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Agrawal K, Prabhakar S, Bakthavachalu B, Chaturvedi D. Distinct developmental patterns in Anopheles stephensi organ systems. Dev Biol 2024; 508:107-122. [PMID: 38272285 PMCID: PMC7615899 DOI: 10.1016/j.ydbio.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/01/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Anatomical profiles of insects inform vector biology, comparative development and evolutionary studies with applications in forensics, agriculture and disease control. This study presents a comprehensive, high-resolution developmental profile of Anopheles stephensi, encompassing larval, pupal, and adult stages, obtained through microCT scanning. The results indicate in situ anatomical changes in most organ systems, including the central nervous system, eyes, musculature, alimentary canal, salivary glands, and ovaries, among other organ systems, except for the developing heart. We find significant differences in the mosquito gut, body-wall, and flight muscle development during metamorphosis from other dipterans like Drosophila. Specifically, indirect flight muscle specification and growth can be traced back at least to the 4th instar A. stephensi larvae, as opposed to post-puparial development in other Dipterans like Drosophila and Calliphora. Further, while Drosophila larval body-wall muscles and gut undergo histolysis, changes to these organs during mosquito metamorphosis are less pronounced. These observations, and raw data therein may serve as a reference for studies on the development and the genetics of mosquitoes. Overall, the detailed developmental profile of A. stephensi presented here illuminates the unique anatomy and developmental processes of Culicidae, with important implications for vector biology, disease control, and comparative evolutionary studies.
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Affiliation(s)
- Khushboo Agrawal
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, 560065, India; School of Biotechnology, Amrita University, Kollam, 690525, Kerala, India
| | - Sunil Prabhakar
- Centre for Cellular and Molecular Platforms, Bellary Road, Bangalore, 560065, India
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, 560065, India; School of Basic Sciences, Indian Institute of Technology, Mandi, 175005, India.
| | - Dhananjay Chaturvedi
- National Centre for Biological Sciences, TIFR, Bangalore, 560065, India; CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.
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2
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Prasad A, Sreedharan S, Bakthavachalu B, Laxman S. Eggs of the mosquito Aedes aegypti survive desiccation by rewiring their polyamine and lipid metabolism. PLoS Biol 2023; 21:e3002342. [PMID: 37874799 PMCID: PMC10597479 DOI: 10.1371/journal.pbio.3002342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Upon water loss, some organisms pause their life cycles and escape death. While widespread in microbes, this is less common in animals. Aedes mosquitoes are vectors for viral diseases. Aedes eggs can survive dry environments, but molecular and cellular principles enabling egg survival through desiccation remain unknown. In this report, we find that Aedes aegypti eggs, in contrast to Anopheles stephensi, survive desiccation by acquiring desiccation tolerance at a late developmental stage. We uncover unique proteome and metabolic state changes in Aedes embryos during desiccation that reflect reduced central carbon metabolism, rewiring towards polyamine production, and enhanced lipid utilisation for energy and polyamine synthesis. Using inhibitors targeting these processes in blood-fed mosquitoes that lay eggs, we infer a two-step process of desiccation tolerance in Aedes eggs. The metabolic rewiring towards lipid breakdown and dependent polyamine accumulation confers resistance to desiccation. Furthermore, rapid lipid breakdown is required to fuel energetic requirements upon water reentry to enable larval hatching and survival upon rehydration. This study is fundamental to understanding Aedes embryo survival and in controlling the spread of these mosquitoes.
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Affiliation(s)
- Anjana Prasad
- Tata Institute for Genetics and Society (TIGS) Centre at inStem, Bangalore, India
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society (TIGS) Centre at inStem, Bangalore, India
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem), Bangalore, India
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3
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Chen N, Zhang Y, Adel M, Kuklin EA, Reed ML, Mardovin JD, Bakthavachalu B, VijayRaghavan K, Ramaswami M, Griffith LC. Local translation provides the asymmetric distribution of CaMKII required for associative memory formation. Curr Biol 2022; 32:2730-2738.e5. [PMID: 35545085 DOI: 10.1016/j.cub.2022.04.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/18/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
How compartment-specific local proteomes are generated and maintained is inadequately understood, particularly in neurons, which display extreme asymmetries. Here we show that local enrichment of Ca2+/calmodulin-dependent protein kinase II (CaMKII) in axons of Drosophila mushroom body neurons is necessary for cellular plasticity and associative memory formation. Enrichment is achieved via enhanced axoplasmic translation of CaMKII mRNA, through a mechanism requiring the RNA-binding protein Mub and a 23-base Mub-recognition element in the CaMKII 3' UTR. Perturbation of either dramatically reduces axonal, but not somatic, CaMKII protein without altering the distribution or amount of mRNA in vivo, and both are necessary and sufficient to enhance axonal translation of reporter mRNA. Together, these data identify elevated levels of translation of an evenly distributed mRNA as a novel strategy for generating subcellular biochemical asymmetries. They further demonstrate the importance of distributional asymmetry in the computational and biological functions of neurons.
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Affiliation(s)
- Nannan Chen
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Yunpeng Zhang
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Mohamed Adel
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Elena A Kuklin
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Martha L Reed
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Jacob D Mardovin
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
| | - Baskar Bakthavachalu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - K VijayRaghavan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology and School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Leslie C Griffith
- Department of Biology, Volen National Center for Complex Systems, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA.
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Singh A, Kandi AR, Jayaprakashappa D, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M, Bakthavachalu B. The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation. Mol Biol Cell 2022; 33:ar25. [PMID: 34985933 PMCID: PMC9250384 DOI: 10.1091/mbc.e21-08-0418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Oxidative stress for 3-hours predominantly resulted in induction or upregulation of stress-responsive mRNAs whose levels peaked during recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for chaperones, including HSP70s, small heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced cytoplasmic SGs that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/Rasputin protein inhibited SG assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced gene expression alterations appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
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Affiliation(s)
- Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arvind Reddy Kandi
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India
| | | | - Guillaume Thuery
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Devam J Purohit
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Rashi Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | | | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India.,Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India.,School of Basic Sciences, Indian Institute of Technology, Mandi 175005, India
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Huelsmeier J, Walker E, Bakthavachalu B, Ramaswami M. A C-terminal ataxin-2 disordered region promotes Huntingtin protein aggregation and neurodegeneration in Drosophila models of Huntington’s disease. G3 Genes|Genomes|Genetics 2021; 11:6385240. [PMID: 34718534 PMCID: PMC8664476 DOI: 10.1093/g3journal/jkab355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/01/2021] [Indexed: 11/15/2022]
Abstract
The Ataxin-2 (Atx2) protein contributes to the progression of neurodegenerative phenotypes in animal models of amyotrophic lateral sclerosis (ALS), type 2 spinocerebellar ataxia (SCA-2), Parkinson’s disease, and Huntington’s disease (HD). However, because the Atx2 protein contains multiple separable activities, deeper understanding requires experiments to address the exact mechanisms by which Atx2 modulates neurodegeneration (ND) progression. Recent work on two ALS models, C9ORF72 and FUS, in Drosophila has shown that a C-terminal intrinsically disordered region (cIDR) of Atx2 protein, required for assembly of ribonucleoprotein (RNP) granules, is essential for the progression of neurodegenerative phenotypes as well as for accumulation of protein inclusions associated with these ALS models. Here, we show that the Atx2-cIDR also similarly contributes to the progression of degenerative phenotypes and accumulation of Huntingtin protein aggregates in Drosophila models of HD. Because Huntingtin is not an established component of RNP granules, these observations support a recently hypothesized, unexpected protein-handling function for RNP granules, which could contribute to the progression of Huntington’s disease and, potentially, other proteinopathies.
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Affiliation(s)
- Joern Huelsmeier
- School of Genetics and Microbiology, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Emily Walker
- School of Genetics and Microbiology, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Baskar Bakthavachalu
- School of Basic Science, Indian Institute of Technology, Mandi, Suran 175075, India
| | - Mani Ramaswami
- School of Genetics and Microbiology, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
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Singh A, Hulsmeier J, Kandi AR, Pothapragada SS, Hillebrand J, Petrauskas A, Agrawal K, RT K, Thiagarajan D, Jayaprakashappa D, VijayRaghavan K, Ramaswami M, Bakthavachalu B. Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation. eLife 2021; 10:e60326. [PMID: 33689682 PMCID: PMC7946432 DOI: 10.7554/elife.60326] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Ataxin-2 (Atx2) is a translational control molecule mutated in spinocerebellar ataxia type II and amyotrophic lateral sclerosis. While intrinsically disordered domains (IDRs) of Atx2 facilitate mRNP condensation into granules, how IDRs work with structured domains to enable positive and negative regulation of target mRNAs remains unclear. Using the Targets of RNA-Binding Proteins Identified by Editing technology, we identified an extensive data set of Atx2-target mRNAs in the Drosophila brain and S2 cells. Atx2 interactions with AU-rich elements in 3'UTRs appear to modulate stability/turnover of a large fraction of these target mRNAs. Further genomic and cell biological analyses of Atx2 domain deletions demonstrate that Atx2 (1) interacts closely with target mRNAs within mRNP granules, (2) contains distinct protein domains that drive or oppose RNP-granule assembly, and (3) has additional essential roles outside of mRNP granules. These findings increase the understanding of neuronal translational control mechanisms and inform strategies for Atx2-based interventions under development for neurodegenerative disease.
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Affiliation(s)
- Amanjot Singh
- National Centre for Biological SciencesBangaloreIndia
| | - Joern Hulsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College DublinDublinIreland
| | - Arvind Reddy Kandi
- National Centre for Biological SciencesBangaloreIndia
- Tata Institute for Genetics and Society Centre at inStem, Bellary RoadBangaloreIndia
| | | | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College DublinDublinIreland
| | - Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College DublinDublinIreland
| | - Khushboo Agrawal
- Tata Institute for Genetics and Society Centre at inStem, Bellary RoadBangaloreIndia
- School of Biotechnology, Amrita Vishwa Vidyapeetham UniversityKollamIndia
| | - Krishnan RT
- National Centre for Biological SciencesBangaloreIndia
| | | | | | | | - Mani Ramaswami
- National Centre for Biological SciencesBangaloreIndia
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College DublinDublinIreland
| | - Baskar Bakthavachalu
- National Centre for Biological SciencesBangaloreIndia
- Tata Institute for Genetics and Society Centre at inStem, Bellary RoadBangaloreIndia
- School of Basic Sciences, Indian Institute of TechnologyMandiIndia
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7
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Bakthavachalu B, Huelsmeier J, Sudhakaran IP, Hillebrand J, Singh A, Petrauskas A, Thiagarajan D, Sankaranarayanan M, Mizoue L, Anderson EN, Pandey UB, Ross E, VijayRaghavan K, Parker R, Ramaswami M. RNP-Granule Assembly via Ataxin-2 Disordered Domains Is Required for Long-Term Memory and Neurodegeneration. Neuron 2018; 98:754-766.e4. [PMID: 29772202 DOI: 10.1016/j.neuron.2018.04.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/07/2018] [Accepted: 04/23/2018] [Indexed: 02/07/2023]
Abstract
Human Ataxin-2 is implicated in the cause and progression of amyotrophic lateral sclerosis (ALS) and type 2 spinocerebellar ataxia (SCA-2). In Drosophila, a conserved atx2 gene is essential for animal survival as well as for normal RNP-granule assembly, translational control, and long-term habituation. Like its human homolog, Drosophila Ataxin-2 (Atx2) contains polyQ repeats and additional intrinsically disordered regions (IDRs). We demonstrate that Atx2 IDRs, which are capable of mediating liquid-liquid phase transitions in vitro, are essential for efficient formation of neuronal mRNP assemblies in vivo. Remarkably, ΔIDR mutants that lack neuronal RNP granules show normal animal development, survival, and fertility. However, they show defects in long-term memory formation/consolidation as well as in C9ORF72 dipeptide repeat or FUS-induced neurodegeneration. Together, our findings demonstrate (1) that higher-order mRNP assemblies contribute to long-term neuronal plasticity and memory, and (2) that a targeted reduction in RNP-granule formation efficiency can alleviate specific forms of neurodegeneration.
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Affiliation(s)
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | | | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | - Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland
| | | | | | - Laura Mizoue
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Eric Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - K VijayRaghavan
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Roy Parker
- Department of Chemistry, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India; Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2, Ireland.
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Wein N, Vulin A, Falzarano MS, Szigyarto CAK, Maiti B, Findlay A, Heller KN, Uhlén M, Bakthavachalu B, Messina S, Vita G, Passarelli C, Brioschi S, Bovolenta M, Neri M, Gualandi F, Wilton SD, Rodino-Klapac LR, Yang L, Dunn DM, Schoenberg DR, Weiss RB, Howard MT, Ferlini A, Flanigan KM. Erratum: Corrigendum: Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med 2015; 21:537. [DOI: 10.1038/nm0515-537c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mukherjee C, Bakthavachalu B, Schoenberg DR. The cytoplasmic capping complex assembles on adapter protein nck1 bound to the proline-rich C-terminus of Mammalian capping enzyme. PLoS Biol 2014; 12:e1001933. [PMID: 25137142 PMCID: PMC4138027 DOI: 10.1371/journal.pbio.1001933] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/11/2014] [Indexed: 12/03/2022] Open
Abstract
mRNA capping and decapping requires a cytoplasmic complex to maintain and/or restore the 5′ cap on a subset of the mammalian transcriptome; Nck1, an SH2/SH3 adapter, creates a scaffold upon which the cytoplasmic capping complex forms. Cytoplasmic capping is catalyzed by a complex that contains capping enzyme (CE) and a kinase that converts RNA with a 5′-monophosphate end to a 5′ diphosphate for subsequent addition of guanylic acid (GMP). We identify the proline-rich C-terminus as a new domain of CE that is required for its participation in cytoplasmic capping, and show the cytoplasmic capping complex assembles on Nck1, an adapter protein with functions in translation and tyrosine kinase signaling. Binding is specific to Nck1 and is independent of RNA. We show by sedimentation and gel filtration that Nck1 and CE are together in a larger complex, that the complex can assemble in vitro on recombinant Nck1, and Nck1 knockdown disrupts the integrity of the complex. CE and the 5′ kinase are juxtaposed by binding to the adjacent domains of Nck1, and cap homeostasis is inhibited by Nck1 with inactivating mutations in each of these domains. These results identify a new domain of CE that is specific to its function in cytoplasmic capping, and a new role for Nck1 in regulating gene expression through its role as the scaffold for assembly of the cytoplasmic capping complex. We previously described a cyclical process of mRNA decapping and recapping termed “cap homeostasis.” Recapping is catalyzed by a complex of cytoplasmic proteins that includes the enzyme known to catalyze nuclear capping, and a kinase that converts RNA with a 5′-monophosphate end to a 5′-diphosphate capping substrate. The current study shows these two enzymatic activities are brought together in the cytoplasmic capping complex as both bind to adjacent domains of the adapter protein Nck1. Nck1 is a cytoplasmic protein best known for transducing receptor tyrosine kinase signaling. We identify a proline-rich sequence at the C-terminus of a human capping enzyme that is required for binding to Nck1, and we show that this interaction is required for integrity of the cytoplasmic capping complex. Depletion of Nck1 causes the cytoplasmic capping complex to dissociate. The inhibition of cytoplasmic capping by Nck1 with mutations in either the 5′-kinase or capping enzyme binding sites identified a functional role for Nck1 in cap homeostasis and a previously unknown function for Nck1 in cell biology.
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Affiliation(s)
- Chandrama Mukherjee
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Baskar Bakthavachalu
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Daniel R. Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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10
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Wein N, Vulin A, Falzarano MS, Szigyarto CAK, Maiti B, Findlay A, Heller KN, Uhlén M, Bakthavachalu B, Messina S, Vita G, Passarelli C, Brioschi S, Bovolenta M, Neri M, Gualandi F, Wilton SD, Rodino-Klapac LR, Yang L, Dunn DM, Schoenberg DR, Weiss RB, Howard MT, Ferlini A, Flanigan KM. Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med 2014; 20:992-1000. [PMID: 25108525 PMCID: PMC4165597 DOI: 10.1038/nm.3628] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/05/2014] [Indexed: 12/26/2022]
Abstract
Most mutations that truncate the reading frame of the DMD gene cause loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity can result from alternate translation initiation beginning in DMD exon 6 that leads to expression of a highly functional N-truncated dystrophin. This novel isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid-inducible. IRES activity is confirmed in patient muscle by both peptide sequencing and ribosome profiling. Generation of a truncated reading frame upstream of the IRES by exon skipping leads to synthesis of a functional N-truncated isoform in both patient-derived cell lines and in a new DMD mouse model, where expression protects muscle from contraction-induced injury and corrects muscle force to the same level as control mice. These results support a novel therapeutic approach for patients with mutations within the 5’ exons of DMD.
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Affiliation(s)
- Nicolas Wein
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2]
| | - Adeline Vulin
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2]
| | - Maria S Falzarano
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Christina Al-Khalili Szigyarto
- Department of Proteomics and Nanobiotechnology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Baijayanta Maiti
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew Findlay
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Kristin N Heller
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Mathias Uhlén
- Department of Proteomics and Nanobiotechnology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Baskar Bakthavachalu
- 1] Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA. [2] Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sonia Messina
- Department of Neuroscience, University of Messina and Centro Clinico Nemo Sud, Messina, Italy
| | - Giuseppe Vita
- Department of Neuroscience, University of Messina and Centro Clinico Nemo Sud, Messina, Italy
| | | | | | | | | | - Francesca Gualandi
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Steve D Wilton
- Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, Australia
| | - Louise R Rodino-Klapac
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Lin Yang
- Division of Biomedical Informatics, Department of Computer Science, University of Kentucky Lexington, Kentucky, USA
| | - Diane M Dunn
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Daniel R Schoenberg
- 1] Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA. [2] Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Michael T Howard
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alessandra Ferlini
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Kevin M Flanigan
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA. [3] Department of Neurology, The Ohio State University, Columbus, Ohio, USA
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11
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Mukherjee C, Patil DP, Kennedy BA, Bakthavachalu B, Bundschuh R, Schoenberg DR. Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Rep 2012; 2:674-84. [PMID: 22921400 DOI: 10.1016/j.celrep.2012.07.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/20/2012] [Accepted: 07/26/2012] [Indexed: 10/28/2022] Open
Abstract
The notion that decapping leads irreversibly to messenger RNA (mRNA) decay was contradicted by the identification of capped transcripts missing portions of their 5' ends and a cytoplasmic complex that can restore the cap on uncapped mRNAs. In this study, we used accumulation of uncapped transcripts in cells inhibited for cytoplasmic capping to identify the targets of this pathway. Inhibition of cytoplasmic capping results in the destabilization of some transcripts and the redistribution of others from polysomes to nontranslating messenger ribonucleoproteins, where they accumulate in an uncapped state. Only a portion of the mRNA transcriptome is affected by cytoplasmic capping, and its targets encode proteins involved in nucleotide binding, RNA and protein localization, and the mitotic cell cycle. The 3' untranslated regions of recapping targets are enriched for AU-rich elements and microRNA binding sites, both of which function in cap-dependent mRNA silencing. These findings identify a cyclical process of decapping and recapping that we term cap homeostasis.
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Gu SQ, Bakthavachalu B, Han J, Patil DP, Otsuka Y, Guda C, Schoenberg DR. Identification of the human PMR1 mRNA endonuclease as an alternatively processed product of the gene for peroxidasin-like protein. RNA 2012; 18:1186-1196. [PMID: 22543864 PMCID: PMC3358641 DOI: 10.1261/rna.031369.111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/07/2012] [Indexed: 05/31/2023]
Abstract
The PMR1 endonuclease was discovered in Xenopus liver and identified as a member of the large and diverse peroxidase gene family. The peroxidase genes arose from multiple duplication and rearrangement events, and their high degree of sequence similarity confounded attempts to identify human PMR1. The functioning of PMR1 in mRNA decay depends on the phosphorylation of a tyrosine in the C-terminal polysome targeting domain by c-Src. The sequences of regions that are required for c-Src binding and phosphorylation of Xenopus PMR1 were used to inform a bioinformatics search that identified two related genes as potential candidates for human PMR1: peroxidasin homolog (PXDN) and peroxidasin homolog-like (PXDNL) protein. Although each of these genes is predicted to encode a large, multidomain membrane-bound peroxidase, alternative splicing of PXDNL pre-mRNA yields a transcript whose predicted product is a 57-kDa protein with 42% sequence identity to Xenopus PMR1. Results presented here confirm the existence of the predicted 57-kDa protein, show this is the only form of PXDNL detected in any of the human cell lines examined, and confirm its identity as human PMR1. Like the Xenopus protein, human PMR1 binds to c-Src, is tyrosine phosphorylated, sediments on polysomes, and catalyzes the selective decay of a PMR1 substrate mRNA. Importantly, the expression of human PMR1 stimulates cell motility in a manner similar to that of the Xenopus PMR1 expressed in human cells, thus providing definitive evidence linking endonuclease decay to the regulation of cell motility.
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Affiliation(s)
- Shan-Qing Gu
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
| | - Baskar Bakthavachalu
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
| | - Joonhee Han
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
| | - Deepak P. Patil
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
| | - Yuichi Otsuka
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
| | - Chittibabu Guda
- Center for Bioinformatics and Systems Biology, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68118-5145, USA
| | - Daniel R. Schoenberg
- Center for RNA Biology
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210-1218, USA
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Kulkarni SD, Muralidharan B, Panda AC, Bakthavachalu B, Vindu A, Seshadri V. Glucose-stimulated translation regulation of insulin by the 5' UTR-binding proteins. J Biol Chem 2011; 286:14146-56. [PMID: 21357685 DOI: 10.1074/jbc.m110.190553] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Insulin is the key regulator of glucose homeostasis in mammals, and glucose-stimulated insulin biosynthesis is essential for maintaining glucose levels in a narrow range in mammals. Glucose specifically promotes the translation of insulin in pancreatic β-islet, and the untranslated regions of insulin mRNA play a role in such regulation. Specific factors in the β-islets bind to the insulin 5' UTR and regulate its translation. In the present study we identify protein-disulfide isomerase (PDI) as a key regulator of glucose-stimulated insulin biosynthesis. We show that both in vitro and in vivo PDI can specifically associate with the 5' UTR of insulin mRNA. Immunodepletion of PDI from the islet extract results in loss of glucose-stimulated translation indicating a critical role for PDI in insulin biosynthesis. Similarly, transient overexpression of PDI resulted in specific translation activation by glucose. We show that the RNA binding activity of PDI is mediated through PABP. PDI catalyzes the reduction of the PABP disulfide bond resulting in specific binding of PABP to the insulin 5' UTR. We also show that glucose stimulation of the islets results in activation of a specific kinase that can phosphorylate PDI. These findings identify PDI and PABP as important players in glucose homeostasis.
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Panda AC, Kulkarni SD, Muralidharan B, Bakthavachalu B, Seshadri V. Novel splice variant of mouse insulin2 mRNA: implications for insulin expression. FEBS Lett 2010; 584:1169-73. [PMID: 20153322 DOI: 10.1016/j.febslet.2010.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/29/2022]
Abstract
Insulin is a secreted peptide that controls glucose homeostasis in mammals, and insulin biosynthesis is regulated by glucose at many levels. Rodent insulin is encoded by two non-allelic genes. We have identified a novel splice variant of the insulin2 gene in mice that constitutes about 75% of total insulin2 mRNA. The alternate splicing does not alter the ORF but reduces the 5'UTR by 12 bases. A reporter gene containing the novel short 5'UTR, is more efficiently expressed in cells, suggesting that alternative splicing of insulin mRNA in mice could result in an additional level of regulation in insulin biosynthesis.
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Muralidharan B, Bakthavachalu B, Pathak A, Seshadri V. A minimal element in 5'UTR of insulin mRNA mediates its translational regulation by glucose. FEBS Lett 2007; 581:4103-8. [PMID: 17686473 DOI: 10.1016/j.febslet.2007.07.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 07/16/2007] [Accepted: 07/24/2007] [Indexed: 11/17/2022]
Abstract
Glucose induced translation of insulin in pancreatic beta cells is mediated by the 5'UTR of insulin mRNA. We determined the minimal sequence/structure in the 5'UTR of rat insulin gene1 for this regulation. We show that specific factors in the pancreatic islets bind to the 5'UTR of the insulin mRNA upon glucose stimulation. We identified a minimal 29-nucleotide element in the 5'UTR that is sufficient to form the complex, and confer glucose mediated translation activation. Conserved residues in the predicted stem loop region of the un-translated region (UTR) seem to be important for the complex formation and the translation regulation.
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