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Earwood R, Ninomiya H, Wang H, Shimada IS, Stroud M, Perez D, Uuganbayar U, Yamada C, Akiyama-Miyoshi T, Stefanovic B, Kato Y. The binding of LARP6 and DNAAF6 in biomolecular condensates influences ciliogenesis of multiciliated cells. J Biol Chem 2024; 300:107373. [PMID: 38762183 PMCID: PMC11208920 DOI: 10.1016/j.jbc.2024.107373] [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: 12/08/2023] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
Motile cilia on the cell surface produce fluid flows in the body and abnormalities in motile cilia cause primary ciliary dyskinesia. Dynein axonemal assembly factor 6 (DNAAF6), a causative gene of primary ciliary dyskinesia, was isolated as an interacting protein with La ribonucleoprotein 6 (LARP6) that regulates ciliogenesis in multiciliated cells (MCCs). In MCCs of Xenopus embryos, LARP6 and DNAAF6 were colocalized in biomolecular condensates termed dynein axonemal particles and synergized to control ciliogenesis. Moreover, tubulin alpha 1c-like mRNA encoding α-tubulin protein, that is a major component of ciliary axoneme, was identified as a target mRNA regulated by binding LARP6. While DNAAF6 was necessary for high α-tubulin protein expression near the apical side of Xenopus MCCs during ciliogenesis, its mutant, which abolishes binding with LARP6, was unable to restore the expression of α-tubulin protein near the apical side of MCCs in Xenopus DNAAF6 morphant. These results indicated that the binding of LARP6 and DNAAF6 in dynein axonemal particles regulates highly expressed α-tubulin protein near the apical side of Xenopus MCCs during ciliogenesis.
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Affiliation(s)
- Ryan Earwood
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Hiromasa Ninomiya
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Hao Wang
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Issei S Shimada
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Mia Stroud
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Diana Perez
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA
| | - Udval Uuganbayar
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Chisato Yamada
- Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan
| | - Toru Akiyama-Miyoshi
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Branko Stefanovic
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA.
| | - Yoichi Kato
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA; Department of Cell Biology, Nagoya City University, Graduate School of Medical Sciences, Mizuho-ku, Nagoya, Japan.
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Xiang X, Deng Q, Zheng Y, He Y, Ji D, Vejlupkova Z, Fowler JE, Zhou L. Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen. BMC PLANT BIOLOGY 2024; 24:348. [PMID: 38684961 PMCID: PMC11057080 DOI: 10.1186/s12870-024-05054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. RESULTS In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type. CONCLUSIONS The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination.
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Affiliation(s)
- Xiaoqin Xiang
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Qianxia Deng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi Zheng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi He
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Dongpu Ji
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Lian Zhou
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry. Genes (Basel) 2023; 14:genes14030665. [PMID: 36980938 PMCID: PMC10048728 DOI: 10.3390/genes14030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023] Open
Abstract
Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.
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Chen L, Su Y, Yin B, Li S, Cheng X, He Y, Jia C. LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen. J Invest Dermatol 2022; 142:2395-2405.e7. [PMID: 35176288 DOI: 10.1016/j.jid.2022.01.028] [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] [Received: 01/06/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
Keloid is a skin fibroproliferative disease currently having no uniformly successful treatment. The lesion is composed of actively proliferating and collagen-overproducing fibroblasts. LARP6 is an RNA-binding protein able to regulate collagen synthesis in fibroblasts and to promote proliferation and invasion of tumor cells. To explore LARP6's likely functions in keloid pathogenesis, we performed immunohistochemistry staining on human keloid tissues and discovered markedly upregulated LARP6 expression in lesion fibroblasts compared with that of normal skin and hypertrophic scar tissues. In addition, the keloid tissue‒derived fibroblasts showed constitutive upregulation of LARP6 expression as well as significantly upregulated mRNA and protein expressions of type I collagen and enhanced cell proliferation and invasive behavior in cell culture system. Intriguingly, LARP6 knockdown by targeting with small interfering RNAs significantly inhibited type I collagen expression, proliferation, and invasion capability of keloid tissue‒derived fibroblasts relative to that of normal skin‒ and hypertrophic scar‒derived fibroblasts and control keloid tissue‒derived fibroblasts that were transfected with a scrambled small interfering RNA. In conclusion, the abnormally upregulated expression of LARP6 in fibroblasts may play an important role in the growth and invasive behavior of keloid lesions.
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Affiliation(s)
- Lingxi Chen
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yingjun Su
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Plastic Surgery Hospital, Xi'an International Medical Center Hospital, Xi'an, China
| | - Bin Yin
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Shu Li
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xialin Cheng
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yan He
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chiyu Jia
- Department of Burns and Plastic Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
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Billey E, Hafidh S, Cruz-Gallardo I, Litholdo CG, Jean V, Carpentier MC, Picart C, Kumar V, Kulichova K, Maréchal E, Honys D, Conte MR, Deragon JM, Bousquet-Antonelli C. LARP6C orchestrates posttranscriptional reprogramming of gene expression during hydration to promote pollen tube guidance. THE PLANT CELL 2021; 33:2637-2661. [PMID: 34124761 PMCID: PMC8408461 DOI: 10.1093/plcell/koab131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2021] [Indexed: 05/15/2023]
Abstract
Increasing evidence suggests that posttranscriptional regulation is a key player in the transition between mature pollen and the progamic phase (from pollination to fertilization). Nonetheless, the actors in this messenger RNA (mRNA)-based gene expression reprogramming are poorly understood. We demonstrate that the evolutionarily conserved RNA-binding protein LARP6C is necessary for the transition from dry pollen to pollen tubes and the guided growth of pollen tubes towards the ovule in Arabidopsis thaliana. In dry pollen, LARP6C binds to transcripts encoding proteins that function in lipid synthesis and homeostasis, vesicular trafficking, and polarized cell growth. LARP6C also forms cytoplasmic granules that contain the poly(A) binding protein and possibly represent storage sites for translationally silent mRNAs. In pollen tubes, the loss of LARP6C negatively affects the quantities and distribution of storage lipids, as well as vesicular trafficking. In Nicotiana benthamiana leaf cells and in planta, analysis of reporter mRNAs designed from the LARP6C target MGD2 provided evidence that LARP6C can shift from a repressor to an activator of translation when the pollen grain enters the progamic phase. We propose that LARP6C orchestrates the timely posttranscriptional regulation of a subset of mRNAs in pollen during the transition from the quiescent to active state and along the progamic phase to promote male fertilization in plants.
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Affiliation(s)
- Elodie Billey
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Celso G. Litholdo
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Viviane Jean
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Katarina Kulichova
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS, CEA, INRAE, Université Grenoble Alpes, IRIG, CEA Grenoble, 38054 Grenoble, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Jean-Marc Deragon
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 5, France
| | - Cécile Bousquet-Antonelli
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Billey E, Hafidh S, Cruz-Gallardo I, Litholdo CG, Jean V, Carpentier MC, Picart C, Kumar V, Kulichova K, Maréchal E, Honys D, Conte MR, Deragon JM, Bousquet-Antonelli C. LARP6C orchestrates posttranscriptional reprogramming of gene expression during hydration to promote pollen tube guidance. THE PLANT CELL 2021; 33:2637-2661. [PMID: 34124761 DOI: 10.1101/2020.11.27.401307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2021] [Indexed: 05/19/2023]
Abstract
Increasing evidence suggests that posttranscriptional regulation is a key player in the transition between mature pollen and the progamic phase (from pollination to fertilization). Nonetheless, the actors in this messenger RNA (mRNA)-based gene expression reprogramming are poorly understood. We demonstrate that the evolutionarily conserved RNA-binding protein LARP6C is necessary for the transition from dry pollen to pollen tubes and the guided growth of pollen tubes towards the ovule in Arabidopsis thaliana. In dry pollen, LARP6C binds to transcripts encoding proteins that function in lipid synthesis and homeostasis, vesicular trafficking, and polarized cell growth. LARP6C also forms cytoplasmic granules that contain the poly(A) binding protein and possibly represent storage sites for translationally silent mRNAs. In pollen tubes, the loss of LARP6C negatively affects the quantities and distribution of storage lipids, as well as vesicular trafficking. In Nicotiana benthamiana leaf cells and in planta, analysis of reporter mRNAs designed from the LARP6C target MGD2 provided evidence that LARP6C can shift from a repressor to an activator of translation when the pollen grain enters the progamic phase. We propose that LARP6C orchestrates the timely posttranscriptional regulation of a subset of mRNAs in pollen during the transition from the quiescent to active state and along the progamic phase to promote male fertilization in plants.
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Affiliation(s)
- Elodie Billey
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Celso G Litholdo
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Viviane Jean
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Katarina Kulichova
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 CNRS, CEA, INRAE, Université Grenoble Alpes, IRIG, CEA Grenoble, 38054 Grenoble, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Jean-Marc Deragon
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Institut Universitaire de France, 75231 Paris Cedex 5, France
| | - Cécile Bousquet-Antonelli
- Laboratoire Génome et Développement des Plantes, UMR5096, CNRS, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
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Kim H, Lee YS, Kim SM, Jang S, Choi H, Lee JW, Kim TD, Kim VN. RNA demethylation by FTO stabilizes the FOXJ1 mRNA for proper motile ciliogenesis. Dev Cell 2021; 56:1118-1130.e6. [PMID: 33761320 DOI: 10.1016/j.devcel.2021.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 12/10/2020] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Adenosine N6-methylation (m6A) is one of the most pervasive mRNA modifications, and yet the physiological significance of m6A removal (demethylation) remains elusive. Here, we report that the m6A demethylase FTO functions as a conserved regulator of motile ciliogenesis. Mechanistically, FTO demethylates and thereby stabilizes the mRNA that encodes the master ciliary transcription factor FOXJ1. Depletion of Fto in Xenopus laevis embryos caused widespread motile cilia defects, and Foxj1 was identified as one of the major phenocritical targets. In primary human airway epithelium, FTO depletion also led to FOXJ1 mRNA destabilization and a severe loss of ciliated cells with an increase of neighboring goblet cells. Consistently, Fto knockout mice showed strong asthma-like phenotypes upon allergen challenge, a result owing to defective ciliated cells in the airway epithelium. Altogether, our study reveals a conserved role of the FTO-FOXJ1 axis in embryonic and homeostatic motile ciliogenesis.
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Affiliation(s)
- Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea.
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seok-Min Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Soohyun Jang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Hyunji Choi
- School of the Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae-Won Lee
- Natural Medicine Research Center, KRIBB, Cheongju, Korea
| | - Tae-Don Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of the Biological Sciences, Seoul National University, Seoul 08826, Korea.
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105217. [PMID: 33276167 DOI: 10.1016/j.marenvres.2020.105217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122, NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
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9
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105214. [PMID: 33221553 DOI: 10.1016/j.marenvres.2020.105214] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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Sheel A, Shao R, Brown C, Johnson J, Hamilton A, Sun D, Oppenheimer J, Smith W, Visconti PE, Markstein M, Bigelow C, Schwartz LM. Acheron/Larp6 Is a Survival Protein That Protects Skeletal Muscle From Programmed Cell Death During Development. Front Cell Dev Biol 2020; 8:622. [PMID: 32850788 PMCID: PMC7405549 DOI: 10.3389/fcell.2020.00622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
The term programmed cell death (PCD) was coined in 1965 to describe the loss of the intersegmental muscles (ISMs) of moths at the end of metamorphosis. While it was subsequently demonstrated that this hormonally controlled death requires de novo gene expression, the signal transduction pathway that couples hormone action to cell death is largely unknown. Using the ISMs from the tobacco hawkmoth Manduca sexta, we have found that Acheron/LARP6 mRNA is induced ∼1,000-fold on the day the muscles become committed to die. Acheron functions as a survival protein that protects cells until cell death is initiated at eclosion (emergence), at which point it becomes phosphorylated and degraded in response to the peptide Eclosion Hormone (EH). Acheron binds to a novel BH3-only protein that we have named BBH1 (BAD/BNIP3 homology 1). BBH1 accumulates on the day the ISMs become committed to die and is presumably liberated when Acheron is degraded. This is correlated with the release and rapid degradation of cytochrome c and the subsequent demise of the cell. RNAi experiments in the fruit fly Drosophila confirmed that loss of Acheron results in precocious ecdysial muscle death while targeting BBH1 prevents death altogether. Acheron is highly expressed in neurons and muscles in humans and drives metastatic processes in some cancers, suggesting that it may represent a novel survival protein that protects terminally differentiated cells and some cancers from death.
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Affiliation(s)
- Ankur Sheel
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
| | - Rong Shao
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Pharmacology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Christine Brown
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Joanne Johnson
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Alexandra Hamilton
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Danhui Sun
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
| | - Julia Oppenheimer
- Department of Biology, Barnard College, Columbia University, New York, NY, United States
| | - Wendy Smith
- Department of Biology, College of Science, Northeastern University, Boston, MA, United States
| | - Pablo E Visconti
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, United States
| | - Michele Markstein
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
| | - Carol Bigelow
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lawrence M Schwartz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, United States
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11
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Hau HTA, Ogundele O, Hibbert AH, Monfries CAL, Exelby K, Wood NJ, Nevarez-Mejia J, Carbajal MA, Fleck RA, Dermit M, Mardakheh FK, Williams-Ward VC, Pipalia TG, Conte MR, Hughes SM. Maternal Larp6 controls oocyte development, chorion formation and elevation. Development 2020; 147:dev187385. [PMID: 32054660 PMCID: PMC7055395 DOI: 10.1242/dev.187385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/23/2020] [Indexed: 12/19/2022]
Abstract
La-related protein 6 (Larp6) is a conserved RNA-binding protein found across eukaryotes that has been suggested to regulate collagen biogenesis, muscle development, ciliogenesis, and various aspects of cell proliferation and migration. Zebrafish have two Larp6 family genes: larp6a and larp6b Viable and fertile single and double homozygous larp6a and larp6b zygotic mutants revealed no defects in muscle structure, and were indistinguishable from heterozygous or wild-type siblings. However, larp6a mutant females produced eggs with chorions that failed to elevate fully and were fragile. Eggs from larp6b single mutant females showed minor chorion defects, but chorions from eggs laid by larp6a;larp6b double mutant females were more defective than those from larp6a single mutants. Electron microscopy revealed defective chorionogenesis during oocyte development. Despite this, maternal zygotic single and double mutants were viable and fertile. Mass spectrometry analysis provided a description of chorion protein composition and revealed significant reductions in a subset of zona pellucida and lectin-type proteins between wild-type and mutant chorions that paralleled the severity of the phenotype. We conclude that Larp6 proteins are required for normal oocyte development, chorion formation and egg activation.
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Affiliation(s)
- Hoi Ting A Hau
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Oluwaseun Ogundele
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Andrew H Hibbert
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Clinton A L Monfries
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Katherine Exelby
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Natalie J Wood
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Jessica Nevarez-Mejia
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | | | - Roland A Fleck
- Centre for Ultrastructural Imaging, King's College London, London SE1 1UL, UK
| | - Maria Dermit
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Victoria C Williams-Ward
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Tapan G Pipalia
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
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12
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Stefanovic B, Manojlovic Z, Vied C, Badger CD, Stefanovic L. Discovery and evaluation of inhibitor of LARP6 as specific antifibrotic compound. Sci Rep 2019; 9:326. [PMID: 30674965 PMCID: PMC6344531 DOI: 10.1038/s41598-018-36841-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 01/17/2023] Open
Abstract
Fibrosis is characterized by excessive production of type I collagen. Biosynthesis of type I collagen in fibrosis is augmented by binding of protein LARP6 to the 5' stem-loop structure (5'SL), which is found exclusively in type I collagen mRNAs. A high throughput screen was performed to discover inhibitors of LARP6 binding to 5'SL, as potential antifibrotic drugs. The screen yielded one compound (C9) which was able to dissociate LARP6 from 5' SL RNA in vitro and to inactivate the binding of endogenous LARP6 in cells. Treatment of hepatic stellate cells (liver cells responsible for fibrosis) with nM concentrations of C9 reduced secretion of type I collagen. In precision cut liver slices, as an ex vivo model of hepatic fibrosis, C9 attenuated the profibrotic response at 1 μM. In prophylactic and therapeutic animal models of hepatic fibrosis C9 prevented development of fibrosis or hindered the progression of ongoing fibrosis when administered at 1 mg/kg. Toxicogenetics analysis revealed that only 42 liver genes changed expression after administration of C9 for 4 weeks, suggesting minimal off target effects. Based on these results, C9 represents the first LARP6 inhibitor with significant antifibrotic activity.
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Affiliation(s)
- Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
| | - Zarko Manojlovic
- Keck School of Medicine of University of Southern California, 1450 Biggy Street, NRT 4510, Los Angeles, CA, 90033, USA
| | - Cynthia Vied
- Translational Science Laboratory, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Crystal-Dawn Badger
- Translational Science Laboratory, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
- Proteomics and Metabolomics Facility, Colorado State University, 401 West Pitkin Street, Fort Collins, CO, 80521, USA
| | - Lela Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
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