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Murari E, Meadows D, Cuda N, Mangone M. A comprehensive analysis of 3'UTRs in Caenorhabditis elegans. Nucleic Acids Res 2024:gkae543. [PMID: 38917330 DOI: 10.1093/nar/gkae543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/29/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
3'Untranslated regions (3'UTRs) are essential portions of genes containing elements necessary for pre-mRNA 3'end processing and are involved in post-transcriptional gene regulation. Despite their importance, they remain poorly characterized in eukaryotes. Here, we have used a multi-pronged approach to extract and curate 3'UTR data from 11533 publicly available datasets, corresponding to the entire collection of Caenorhabditis elegans transcriptomes stored in the NCBI repository from 2009 to 2023. We have also performed high throughput cloning pipelines to identify and validate rare 3'UTR isoforms and incorporated and manually curated 3'UTR isoforms from previously published datasets. This updated C. elegans 3'UTRome (v3) is the most comprehensive resource in any metazoan to date, covering 97.4% of the 20362 experimentally validated protein-coding genes with refined and updated 3'UTR boundaries for 23489 3'UTR isoforms. We also used this novel dataset to identify and characterize sequence elements involved in pre-mRNA 3'end processing and update miRNA target predictions. This resource provides important insights into the 3'UTR formation, function, and regulation in eukaryotes.
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Affiliation(s)
- Emma Murari
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Dalton Meadows
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Nicholas Cuda
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, USA
| | - Marco Mangone
- The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA
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Jones M, Norman M, Tiet AM, Lee J, Lee MH. C. elegans Germline as Three Distinct Tumor Models. BIOLOGY 2024; 13:425. [PMID: 38927305 PMCID: PMC11200432 DOI: 10.3390/biology13060425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand the molecular mechanisms associated with tumorigenesis in diverse regards. However, our comprehension of how non-tumor cells transform into tumor cells at molecular and cellular levels remains incomplete. The nematode C. elegans has emerged as an excellent model organism for exploring various phenomena, including tumorigenesis. Although C. elegans does not naturally develop cancer, it serves as a valuable platform for identifying oncogenes and the underlying mechanisms within a live organism. In this review, we describe three distinct germline tumor models in C. elegans, highlighting their associated mechanisms and related regulators: (1) ectopic proliferation due to aberrant activation of GLP-1/Notch signaling, (2) meiotic entry failure resulting from the loss of GLD-1/STAR RNA-binding protein, (3) spermatogenic dedifferentiation caused by the loss of PUF-8/PUF RNA-binding protein. Each model requires the mutations of specific genes (glp-1, gld-1, and puf-8) and operates through distinct molecular mechanisms. Despite these differences in the origins of tumorigenesis, the internal regulatory networks within each tumor model display shared features. Given the conservation of many of the regulators implicated in C. elegans tumorigenesis, it is proposed that these unique models hold significant potential for enhancing our comprehension of the broader control mechanisms governing tumorigenesis.
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Affiliation(s)
- Mariah Jones
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Mina Norman
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Alex Minh Tiet
- Neuroscience Program, East Carolina University, Greenville, NC 27858, USA;
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jiwoo Lee
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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3
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Caponnetto A, Ferrara C, Fazzio A, Agosta N, Scribano M, Vento ME, Borzì P, Barbagallo C, Stella M, Ragusa M, Scollo P, Barbagallo D, Purrello M, Di Pietro C, Battaglia R. A Circular RNA Derived from the Pumilio 1 Gene Could Regulate PTEN in Human Cumulus Cells. Genes (Basel) 2024; 15:124. [PMID: 38275605 PMCID: PMC10815046 DOI: 10.3390/genes15010124] [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: 11/30/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
CircRNAs are a class of non-coding RNAs able to regulate gene expression at multiple levels. Their involvement in physiological processes, as well as their altered regulation in different human diseases, both tumoral and non-tumoral, is well documented. However, little is known about their involvement in female reproduction. This study aims to identify circRNAs potentially involved in reproductive women's health. Candidate circRNAs expressed in ovary and sponging miRNAs, already known to be expressed in the ovary, were selected by a computational approach. Using real time PCR, we verified their expression and identified circPUM1 as the most interesting candidate circRNA for further analyses. We assessed the expression of circPUM1 and its linear counterpart in all the follicle compartments and, using a computational and experimental approach, identified circPUM1 direct and indirect targets, miRNAs and mRNAs, respectively, in cumulus cells. We found that both circPUM1 and its mRNA host gene are co-expressed in all the follicle compartments and proposed circPUM1 as a potential regulator of PTEN, finding a strong positive correlation between circPUM1 and PTEN mRNA. These results suggest a possible regulation of PTEN by circPUM1 in cumulus cells and point out the important role of circRNA inside the pathways related to follicle growth and oocyte maturation.
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Affiliation(s)
- Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Carmen Ferrara
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Anna Fazzio
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Noemi Agosta
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Marianna Scribano
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Maria Elena Vento
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Placido Borzì
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Paolo Scollo
- Department of Medicine and Surgery, Kore University, 94100 Enna, Italy;
- Maternal and Child Department, Obstetrics and Gynecology Unit, Cannizzaro Hospital, 95123 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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Feng W, Zhang H, Cao Y, Yang C, Khalid MHB, Yang Q, Li W, Wang Y, Fu F, Yu H. Comprehensive Identification of the Pum Gene Family and Its Involvement in Kernel Development in Maize. Int J Mol Sci 2023; 24:14036. [PMID: 37762337 PMCID: PMC10530998 DOI: 10.3390/ijms241814036] [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: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The Pumilio (Pum) RNA-binding protein family regulates post-transcription and plays crucial roles in stress response and growth. However, little is known about Pum in plants. In this study, a total of 19 ZmPum genes were identified and classified into two groups in maize. Although each ZmPum contains the conserved Pum domain, the ZmPum members show diversity in the gene and protein architectures, physicochemical properties, chromosomal location, collinearity, cis-elements, and expression patterns. The typical ZmPum proteins have eight α-helices repeats, except for ZmPum2, 3, 5, 7, and 14, which have fewer α-helices. Moreover, we examined the expression profiles of ZmPum genes and found their involvement in kernel development. Except for ZmPum2, ZmPum genes are expressed in maize embryos, endosperms, or whole seeds. Notably, ZmPum4, 7, and 13 exhibited dramatically high expression levels during seed development. The study not only contributes valuable information for further validating the functions of ZmPum genes but also provides insights for improvement and enhancing maize yield.
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Affiliation(s)
- Wenqi Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongwanjun Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Hayder Bin Khalid
- National Research Centre of Intercropping, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Qingqing Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingge Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoqiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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van de Poll F, Sutter BM, Acoba MG, Caballero D, Jahangiri S, Yang YS, Lee CD, Tu BP. Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis. PLoS Genet 2023; 19:e1010774. [PMID: 37216416 PMCID: PMC10237644 DOI: 10.1371/journal.pgen.1010774] [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: 04/04/2023] [Revised: 06/02/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Pbp1 (poly(A)-binding protein-binding protein 1) is a cytoplasmic stress granule marker that is capable of forming condensates that function in the negative regulation of TORC1 signaling under respiratory conditions. Polyglutamine expansions in its mammalian ortholog ataxin-2 lead to spinocerebellar dysfunction due to toxic protein aggregation. Here, we show that loss of Pbp1 in S. cerevisiae leads to decreased amounts of mRNAs and mitochondrial proteins which are targets of Puf3, a member of the PUF (Pumilio and FBF) family of RNA-binding proteins. We found that Pbp1 supports the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase and subunits of mitochondrial ribosomes. We further show that Pbp1 and Puf3 interact through their respective low complexity domains, which is required for Puf3-target mRNA translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration. They may further explain prior associations of Pbp1/ataxin-2 with RNA, stress granule biology, mitochondrial function, and neuronal health.
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Affiliation(s)
- Floortje van de Poll
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Benjamin M. Sutter
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle Grace Acoba
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Daniel Caballero
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Samira Jahangiri
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yu-San Yang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chien-Der Lee
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Benjamin P. Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. The in vivo functional significance of PUF hub partnerships in C. elegans germline stem cells. Development 2023; 150:dev201705. [PMID: 37070766 PMCID: PMC10259659 DOI: 10.1242/dev.201705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 04/19/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of Caenorhabditis elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we previously proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(AmBm) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(AmBm) is used to explore the in vivo functional significance of the LST-1-PUF partnership. Tethered LST-1 requires this partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs in vivo. Comparison of LST-1-PUF and Nanos-Pumilio reveals fundamental molecular differences, making LST-1-PUF a distinct paradigm for PUF partnerships.
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Affiliation(s)
- Ahlan S. Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R. Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H. Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L. Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Yoon DS, Choi Y, Lee KM, Ko EA, Kim EJ, Park KH, Lee JW. Downregulation of the RNA-binding protein PUM2 facilitates MSC-driven bone regeneration and prevents OVX-induced bone loss. J Biomed Sci 2023; 30:26. [PMID: 37088847 PMCID: PMC10122812 DOI: 10.1186/s12929-023-00920-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/14/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Although mRNA dysregulation can induce changes in mesenchymal stem cell (MSC) homeostasis, the mechanisms by which post-transcriptional regulation influences MSC differentiation potential remain understudied. PUMILIO2 (PUM2) represses translation by binding target mRNAs in a sequence-specific manner. METHODS In vitro osteogenic differentiation assays were conducted using human bone marrow-derived MSCs. Alkaline phosphatase and alizarin red S staining were used to evaluate the osteogenic potential of MSCs. A rat xenograft model featuring a calvarial defect to examine effects of MSC-driven bone regeneration. RNA-immunoprecipitation (RNA-IP) assay was used to determine the interaction between PUM2 protein and Distal-Less Homeobox 5 (DLX5) mRNA. Ovariectomized (OVX) mice were employed to evaluate the effect of gene therapy for postmenopausal osteoporosis. RESULTS Here, we elucidated the molecular mechanism of PUM2 in MSC osteogenesis and evaluated the applicability of PUM2 knockdown (KD) as a potential cell-based or gene therapy. PUM2 level was downregulated during MSC osteogenic differentiation, and PUM2 KD enhanced MSC osteogenic potential. Following PUM2 KD, MSCs were transplanted onto calvarial defects in 12-week-old rats; after 8 weeks, transplanted MSCs promoted bone regeneration. PUM2 KD upregulated the expression of DLX5 mRNA and protein and the reporter activity of its 3'-untranslated region. RNA-IP revealed direct binding of PUM2 to DLX5 mRNA. We then evaluated the potential of adeno-associated virus serotype 9 (AAV9)-siPum2 as a gene therapy for osteoporosis in OVX mice. CONCLUSION Our findings suggest a novel role for PUM2 in MSC osteogenesis and highlight the potential of PUM2 KD-MSCs in bone regeneration. Additionally, we showed that AAV9-siPum2 is a potential gene therapy for osteoporosis.
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Affiliation(s)
- Dong Suk Yoon
- Department of Biomedical Science, Hwasung Medi-Science University, Hwaseong-Si 18274, Gyeonggi-Do, South Korea
| | - Yoorim Choi
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Kyoung-Mi Lee
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Eun Ae Ko
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Eun-Ji Kim
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Kwang Hwan Park
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jin Woo Lee
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea.
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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Fusarium oxysporum f. sp. niveum Pumilio 1 Regulates Virulence on Watermelon through Interacting with the ARP2/3 Complex and Binding to an A-Rich Motif in the 3' UTR of Diverse Transcripts. mBio 2023; 14:e0015723. [PMID: 36856417 PMCID: PMC10128047 DOI: 10.1128/mbio.00157-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Fusarium oxysporum f. sp. niveum (Fon), a soilborne phytopathogenic fungus, causes watermelon Fusarium wilt, resulting in serious yield losses worldwide. However, the underlying molecular mechanism of Fon virulence is largely unknown. The present study investigated the biological functions of six FonPUFs, encoding RNA binding Pumilio proteins, and especially explored the molecular mechanism of FonPUF1 in Fon virulence. A series of phenotypic analyses indicated that FonPUFs have distinct but diverse functions in vegetative growth, asexual reproduction, macroconidia morphology, spore germination, cell wall, or abiotic stress response of Fon. Notably, the deletion of FonPUF1 attenuates Fon virulence by impairing the invasive growth and colonization ability inside the watermelon plants. FonPUF1 possesses RNA binding activity, and its biochemical activity and virulence function depend on the RNA recognition motif or Pumilio domains. FonPUF1 associates with the actin-related protein 2/3 (ARP2/3) complex by interacting with FonARC18, which is also required for Fon virulence and plays an important role in regulating mitochondrial functions, such as ATP generation and reactive oxygen species production. Transcriptomic profiling of ΔFonPUF1 identified a set of putative FonPUF1-dependent virulence-related genes in Fon, possessing a novel A-rich binding motif in the 3' untranslated region (UTR), indicating that FonPUF1 participates in additional mechanisms critical for Fon virulence. These findings highlight the functions and molecular mechanism of FonPUFs in Fon virulence. IMPORTANCE Fusarium oxysporum is a devastating plant-pathogenic fungus that causes vascular wilt disease in many economically important crops, including watermelon, worldwide. F. oxysporum f. sp. nievum (Fon) causes serious yield loss in watermelon production. However, the molecular mechanism of Fusarium wilt development by Fon remains largely unknown. Here, we demonstrate that six putative Pumilio proteins-encoding genes (FonPUFs) differentially operate diverse basic biological processes, including stress response, and that FonPUF1 is required for Fon virulence. Notably, FonPUF1 possesses RNA binding activity and associates with the actin-related protein 2/3 complex to control mitochondrial functions. Furthermore, FonPUF1 coordinates the expression of a set of putative virulence-related genes in Fon by binding to a novel A-rich motif present in the 3' UTR of a diverse set of target mRNAs. Our study disentangles the previously unexplored molecular mechanism involved in regulating Fon virulence, providing a possibility for the development of novel strategies for disease management.
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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11
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Ferdous AS, Costa Dos Santos SJ, Kanzler CR, Shin H, Carrick BH, Crittenden SL, Wickens M, Kimble J. Functional significance of PUF partnerships in C. elegans germline stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528708. [PMID: 36824876 PMCID: PMC9949348 DOI: 10.1101/2023.02.15.528708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
PUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal of C. elegans germline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1-PUF and SYGL-1-PUF partnerships and their molecular activities in their natural context - nematode stem cells. We confirm LST-1-PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(A m B m ) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(A m B m ) is used to explore the functional significance of the LST-1-PUF partnership. Tethered LST-1 requires the partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs. Comparison of PUF-LST-1 and Pumilio-Nanos reveals fundamental molecular differences, making PUF-LST-1 a distinct paradigm for PUF partnerships. Summary statement Partnerships between PUF RNA-binding proteins and intrinsically disordered proteins are essential for stem cell maintenance and RNA repression.
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Affiliation(s)
- Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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12
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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13
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Modulation and function of Pumilio proteins in cancer. Semin Cancer Biol 2022; 86:298-309. [PMID: 35301091 DOI: 10.1016/j.semcancer.2022.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 01/27/2023]
Abstract
Post-transcriptional regulation is involved in tumorigenesis, and in this control, RNA-binding proteins are the main protagonists. Pumilio proteins are highly conserved RNA-binding proteins that regulate many aspects of RNA processing. The dysregulation of Pumilio expression is associated with different types of cancer. This review summarizes the roles of Pumilio 1 and Pumilio 2 in cancer and discusses the factors that account for their distinct biological functions. Pumilio levels seem to be related to tumor progression and poor prognoses in some kinds of tumors, such as lung, pancreatic, prostate, and cervical cancers. Pumilio 1 is associated with cancer proliferation, migration, and invasion, and so is Pumilio 2, although there are contradictory reports regarding the latter. Furthermore, the circular RNA, circPUM1, has been described as a miRNAs sponge, regulating miRNA involved in the cell cycle. The expression and function of Pumilio proteins depend on the fine adjustment of a set of modulators, including miRNAs, lncRNAs, and circRNAs; this demonstrates that Pumilio plays an important role in tumorigenesis through a variety of regulatory axes.
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14
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Snoderly-Foster LJ, Olivas WM. Regulation of Parkinson's disease-associated genes by Pumilio proteins and microRNAs in SH-SY5Y neuronal cells. PLoS One 2022; 17:e0275235. [PMID: 36174040 PMCID: PMC9522289 DOI: 10.1371/journal.pone.0275235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease is the second most common age-related, neurodegenerative disease. A small collection of genes has been linked to Parkinson's disease including LRRK2, SAT1, and SNCA, the latter of which encodes the protein alpha-synuclein that aggregates in Lewy bodies as a hallmark of the disease. Overexpression of even wild-type versions of these genes can lead to pathogenesis, yet the regulatory mechanisms that control protein production of the genes are not fully understood. Pumilio proteins belong to the highly conserved PUF family of eukaryotic RNA-binding proteins that post-transcriptionally regulate gene expression through binding conserved motifs in the 3' untranslated region (UTR) of mRNA targets known as PUF Recognition Elements (PREs). The 3'UTRs of LRRK2, SNCA and SAT1 each contain multiple putative PREs. Knockdown (KD) of the two human Pumilio homologs (Pumilio 1 and Pumilio 2) in a neurodegenerative model cell line, SH-SY5Y, resulted in increased SNCA and LRRK2 mRNA, as well as alpha-synuclein levels, suggesting these genes are normally repressed by the Pumilio proteins. Some studies have indicated a relationship between Pumilio and microRNA activities on the same target, especially when their binding sites are close together. LRRK2, SNCA, and SAT1 each contain several putative microRNA-binding sites within the 3'UTR, some of which reside near PREs. Small RNA-seq and microRNA qPCR assays were performed in both wild type and Pumilio KD SH-SY5Y cells to analyze global and differential microRNA expression. One thousand four hundred and four microRNAs were detected across wild type and Pumilio KD cells. Twenty-one microRNAs were differentially expressed between treatments, six of which were previously established to be altered in Parkinson's disease patient samples or research models. Expression of ten miRs predicted to target LRRK2 and SNCA was verified by RT-qPCR. Collectively, our results demonstrate that Pumilios and microRNAs play a multi-faceted role in regulating Parkinson's disease-associated genes.
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Affiliation(s)
- Lisa J. Snoderly-Foster
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
| | - Wendy M. Olivas
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
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15
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Liu Z, Lv C. RNA binding protein PUM2 promotes hepatocellular carcinoma proliferation and apoptosis via binding to the 3'UTR of BTG3. Oncol Lett 2022; 24:346. [PMID: 36072004 PMCID: PMC9434726 DOI: 10.3892/ol.2022.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Affiliation(s)
- Zhenhua Liu
- Department of General Surgery, The First People's Hospital of Lin Ping District, Hangzhou, Zhejiang 311100, P.R. China
| | - Chunye Lv
- Department of General Surgery, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211100, P.R. China
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16
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Rajasekaran S, Khan E, Ching SR, Khan M, Siddiqui J, Gradia DF, Lin C, Bouley SJ, Mercadante D, Manning AL, Gerber AP, Walker J, Miles W. PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. Nucleic Acids Res 2022; 50:7048-7066. [PMID: 35736218 PMCID: PMC9262620 DOI: 10.1093/nar/gkac499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
DICER1 syndrome is a cancer pre-disposition disorder caused by mutations that disrupt the function of DICER1 in miRNA processing. Studying the molecular, cellular and oncogenic effects of these mutations can reveal novel mechanisms that control cell homeostasis and tumor biology. Here, we conduct the first analysis of pathogenic DICER1 syndrome allele from the DICER1 3'UTR. We find that the DICER1 syndrome allele, rs1252940486, abolishes interaction with the PUMILIO RNA binding protein with the DICER1 3'UTR, resulting in the degradation of the DICER1 mRNA by AUF1. This single mutational event leads to diminished DICER1 mRNA and protein levels, and widespread reprogramming of miRNA networks. The in-depth characterization of the rs1252940486 DICER1 allele, reveals important post-transcriptional regulatory events that control DICER1 levels.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Samuel R Ching
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Misbah Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Jalal K Siddiqui
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Daniela F Gradia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Stephanie J Bouley
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dayna L Mercadante
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Amity L Manning
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wayne O Miles
- To whom correspondence should be addressed. Tel: +1 614 366 2869;
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17
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Nishanth MJ, Simon B. Understanding the possible influence of Pumilio RNA binding proteins on terpenoid indole alkaloid biosynthesis in Catharanthus roseus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:963-969. [PMID: 35722510 PMCID: PMC9203614 DOI: 10.1007/s12298-022-01193-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 05/03/2023]
Abstract
Catharanthus roseus is a clinically significant medicinal plant; the sole source of chemotherapy agents, vincristine and vinblastine (specialized metabolites, terpenoid indole alkaloids/TIAs). Owing to large clinical demand and low bioavailability, several studies have focused on biosynthesis and regulation of TIA biosynthesis in C. roseus. However, transcription factor mediated regulation has been a major research focus, and the impact of post-transcriptional regulation remains under-explored. RNA binding proteins (RBPs) are an emerging class of post-transcriptional regulators having a profound influence on transcript stability. Pumilio (Pum) RBPs are evolutionarily conserved post-transcriptional regulators, involved in RNA degradation across eukaryotes. However, their potential influence on TIA biosynthesis has not been studied till date in any medicinal plants including C. roseus. Thus, the present study aimed at identification and computational characterization of Pum in C. roseus, followed by expression and functional analyses. The genome-wide identification and characterization revealed twelve CrPum isoforms. The effect of CrPum2, 3, and 5 knockdown on TIA biosynthesis (specifically vindoline and catharanthine) was analyzed via high performance liquid chromatography. CrPum5 knockdown was associated with increased TIA levels and upregulation of key TIA pathway genes. Thus, the present study is the first to report the potential influence of Pum on TIA biosynthesis in C. roseus. Further studies to elucidate the mechanism of Pum activity could provide new insights into the molecular regulation of TIA biosynthesis. A holistic understanding of regulatory mechanisms could benefit the metabolic engineering programs aimed at higher productivity of plant specialized metabolites. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01193-5.
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Affiliation(s)
- M. J. Nishanth
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu India
| | - Bindu Simon
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu India
- Assistant Professor of Biology, Department of Molecular and Cellular Biology, College of Science and Mathematics, Kennesaw State University, Kennesaw, GA 30144 USA
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18
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Gao M, Su S, Cao J, Xiang S, Huang Y, Shu X, Ma J, Liu J. Targeted Manipulation of Cellular RNA m 6A Methylation at the Single-Base Level. ACS Chem Biol 2022; 17:854-863. [PMID: 35294178 DOI: 10.1021/acschembio.1c00895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of tools for precise manipulation of cellular mRNA m6A methylation at the base level is highly required. Here, we report an RNA-guided RNA modification strategy using a fusion protein containing deactivated nuclease Cas13b and m6A methyltransferase METTL14, namely, dCas13b-M14, which is designedly positioned in the cytoplasm. dCas13b-M14 naturally heterodimerizes with endogenous METTL3 to form a catalytic complex to methylate specific cytoplasmic mRNA under a guide RNA (gRNA). We developed assays to screen and validate the guiding specificity of varied gRNAs at single-base resolution. With an optimum combination of dCas13b-M14 and gRNAs inside cells, we have successfully tuned methylation levels of several selected mRNA m6A sites. The off-target effect was evaluated by whole transcriptome m6A sequencing, and a very minor perturbation on the methylome was revealed. Finally, we successfully utilized the editing tool to achieve de novo methylations on five selected mRNA sites. Together, this study paves the way for studying position-dependent roles of m6A methylation in a particular transcript.
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Affiliation(s)
- Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ye Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
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Bencivenga D, Stampone E, Vastante A, Barahmeh M, Della Ragione F, Borriello A. An Unanticipated Modulation of Cyclin-Dependent Kinase Inhibitors: The Role of Long Non-Coding RNAs. Cells 2022; 11:cells11081346. [PMID: 35456025 PMCID: PMC9028986 DOI: 10.3390/cells11081346] [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: 03/12/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
It is now definitively established that a large part of the human genome is transcribed. However, only a scarce percentage of the transcriptome (about 1.2%) consists of RNAs that are translated into proteins, while the large majority of transcripts include a variety of RNA families with different dimensions and functions. Within this heterogeneous RNA world, a significant fraction consists of sequences with a length of more than 200 bases that form the so-called long non-coding RNA family. The functions of long non-coding RNAs range from the regulation of gene transcription to the changes in DNA topology and nucleosome modification and structural organization, to paraspeckle formation and cellular organelles maturation. This review is focused on the role of long non-coding RNAs as regulators of cyclin-dependent kinase inhibitors’ (CDKIs) levels and activities. Cyclin-dependent kinases are enzymes necessary for the tuned progression of the cell division cycle. The control of their activity takes place at various levels. Among these, interaction with CDKIs is a vital mechanism. Through CDKI modulation, long non-coding RNAs implement control over cellular physiology and are associated with numerous pathologies. However, although there are robust data in the literature, the role of long non-coding RNAs in the modulation of CDKIs appears to still be underestimated, as well as their importance in cell proliferation control.
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20
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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21
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Inoue AH, Domingues PF, Serpeloni M, Hiraiwa PM, Vidal NM, Butterfield ER, del Pino RC, Ludwig A, Boehm C, Field MC, Ávila AR. Proteomics uncovers novel components of an interactive protein network supporting RNA export in trypanosomes. Mol Cell Proteomics 2022; 21:100208. [PMID: 35091090 PMCID: PMC8938319 DOI: 10.1016/j.mcpro.2022.100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022] Open
Abstract
In trypanosomatids, transcription is polycistronic and all mRNAs are processed by trans-splicing, with export mediated by noncanonical mechanisms. Although mRNA export is central to gene regulation and expression, few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components. We previously described conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII (previously Hel45), a core component of the exon junction complex (EJC). Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry. Significant overlap between TcSub2 and TceIF4AIII-interacting protein cohorts suggests that both proteins associate with similar machinery. We identified several interactions with conserved core components of the EJC and multiple additional complexes, together with proteins specific to trypanosomatids. Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events. We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of mRNA metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome mRNA maturation. Gene expression in trypanosomes is mediated by noncanonical mechanisms. Trypanosome mRNA nuclear export system comprises unique proteins to kinetoplastids. The present work highlights an amalgam of kinetoplastid-specific and conserved components. Our data support a highly coupled mRNA maturation pathway.
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22
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The Role of Pumilio RNA Binding Protein in Plants. Biomolecules 2021; 11:biom11121851. [PMID: 34944494 PMCID: PMC8699478 DOI: 10.3390/biom11121851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Eukaryotic organisms have a posttranscriptional/translational regulation system for the control of translational efficiency. RNA binding proteins (RBPs) have been known to control target genes. One type of protein, Pumilio (Pum)/Puf family RNA binding proteins, show a specific binding of 3′ untranslational region (3′ UTR) of target mRNA and function as a post-transcriptional/translational regulator in eukaryotic cells. Plant Pum protein is involved in development and biotic/abiotic stresses. Interestingly, Arabidopsis Pum can control target genes in a sequence-specific manner and rRNA processing in a sequence-nonspecific manner. As shown in in silico Pum gene expression analysis, Arabidopsis and rice Pum genes are responsive to biotic/abiotic stresses. Plant Pum can commonly contribute to host gene regulation at the post-transcriptional/translational step, as can mammalian Pum. However, the function of plant Pum proteins is not yet fully known. In this review, we briefly summarize the function of plant Pum in defense, development, and environmental responses via recent research and bioinformatics data.
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Iannello M, Mezzelani M, Dalla Rovere G, Smits M, Patarnello T, Ciofi C, Carraro L, Boffo L, Ferraresso S, Babbucci M, Mazzariol S, Centelleghe C, Cardazzo B, Carrer C, Varagnolo M, Nardi A, Pittura L, Benedetti M, Fattorini D, Regoli F, Ghiselli F, Gorbi S, Bargelloni L, Milan M. Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam. Evol Appl 2021; 14:2864-2880. [PMID: 34950234 PMCID: PMC8674894 DOI: 10.1111/eva.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marica Mezzelani
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Morgan Smits
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Luciano Boffo
- Associazione “Vongola Verace di Chioggia”ChioggiaItaly
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Carrer
- c/o Magistrato alle Acque di Venezia Ufficio Tecnico Antinquinamento Laboratorio CSMOPadovaItaly
| | | | - Alessandro Nardi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Lucia Pittura
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Maura Benedetti
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Daniele Fattorini
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Francesco Regoli
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Stefania Gorbi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimo Milan
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
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24
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Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Commun Biol 2021; 4:1240. [PMID: 34716407 PMCID: PMC8556268 DOI: 10.1038/s42003-021-02766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/07/2021] [Indexed: 01/16/2023] Open
Abstract
Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function. Jazmine Hallinan et al. report the development of a new generation of circular tandem repeat proteins with enhanced self-assembly. Functionalisation of these constructs with SARS CoV-2 VHH domains resulted in sub-nanomolar binding affinity to the viral receptor binding domain.
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Affiliation(s)
- Jazmine P Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Mesfin M Gewe
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Madison A Kennedy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Della Friend
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - James M Roberts
- Lumen Bioscience Inc., 1441 North 34th Street, Seattle, WA, 98103, USA
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA. .,Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98009, USA.
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
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25
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Feng H, Wan C, Zhang Z, Chen H, Li Z, Jiang H, Yin M, Dong S, Dou D, Wang Y, Zheng X, Ye W. Specific interaction of an RNA-binding protein with the 3'-UTR of its target mRNA is critical to oomycete sexual reproduction. PLoS Pathog 2021; 17:e1010001. [PMID: 34648596 PMCID: PMC8547697 DOI: 10.1371/journal.ppat.1010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/26/2021] [Accepted: 10/03/2021] [Indexed: 01/17/2023] Open
Abstract
Sexual reproduction is an essential stage of the oomycete life cycle. However, the functions of critical regulators in this biological process remain unclear due to a lack of genome editing technologies and functional genomic studies in oomycetes. The notorious oomycete pathogen Pythium ultimum is responsible for a variety of diseases in a broad range of plant species. In this study, we revealed the mechanism through which PuM90, a stage-specific Puf family RNA-binding protein, regulates oospore formation in P. ultimum. We developed the first CRISPR/Cas9 system-mediated gene knockout and in situ complementation methods for Pythium. PuM90-knockout mutants were significantly defective in oospore formation, with empty oogonia or oospores larger in size with thinner oospore walls compared with the wild type. A tripartite recognition motif (TRM) in the Puf domain of PuM90 could specifically bind to a UGUACAUA motif in the mRNA 3′ untranslated region (UTR) of PuFLP, which encodes a flavodoxin-like protein, and thereby repress PuFLP mRNA level to facilitate oospore formation. Phenotypes similar to PuM90-knockout mutants were observed with overexpression of PuFLP, mutation of key amino acids in the TRM of PuM90, or mutation of the 3′-UTR binding site in PuFLP. The results demonstrated that a specific interaction of the RNA-binding protein PuM90 with the 3′-UTR of PuFLP mRNA at the post-transcriptional regulation level is critical for the sexual reproduction of P. ultimum. Oomycetes are a class of eukaryotic microorganisms with life cycles and growth habits similar to filamentous fungi, but are not true fungi. Although sexual reproduction, which produce oospores, is an essential stage of life cycle, the functions of critical regulators in this biological process remain unclear due to a lack of genome editing technologies and functional genomic studies in oomycetes. In this study, we developed the first CRISPR/Cas9 system-mediated gene knockout and in situ complementation methods for Pythium ultimum, a notorious oomycete pathogen that is responsible for a variety of diseases in a broad range of plant species. We further identified the Puf family RNA-binding protein PuM90 and the flavodoxin-like protein PuFLP as major functional factors involved in P. ultimum oospore formation. We proposed a new model that PuM90 acts as a stage-specific post-transcriptional regulator by specifically binding to the 3′-UTR of PuFLP and then repressing PuFLP mRNA level. This study describes new technologies and data that will help to elucidate sexual reproduction and post-transcriptional regulation in oomycetes.
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Affiliation(s)
- Hui Feng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Chuanxu Wan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Zhipeng Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Haibin Jiang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Maozhu Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
- * E-mail:
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26
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Kochan DZ, Mawer JSP, Massen J, Tishinov K, Parekh S, Graef M, Spang A, Tessarz P. The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription. J Cell Sci 2021; 134:jcs259051. [PMID: 34350963 PMCID: PMC8353526 DOI: 10.1242/jcs.259051] [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: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a Saccharomyces cerevisiae strain harbouring the H3K56A mutation, which is known to perturb chromatin structure and nascent transcription. We identified Puf5 (also known as Mpt5) as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs, and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A cells compared to wild-type cells. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing deregulated nascent transcription to maintain physiological mRNA levels.
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Affiliation(s)
- David Z. Kochan
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Julia S. P. Mawer
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Kiril Tishinov
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Martin Graef
- Max Planck Research Group ‘Autophagy and Cellular Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anne Spang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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27
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Voronina AS, Pshennikova ES. mRNPs: Structure and role in development. Cell Biochem Funct 2021; 39:832-843. [PMID: 34212408 DOI: 10.1002/cbf.3656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 11/11/2022]
Abstract
In eukaryotic cells, mRNA molecules are coated with numerous RNA-binding proteins and so exist in ribonucleoproteins (mRNPs). The proteins associated with the mRNA regulate the fate of mRNA, including its localization, translation and decay. Before activation of translation, the mRNA does not display any template functions-it is masked. The coordinated activity of certain RNA-binding proteins determines the future fate of each mRNA individually. In embryo development, the temporal and spatial regulation of translation can cause a situation when the mRNA and the encoded protein are localized in different compartments and so the differentiation of the cells can be determined. The fundamentals of regulation of the mRNAs fate and functioning in nerves are similar to those already described for oo- and embryogenesis. Disorders in the mRNA masking and demasking result in the emergence of various diseases, in particular cancers and neuro-degenerative diseases.
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Affiliation(s)
- Anna S Voronina
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena S Pshennikova
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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28
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Turner DJ, Turner M. RNA Binding Proteins As Regulators of Oxidative Stress Identified by a Targeted CRISPR-Cas9 Single Guide RNA Library. CRISPR J 2021; 4:427-437. [PMID: 34096786 PMCID: PMC8236562 DOI: 10.1089/crispr.2020.0116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing system has been broadly adopted for high-throughput genetic screens. However, the application of genome-wide single guide RNA (sgRNA) libraries can be challenging. We generated a custom sgRNA library, an order of magnitude smaller than genome-wide alternatives, to facilitate the genetic screening of RNA binding proteins (RBPs). We demonstrated the utility of our reagent in a genetic screen for RBPs that conveyed cellular resistance or sensitivity to oxidative stress induced by paraquat. This identified that CSDE1 and STRAP, proteins that interact with each other, convey sensitivity to oxidative stress and that Pumilio homologues (PUM1 and PUM2) convey resistance. Targeting eIF4-E1 and -A1 protected cells from high-dose paraquat, whereas eIF4E2 targeted cells did less well. We also found that G3BP1 promoted sensitivity to a low dose of paraquat but protected cells at a higher dose. Our study highlights the use of genetic screens to identify roles of RBPs and identifies novel genes regulating sensitivity to oxidative stress.
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Affiliation(s)
- David J. Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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29
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Wilson KA, Kung RW, D'souza S, Wetmore SD. Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes. Nucleic Acids Res 2021; 49:2213-2225. [PMID: 33544852 PMCID: PMC7913691 DOI: 10.1093/nar/gkab008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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30
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Shropshire JD, Kalra M, Bordenstein SR. Evolution-guided mutagenesis of the cytoplasmic incompatibility proteins: Identifying CifA's complex functional repertoire and new essential regions in CifB. PLoS Pathog 2020; 16:e1008794. [PMID: 32813725 PMCID: PMC7458348 DOI: 10.1371/journal.ppat.1008794] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/31/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022] Open
Abstract
Wolbachia are the world's most common, maternally-inherited, arthropod endosymbionts. Their worldwide distribution is due, in part, to a selfish drive system termed cytoplasmic incompatibility (CI) that confers a relative fitness advantage to females that transmit Wolbachia to their offspring. CI results in embryonic death when infected males mate with uninfected females but not infected females. Under the Two-by-One genetic model of CI, males expressing the two phage WO proteins CifA and CifB cause CI, and females expressing CifA rescue CI. While each protein is predicted to harbor three functional domains, there is no knowledge on how sites across these Cif domains, rather than in any one particular domain, contribute to CI and rescue. Here, we use evolution-guided, substitution mutagenesis of conserved amino acids across the Cif proteins, coupled with transgenic expression in uninfected Drosophila melanogaster, to determine the functional impacts of conserved residues evolving mostly under purifying selection. We report that amino acids in CifA's N-terminal unannotated region and annotated catalase-related domain are important for both complete CI and rescue, whereas C-terminal residues in CifA's putative domain of unknown function are solely important for CI. Moreover, conserved CifB amino acids in the predicted nucleases, peptidase, and unannotated regions are essential for CI. Taken together, these findings indicate that (i) all CifA amino acids determined to be crucial in rescue are correspondingly crucial in CI, (ii) an additional set of CifA amino acids are uniquely important in CI, and (iii) CifB amino acids across the protein, rather than in one particular domain, are all crucial for CI. We discuss how these findings advance an expanded view of Cif protein evolution and function, inform the mechanistic and biochemical bases of Cif-induced CI/rescue, and continue to substantiate the Two-by-One genetic model of CI.
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Affiliation(s)
- J. Dylan Shropshire
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (JDS); (SRB)
| | - Mahip Kalra
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail: (JDS); (SRB)
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