Targeting endogenous proteins for spatial and temporal knockdown using auxin-inducible degron in Caenorhabditis elegans

Protocol for auxin-inducible protein degradation in C. elegans using different auxins and TIR1-expressing strains

The auxin-inducible degron (AID) system is a powerful tool to deplete proteins in vivo. Here, we present a protocol for AID-mediated depletion of two proteins (CFI-1/AT-rich interaction domain 3 [ARID3] and Y47D3A.21/density-regulated re-initiation and release factor [DENR]) in C. elegans tissues using different auxins and transport inhibitor response 1 (TIR1)-expressing strains. We describe steps for genetic crossing, sample preparation, fluorescent microscopy, and treatment with either natural (indole-3-acetic acid [IAA]) or synthetic (1-naphthaleneacetic acid, potassium salt [K-NAA]) auxins. We then detail procedures for comparing the degree of CFI-1 depletion in C. elegans neurons upon panneuronal or pansomatic TIR1 expression. For complete details on the use and execution of this protocol, please refer to Li et al.1,2.

C. elegans: a prominent platform for modeling and drug screening in neurological disorders

INTRODUCTION

Human neurodevelopmental and neurodegenerative diseases (NDevDs and NDegDs, respectively) encompass a broad spectrum of disorders affecting the nervous system with an increasing incidence. In this context, the nematode C. elegans, has emerged as a benchmark model for biological research, especially in the field of neuroscience.

AREAS COVERED

The authors highlight the numerous advantages of this tiny worm as a model for exploring nervous system pathologies and as a platform for drug discovery. There is a particular focus given to describing the existing models of C. elegans for the study of NDevDs and NDegDs. Specifically, the authors underscore their strong applicability in preclinical drug development. Furthermore, they place particular emphasis on detailing the common techniques employed to explore the nervous system in both healthy and diseased states.

EXPERT OPINION

Drug discovery constitutes a long and expensive process. The incorporation of invertebrate models, such as C. elegans, stands as an exemplary strategy for mitigating costs and expediting timelines. The utilization of C. elegans as a platform to replicate nervous system pathologies and conduct high-throughput automated assays in the initial phases of drug discovery is pivotal for rendering therapeutic options more attainable and cost-effective.

Efficacy of auxin-inducible protein degradation in C. elegans tissues using different auxins and TIR1-expressing strains

The auxin-inducible degradation system has emerged as a powerful tool to deplete proteins of interest in cells and tissues of various model organisms, including C. elegans 2-5 . Here, we present a detailed protocol to perform AID-driven spatiotemporal depletion of specific proteins in C. elegans tissues. First, we introduced the AID degron and a fluorescent reporter at two conserved proteins: (a) the transcription factor CFI-1 (human ARID3), which is expressed in the nucleus of multiple C. elegans neurons and head muscle cells 6,7 , and (b) the broadly expressed translation initiation factor Y47D3A.21 (human DENR) that localizes in the cytoplasm. Second, we provide a step-by-step guide on how to generate C. elegans strains suitable for AID-mediated protein (CFI-1 and DENR) depletion. Third, we find that the degree of CFI-1 and DENR depletion in C. elegans tissues is comparable upon treatment with either natural auxin (indole-3-acetic acid (IAA) or a water-soluble synthetic auxin analog (K-NAA). Last, we compare the degree of AID-mediated CFI-1 depletion in C. elegans neurons when the transport inhibitor response 1 (TIR1), component of the SCF ubiquitin ligase complex, is provided in neurons or all somatic cells. Altogether, this protocol provides side-by-side comparisons of different auxins and TIR1-expressing lines. Such comparisons may benefit future studies of AID-mediated protein depletion in C. elegans .

Graphical abstract

Image provided as pdf (together with Figures).

Highlights

Efficient protein depletion in C. elegans tissues upon treatment with either natural or synthetic auxins. Pansomatic TIR1 expression leads to efficient depletion of CFI-1 and DENR.Panneuronal TIR1 expression leads to neuron-specific, yet variable CFI-1 depletion.The AID system is compatible with fluorescence microscopy, Western blotting and behavioral assays.

The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling

The elimination of synapses during circuit remodeling is critical for brain maturation; however, the molecular mechanisms directing synapse elimination and its timing remain elusive. We show that the transcriptional regulator DVE-1, which shares homology with special AT-rich sequence-binding (SATB) family members previously implicated in human neurodevelopmental disorders, directs the elimination of juvenile synaptic inputs onto remodeling C. elegans GABAergic neurons. Juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during the maturation of wild-type GABAergic neurons but persist into adulthood in dve-1 mutants, producing heightened motor connectivity. DVE-1 localization to GABAergic nuclei is required for synapse elimination, consistent with DVE-1 regulation of transcription. Pathway analysis of putative DVE-1 target genes, proteasome inhibitor, and genetic experiments implicate the ubiquitin-proteasome system in synapse elimination. Together, our findings define a previously unappreciated role for a SATB family member in directing synapse elimination during circuit remodeling, likely through transcriptional regulation of protein degradation processes.