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Kamaraju D, Chatterjee M, Papolu PK, Shivakumara TN, Sreevathsa R, Hada A, Rao U. Host-induced RNA interference targeting the neuromotor gene FMRFamide-like peptide-14 (Mi-flp14) perturbs Meloidogyne incognita parasitic success in eggplant. PLANT CELL REPORTS 2024; 43:178. [PMID: 38907748 DOI: 10.1007/s00299-024-03259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/04/2024] [Indexed: 06/24/2024]
Abstract
KEY MESSAGE The study demonstrates the successful management of Meloidogyne incognita in eggplant using Mi-flp14 RNA interference, showing reduced nematode penetration and reproduction without off-target effects across multiple generations. Root-knot nematode, Meloidogyne incognita, causes huge yield losses worldwide. Neuromotor function in M. incognita governed by 19 neuropeptides is vital for parasitism and parasite biology. The present study establishes the utility of Mi-flp14 for managing M. incognita in eggplant in continuation of our earlier proof of concept in tobacco (US patent US2015/0361445A1). Mi-flp14 hairpin RNA construct was used for generating 19 independent transgenic eggplant events. PCR and Southern hybridization analysis confirmed transgene integration and its orientation, while RT-qPCR and Northern hybridization established the generation of dsRNA and siRNA of Mi-flp14. In vitro and in vivo bio-efficacy analysis of single-copy events against M. incognita showed reduced nematode penetration and development at various intervals that negatively impacted reproduction. Interestingly, M. incognita preferred wild-type plants over the transgenics even when unbiased equal opportunity was provided for the infection. A significant reduction in disease parameters was observed in transgenic plants viz., galls (40-48%), females (40-50%), egg masses (35-40%), eggs/egg mass (50-55%), and derived multiplication factor (60-65%) compared to wild type. A unique demonstration of perturbed expression of Mi-flp14 in partially penetrated juveniles and female nematodes established successful host-mediated RNAi both at the time of penetration even before the nematodes started withdrawing plant nutrients and later stage, respectively. The absence of off-target effects in transgenic plants was supported by the normal growth phenotype of the plants and T-DNA integration loci. Stability in the bio-efficacy against M. incognita across T1- to T4-generation transgenic plants established the utility of silencing Mi-flp14 for nematode management. This study demonstrates the significance of targeting Mi-flp14 in eggplant for nematode management, particularly to address global agricultural challenges posed by M. incognita.
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Affiliation(s)
- Divya Kamaraju
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - Madhurima Chatterjee
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, 7505101, Bet Dagan, Israel.
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
- Engrave Biolabs Pvt Ltd. , Shanthipuram, Kukatpally, Hyderabad, 500072, India.
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Mountoufaris G, Nair A, Yang B, Kim DW, Anderson DJ. Neuropeptide Signaling is Required to Implement a Line Attractor Encoding a Persistent Internal Behavioral State. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565073. [PMID: 37961374 PMCID: PMC10635056 DOI: 10.1101/2023.11.01.565073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Internal states drive survival behaviors, but their neural implementation is not well understood. Recently we identified a line attractor in the ventromedial hypothalamus (VMH) that represents an internal state of aggressiveness. Line attractors can be implemented by recurrent connectivity and/or neuromodulatory signaling, but evidence for the latter is scant. Here we show that neuropeptidergic signaling is necessary for line attractor dynamics in this system, using a novel approach that integrates cell type-specific, anatomically restricted CRISPR/Cas9-based gene editing with microendoscopic calcium imaging. Co-disruption of receptors for oxytocin and vasopressin in adult VMH Esr1 + neurons that control aggression suppressed attack, reduced persistent neural activity and eliminated line attractor dynamics, while only modestly impacting neural activity and sex- or behavior-tuning. These data identify a requisite role for neuropeptidergic signaling in implementing a behaviorally relevant line attractor. Our approach should facilitate mechanistic studies in neuroscience that bridge different levels of biological function and abstraction.
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Blazie SM, Jin Y. Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans. STAR Protoc 2023; 4:101959. [PMID: 36566382 PMCID: PMC9803825 DOI: 10.1016/j.xpro.2022.101959] [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: 09/29/2022] [Revised: 11/03/2022] [Accepted: 12/02/2022] [Indexed: 12/25/2022] Open
Abstract
The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorhabditis elegans. We begin with steps and recommendations for transgene construction and Cas9-mediated chromosomal integration. We provide detailed procedures for isolation of RBP-associated RNA fragments, subsequent library preparation, and sequencing. We further discuss best practices for data analysis, interpretation of results, and troubleshooting. For complete details on the use and execution of this protocol, please refer to Blazie et al. (2021).1.
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Affiliation(s)
- Stephen M Blazie
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Insulin-like growth factor I mitigates post-traumatic stress by inhibiting AMP-kinase in orexin neurons. Mol Psychiatry 2022; 27:2182-2196. [PMID: 35115701 PMCID: PMC9126821 DOI: 10.1038/s41380-022-01442-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/14/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Maladaptive coping behaviors are probably involved in post-traumatic stress disorders (PTSD), but underlying mechanisms are incompletely understood. We now report that mice lacking functional insulin-like growth factor I (IGF-I) receptors in orexin neurons of the lateral hypothalamus (Firoc mice) are unresponsive to the anxiolytic actions of IGF-I and develop PTSD-like behavior that is ameliorated by inhibition of orexin neurons. Conversely, systemic IGF-I treatment ameliorated PTSD-like behavior in a wild-type mouse model of PTSD (PTSD mice). Further, systemic IGF-I modified the GABA/Glutamate synaptic structure in orexin neurons of naïve wild-type mice by increasing the dephosphorylation of GABA(B) receptor subunit through inhibition of AMP-kinase (AMPK). Significantly, pharmacological inhibition of AMPK mimicked IGF-I, normalizing fear behavior in PTSD mice. Thus, we suggest that IGF-I enables coping behaviors by balancing E/I input onto orexin neurons in a context-dependent manner. These observations provide a novel therapeutic approach to PTSD through modulation of AMPK.
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Oliver D, Ramachandran S, Philbrook A, Lambert CM, Nguyen KCQ, Hall DH, Francis MM. Kinesin-3 mediated axonal delivery of presynaptic neurexin stabilizes dendritic spines and postsynaptic components. PLoS Genet 2022; 18:e1010016. [PMID: 35089924 PMCID: PMC8827443 DOI: 10.1371/journal.pgen.1010016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/09/2022] [Accepted: 01/03/2022] [Indexed: 12/02/2022] Open
Abstract
The functional properties of neural circuits are defined by the patterns of synaptic connections between their partnering neurons, but the mechanisms that stabilize circuit connectivity are poorly understood. We systemically examined this question at synapses onto newly characterized dendritic spines of C. elegans GABAergic motor neurons. We show that the presynaptic adhesion protein neurexin/NRX-1 is required for stabilization of postsynaptic structure. We find that early postsynaptic developmental events proceed without a strict requirement for synaptic activity and are not disrupted by deletion of neurexin/nrx-1. However, in the absence of presynaptic NRX-1, dendritic spines and receptor clusters become destabilized and collapse prior to adulthood. We demonstrate that NRX-1 delivery to presynaptic terminals is dependent on kinesin-3/UNC-104 and show that ongoing UNC-104 function is required for postsynaptic maintenance in mature animals. By defining the dynamics and temporal order of synapse formation and maintenance events in vivo, we describe a mechanism for stabilizing mature circuit connectivity through neurexin-based adhesion.
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Affiliation(s)
- Devyn Oliver
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Shankar Ramachandran
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Alison Philbrook
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Christopher M. Lambert
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ken C. Q. Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Michael M. Francis
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
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Hada A, Singh D, Papolu PK, Banakar P, Raj A, Rao U. Host-mediated RNAi for simultaneous silencing of different functional groups of genes in Meloidogyne incognita using fusion cassettes in Nicotiana tabacum. PLANT CELL REPORTS 2021; 40:2287-2302. [PMID: 34387737 DOI: 10.1007/s00299-021-02767-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/05/2021] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE This study establishes possibility of combinatorial silencing of more than one functional gene for their efficacy against root-knot nematode, M. incognita. Root-knot nematodes (RKN) of the genus Meloidogyne are the key important plant parasitic nematodes (PPNs) in agricultural and horticultural crops worldwide. Among RKNs, M. incognita is the most notorious that demand exploration of novel strategies for their management. Due to its sustainable and target-specific nature, RNA interference (RNAi) has gained unprecedented importance to combat RKNs. However, based on the available genomic information and interaction studies, it can be presumed that RKNs are dynamic and not dependent on single genes for accomplishing a particular function. Therefore, it becomes extremely important to consider silencing of more than one gene to establish any synergistic or additive effect on nematode parasitism. In this direction, we have combined three effectors specific to subventral gland cells of M. incognita, Mi-msp1, Mi-msp16, Mi-msp20 as fusion cassettes-1 and two FMRFamide-like peptides, Mi-flp14, Mi-flp18, and Mi-msp20 as fusion cassettes-2 to establish their possible utility for M. incognita management. In vitro RNAi assay in tomato and adzuki bean using these two fusion gene negatively altered nematode behavior in terms of reduced attraction, invasion, development, and reproduction. Subsequently, Nicotiana tabacum plants were transformed with these two fusion gene hairpin RNA-expressing vectors (hpRNA), and characterized via PCR, qRT-PCR, and Southern blot hybridization. Production of siRNAs specific to Mi-flp18 and Mi-msp1 was also confirmed by Northern hybridization. Further, transgenic events expressing single copy insertions of hpRNA constructs of fusion 1 and fusion-2 conferred up to 85% reduction in M. incognita multiplication. Besides, expression quantification revealed a significant reduction in mRNA abundance of target genes (up to 1.8-fold) in M. incognita females extracted from transgenic plants, and provided additional evidence for successful gene silencing.
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Affiliation(s)
- Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Divya Singh
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prakash Banakar
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ankita Raj
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Blazie SM, Takayanagi-Kiya S, McCulloch KA, Jin Y. Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. eLife 2021; 10:68336. [PMID: 34323215 PMCID: PMC8354637 DOI: 10.7554/elife.68336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
The translation initiation complex eIF3 imparts specialized functions to regulate protein expression. However, understanding of eIF3 activities in neurons remains limited despite widespread dysregulation of eIF3 subunits in neurological disorders. Here, we report a selective role of the C. elegans RNA-binding subunit EIF-3.G in shaping the neuronal protein landscape. We identify a missense mutation in the conserved Zinc-Finger (ZF) of EIF-3.G that acts in a gain-of-function manner to dampen neuronal hyperexcitation. Using neuron-type-specific seCLIP, we systematically mapped EIF-3.G-mRNA interactions and identified EIF-3.G occupancy on GC-rich 5′UTRs of a select set of mRNAs enriched in activity-dependent functions. We demonstrate that the ZF mutation in EIF-3.G alters translation in a 5′UTR-dependent manner. Our study reveals an in vivo mechanism for eIF3 in governing neuronal protein levels to control neuronal activity states and offers insights into how eIF3 dysregulation contributes to neurological disorders.
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Affiliation(s)
- Stephen M Blazie
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Seika Takayanagi-Kiya
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Katherine A McCulloch
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, United States
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