breuker CJ. Unscrambling butterfly oogenesis. BMC Genomics 2013; 14:283. [PMID: 23622113 PMCID: PMC3654919 DOI: 10.1186/1471-2164-14-283] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/05/2013] [Indexed: 12/16/2022] Open
Abstract
Background Butterflies are popular model organisms to study physiological mechanisms
underlying variability in oogenesis and egg provisioning in response to
environmental conditions. Nothing is known, however, about; the
developmental mechanisms governing butterfly oogenesis, how polarity in the
oocyte is established, or which particular maternal effect genes regulate
early embryogenesis. To gain insights into these developmental mechanisms
and to identify the conserved and divergent aspects of butterfly oogenesis,
we analysed a de novo ovarian transcriptome of the Speckled Wood
butterfly Pararge aegeria (L.), and compared the results with known
model organisms such as Drosophila melanogaster and Bombyx
mori. Results A total of 17306 contigs were annotated, with 30% possibly novel or highly
divergent sequences observed. Pararge aegeria females expressed
74.5% of the genes that are known to be essential for D.
melanogaster oogenesis. We discuss the genes involved in all
aspects of oogenesis, including vitellogenesis and choriogenesis, plus those
implicated in hormonal control of oogenesis and transgenerational hormonal
effects in great detail. Compared to other insects, a number of significant
differences were observed in; the genes involved in stem cell maintenance
and differentiation in the germarium, establishment of oocyte polarity, and
in several aspects of maternal regulation of zygotic development. Conclusions This study provides valuable resources to investigate a number of divergent
aspects of butterfly oogenesis requiring further research. In order to fully
unscramble butterfly oogenesis, we also now also have the resources to
investigate expression patterns of oogenesis genes under a range of
environmental conditions, and to establish their function.
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Affiliation(s)
- Jean-Michel Carter
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford, OX3 0BP, UK
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21
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Scherrer K. Regulation of gene expression and the transcription factor cycle hypothesis. Biochimie 2012; 94:1057-68. [PMID: 22234303 DOI: 10.1016/j.biochi.2011.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 12/09/2011] [Indexed: 11/26/2022]
Abstract
Post-genomic data show unexpected extent of the transcribed genome and the size of individual primary transcripts. Hence, most cis-regulatory modules (CRMs) binding transcription factors (TFs) at promotor, enhancer and other sites are actually transcribed within full domain transcripts (FDTs). The ensemble of these CRMs placed way upstream of exon clusters, downstream and in intronic or intergenic positions represent a program of gene expression which has been formally analysed within the Gene and Genon concept [1,2]. This concept has emphasised the necessity to separate product information from regulative information to allow information-theoretic analysis of gene expression. Classically, TFs have been assumed to act at DNA level exclusively but evidence has accumulated indicating eventual post-transcriptional functions. The transcription factor cycle (TFC) hypothesis suggests the transfer of DNA-bound factors to nascent RNA. Exerting downstream functions in RNA processing and transport, these factors would be liberated by RNA processing and cycle back to the DNA maintaining active transcription. Sequestered on RNA in absence of processing they would constitute a negative feedback loop. The TFC concept may explain epigenetic regulation in mitosis and meiosis. In mitosis control factors may survive as single proteins but also attached to FDTs as organised complexes. This process might perpetuate in cell division conditioning of chromatin for transcription. As observed on lampbrush chromosomes formed in avian and amphibian oogenesis, in meiosis the genome is fully transcribed and oocytes conserve high Mr RNA of high sequence complexity. When new interphase chromosomes form in daughter cells and early embryogenesis, TFs and other factors attached to RNA might be reinserted onto the DNA.
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Affiliation(s)
- Klaus Scherrer
- Inst. J. Monod, CNRS and University Paris Diderot, 9, rue Larrey, 75005 Paris, France
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22
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Schisa JA. New insights into the regulation of RNP granule assembly in oocytes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 295:233-89. [PMID: 22449492 DOI: 10.1016/b978-0-12-394306-4.00013-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In a variety of cell types in plants, animals, and fungi, ribonucleoprotein (RNP) complexes play critical roles in regulating RNA metabolism. These RNP granules include processing bodies and stress granules that are found broadly across cell types, as well as RNP granules unique to the germline, such as P granules, polar granules, sponge bodies, and germinal granules. This review focuses on RNP granules localized in oocytes of the major model systems, Caenorhabditis elegans, Drosophila, Xenopus, mouse, and zebrafish. The signature families of proteins within oocyte RNPs include Vasa and other RNA-binding proteins, decapping activators and enzymes, Argonaute family proteins, and translation initiation complex proteins. This review describes the many recent insights into the dynamics and functions of RNP granules, including their roles in mRNA degradation, mRNA localization, translational regulation, and fertility. The roles of the cytoskeleton and cell organelles in regulating RNP granule assembly are also discussed.
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Affiliation(s)
- Jennifer A Schisa
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan, USA
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23
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Kato Y, Nakamura A. Roles of cytoplasmic RNP granules in intracellular RNA localization and translational control in the Drosophila oocyte. Dev Growth Differ 2011; 54:19-31. [PMID: 22111938 DOI: 10.1111/j.1440-169x.2011.01314.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Intracellular mRNA localization and translation are ways to achieve asymmetric protein sorting in polarized cells, and they play fundamental roles in cell-fate decisions and body patterning during animal development. These processes are regulated by the interplay between cis-acting elements and trans-acting RNA-binding proteins that form and occur within a ribonucleoprotein (RNP) complex. Recent studies in the Drosophila oocyte have revealed that RNP complex assembly in the nucleus is critical for the regulation of cytoplasmic mRNA localization and translation. Furthermore, several trans-acting factors promote the reorganization of target mRNAs in the cytoplasm into higher-order RNP granules, which are often visible by light microscopy. Therefore, RNA localization and translation are likely to be coupled within these RNP granules. Notably, diverse cytoplasmic RNP granules observed in different cell types share conserved sets of proteins, suggesting they have fundamental and common cellular functions.
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Affiliation(s)
- Yasuko Kato
- Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
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