A neurotransmitter atlas of the nervous system of C. elegans males and hermaphrodites

Reviewer #1 (Public Review):

Wang and colleagues conducted a study to determine the neurotransmitter identity of all neurons in C. elegans hermaphrodites and males. They used CRISPR technology to introduce fluorescent gene expression reporters into the genomic loci of NT pathway genes. This approach is expected to better reflect in vivo gene expression compared to other methods like promoter- or fosmid-based transgenes, or available scRNA datasets. The study presents several noteworthy findings, including sexual dimorphisms, patterns of NT co-transmission, neuronal classes that likely use NTs without direct synthesis, and potential identification of unconventional NTs (e.g. betaine releasing neurons). The data is well-described and critically discussed, including a comparison with alternative methods. Although many of the observations and proposals have been previously discussed by the Hobert lab, the current study is particularly valuable due to its comprehensiveness. This NT atlas is the most complete and comprehensive of any nervous system that I am aware of, making it an extremely useful tool for the community.

Reviewer #2 (Public Review):

Summary:

Together with the known anatomical connectivity of C. elegans, a neurotransmitter atlas paves the way toward a functional connectivity map. This study refines the expression patterns of key genes for neurotransmission by analyzing the expression patterns from CRISPR-knocked-in GFP reporter strains using the color-coded Neuropal strain to identify neurons. Along with data from previous scRNA sequencing and other reporter strains, examining these expression patterns enhances our understanding of neurotransmitter identity for each neuron in hermaphrodites and the male nervous system. Beyond the known neurotransmitters (GABA, Acetylcholine, Glutamate, dopamine, serotonin, tyramine, octopamine), the atlas also identifies neurons likely using betaine and suggests sets of neurons employing new unknown monoaminergic transmission, or using exclusively peptidergic transmission.

Strengths:

The use of CRISPR reporter alleles and of the Neuropal strain to assign neurotransmitter usage to each neuron is much more rigorous than previous analysis and reveals intriguing differences between scRNA seq, fosmid reporter, and CRISPR knock-in approaches. Among other mechanisms, these differences between approaches could be attributed to 3'UTR regulatory mechanisms for scRNA vs. knockin or titration of rate-limited negative regulatory mechanisms for fosmid vs. knockin. It would be interesting to discuss this and highlight the occurrences of these potential phenomena for future studies.

Weaknesses:

For GABAergic transmission, one shortcoming arises from the lack of improved expression pattern by a knockin reporter strain for the GABA recapture symporter snf-11. In its absence, it is difficult to make a final conclusion on GABA recapture vs GABA clearance for all neurons expressing the vesicular GABA transporter neurons (unc-47+) but not expressing the GAD/UNC-25 gene e.g. SIA or R2A neurons. At minima, a comparison of the scRNA seq predictions versus the snf-11 fosmid reporter strain expression pattern would help to better judge the proposed role of each neuron in GABA clearance or recycling.

Considering the complexities of different tagging approaches, like T2A-GFP and SL2-GFP cassettes, in capturing post-translational and 3'UTR regulation is important. The current formulation is simplistic. e.g. after SL2 trans-splicing the GFP RNA lacks the 5' regulatory elements, T2A-GFP self-cleavage has its own issues, and the his-44-GFP reporter protein does certainly have a different post-translational life than vesicular transporters or cytoplasmic enzymes.

Do all splicing variants of neurotransmitter-related genes translate into functional proteins? The possibility that some neurons express a non-functional splice variant, leading to his-74-GFP reporter expression without functional neurotransmitter-related protein production is not addressed. Also, one tagged splice variant of unc-25 is expected to fail to produce a GFP reporter, can this cause trouble?

Reviewer #3 (Public Review):

Summary:

In this paper, Wang et al. provide the most comprehensive description and comparison of the expression of the different genes required to synthesize, transport, and recycle the most common neurotransmitters (Glutamate, Acetylcholine, GABA, Serotonin, Dopamine, Octopamine, and Tyramine) used by hermaphrodite and male C. elegans. This paper will be a seminal reference in the field. Building and contrasting observations from previous studies using fosmid, multicopy reporters, and single-cell sequencing, they now describe CRISPR/Cas-9-engineered reporter strains that, in combination with the multicolor pan-neuronal labeling of all C. elegans neurons (NeuroPAL), allows rigorous elucidation of neurotransmitter expression patterns. These novel reporters also illuminate previously unappreciated aspects of neurotransmitter biology in C. elegans, including sexual dimorphism of expression patterns, co-transmission, and the elucidation of cell-specific pathways that might represent new forms of neurotransmission.

Strengths:

The authors set out to establish neurotransmitter identities in C. elegans males and hermaphrodites via varying techniques, including integration of previous studies, examination of expression patterns, and generation of endogenous CRISPR-labeled alleles. Their study is comprehensive, detailed, and rigorous, and achieves the aims. It is an excellent reference for the field, particularly those interested in biosynthetic pathways of neurotransmission and their distribution in vivo, in neuronal and non-neuronal cells.

Weaknesses:

No weaknesses were noted. The authors do a great job linking their characterizations with other studies and techniques, giving credence to their findings. As the authors note, there are sexually dimorphic differences across animals and varying expression patterns of enzymes. While it is unlikely there will be huge differences in the reported patterns across individual animals, it is possible that these expression patterns could vary developmentally, or based on physiological or environmental conditions. It is unclear from the study how many animals were imaged for each condition, and if the authors noted changes across individuals during development (could be further acknowledged in the discussion?)