Chemoreception in the Nematode Caenorhabditis elegans Marvin L

Chemoreception in the Nematode Caenorhabditis elegans Marvin L. Bayne, Ph. D.

Why Study Worms? Sydney Brenner “Thus we want a multicellular organism which has a short life cycle, can be easily cultivated, and is small enough to be handled in large numbers, like a micro-organism. It should have relatively few cells, so that exhaustive studies of lineage and patterns can be made, and should be amenable to genetic analysis. ” --Excerpts from Proposal to the Medical Research Council, 1963

C. elegans as a Model System • Easy to cultivate – Small: ~1 mm in length – Grown on agar plates of E. coli, scale up in liquid culture – Large brood size: ~300; short generation time: ~3 days • Genetic analysis – Maintained as self-fertilizing hermaphrodite facilitating the expansion of mutant phenotypes. Males available for mating experiments. – Reverse genetics through RNAi; bacterial delivery system of genome wide or chromosome specific libraries – First multicellular organism with a completely sequenced genome (1998) • Transparency – Allowed cell lineage mapping of all invariant 959 cells in adult hermaphrodite – Allows use of GFP tagged promoter and proteins to follow expression in vivo – Enables in vivo compound screening protocols

Self-Fertilizing Hermaphrodites Hermaphrodite (XX) Males (X 0) Photo credit: http: //homepages. ucalgary. ca/~dhansen/worms. gif

Resources Available • C. elegans Genetic Stock Center, U of Minnesota – – Mutant strains Transgenic strains with GFP fusions Wild type strains isolated from different ecosystems Related, sequenced species eg C. briggsea • C. elegans scientific community – Worm. Book • reviews of all aspects of worm biology – Worm. Base • gene sequences, genotypes, mutations – Worm Breeder’s Gazette • informal newsletter, new techniques, unpublished observations – Worm. Atlas • Handbook of C. elegans anatomy, images, movies – New York Area Worm Discussion Group: NYU

C. elegans Models of Human Disease • Neurobiology – Alzheimer’s Disease – Parkinson’s Disease – Nicotine addiction • Metabolic Disease – Insulin signalling and resistance – Fat accumulation • Aging • Cancer pathways

C. elegans as an in vivo Assay System • Traditional Chinese Medicines and other natural products – Mechanism of action studies – Purification of active substances • Drug screening in transgenic models of human disease – Huntington’s, Alzheimer’s, Parkinson’s – 384 well screening using image analysis systems

C. Elegans Visualized on Cellomics Array. Scan Wildtype (ATM) or mutant aggregation prone (ATZ) forms of human alpha-1 antitrypsin

Establishing a C. elegans Research Laboratory at RISE

Initial Project: Chemoreception • Chemoreception of environmental stimuli is a major sensory system in small soil nematodes like C. elegans • C. elegans responds to volatile odorants produced by bacteria feeding on rotting vegetables and fruit • Odorants signals are mediated through chemoreceptors, a subclass of G protein-Coupled Receptors (GPCRs) • Chemotaxis assays straightforward • Good balance between enough details known to establish protocols and enough questions left to be addressed

Nervous System of C. elegans • 959 cells, 302 neurons, 32 chemosensory neurons – Function of individual neurons determined by laser ablation • Complete “connectosome”determined – 5000 chemical synapses – 2000 neuromuscular junctions – 600 gap junctions

Amphid Chemosensory Neurons

Chemosensory Neurons • • • ASE AWC AWA AWB ASH ASI, ADF, ASG, ASJ ASK ADL URX, AQR, PQR PHA, PHB water soluble chemotaxis volatile chemotaxis, lifespan volatile chemotaxis volatile avoidance nociception, osmotic avoidance Dauer formation navigation, lifespan social feeding oxygen/aerotaxis avoidance

Sensory Neurons Responsive to Volatile Odorants Bargmann et al (1993) Cell 74: 515 -527 • Survey of 121 volatile chemicals – 50 strong attractants – Saturation experiments identify at least 7 classes of attractive odorants • AWC: chemotaxis – benzaldehyde, butanone, isoamyl alcohol, – 2, 3 -pentanedione, 2, 4, 5 -trimethylthiazole • AWA: chemotaxis – Diacetyl. Pyrazine, 2, 4, 5 -trimethylthiazole • AWB: avoidance – Nonanone

Chemotaxis Assay Plate

Chemotaxis Assay

Sensory Neurons Responsive to Volatile Odorants Bargmann et al (1993) Cell 74: 515 -527 • Survey of 121 volatile chemicals – 50 strong attractants – Saturation experiments identify at least 7 classes of attractive odorants • AWC: chemotaxis – benzaldehyde, butanone, isoamyl alcohol, – 2, 3 -pentanedione, 2, 4, 5 -trimethylthiazole • AWA: chemotaxis – Diacetyl. Pyrazine, 2, 4, 5 -trimethylthiazole • AWB: avoidance – Nonanone

odr Mutants (Bargmann et al (1993) Cell 74: 515 -527) • odr-1, odr-5 eliminate function of AWC neuron – Normal AWC nucleus and cilia – odr-1 encodes a putative guanylyl cyclase – odr-5 is uncharacterized • odr-2 affects a subset of AWC neuron function; normal AWC nucleus, cilia – odr-2 encodes a predicted membrane –associated protein related to the GPI (glycosylated phosphatidylinositol)-linked signalling proteins, predicted to act downstream of receptor signalling • odr-4 affects a subset of AWA and AWC responses – odr-4 encodes a novel type II membrane protein required for the localization of a subset of GPCRs, including ODR-10, to the cilia of olfactory neurons • odr-7 affects chemotaxis to some volatile odorants and cell fate of AWA neurons. – odr-7 encodes an olfactory –specific member of the nuclear receptor superfamily. Odr-7 appears to lie upstream of odr-10 • odr-10 is a GPCR expressed in AWA neurons and is responsible to chemo attraction to diacetyl. Responses to other AWA odorants normal. Expression of a odr-10 transgene in AWB neurons leads to aversion of transgenic C. elegans to diacetyl

Open Questions Regarding Chemoreception in C. elegans • Remarkably the ODR-10/diacetyl is the only receptor/ligand pair identified • What other bacterial derived attractants can be identified and what are their corresponding receptors ? • How do strains of C. elegans and different species of Caenorhabditis differ in their ability to detect volatile odorants ?

Initial Studies at RISE • Set up chemotaxis assays using diacetyl, pyrazine, benzaldehyde and 2, 4, 5 -trimethylthiazole • Confirm chemotaxis deficits in odr mutants – odr-1, odr-2, odr-4, odr-5, odr-7, odr-10 • Demonstrate chemotaxis deficits through use of odr RNAis • Examine chemotaxis deficits in odr mutants to broad panel of odorants including bacterial derived attractants – Vibrio cholerae autoinducer (S)-3 -hydroxytridecan-4 -one, termed CAI 1, through AWC – Pseudomonas aeruginosa acyl homoserine lactone – Serratia marcescens cyclic lipodepsipentapeptide, serrawettin W 2 – 17 volatile compounds produced by the nematode pathogen Bacillus nematocida • Compare chemotaxis responses in lab strain N 2 to wild isolate strains and additional Caenorhabditis species

Where to begin • Obtain stocks from C. elegans Genetic Stock Center – N 2 standard laboratory stock – odr-1, odr-2, odr-4, odr-5, odr-7, odr-10 mutants – odr-4 -GFP fusion fluorescently label neurons – Wild type isolates: Hawaii, Australia, England – Other species: C. briggsae • Obtain/Construct RNAi reagents for odr-1, odr -4, odr-7, odr-10

Future Directions • Identify novel receptor/odorant pairs – Similar to SPRI’s Orphan GPCR Program • Identified novel receptors for galanin, neuromedin U, ADP (P 2 Y 12), histamine, MCH, leukotriene B 4 • Identified novel bioactive RF-amide peptide as ligand for o. GPCR SP 9155 • Chemoreceptor evolution/diversity – Explore “flatliner” chemoreceptor phenomenon

Chemoreceptors in C. elegans • Genome sequencing identifies ~1300 predictive genes encoding potentially functional chemoreceptors and 400 apparent pseudogenes. ~7% of total genome • str superfamily: 793 members includes odr-10 – srd, str, sri, srd, srj, srm, sm families – 84% located on chromosome V

Candidate Gene Profile for Chemoreceptors • GPCRs expressed in AWA, AWB and AWC olfactory sensory neurons – cell-sorted AWB neurons (Colosimo et al. , 2004) • str-220, srd-16, srd-23 – GPCRs whose expression are controlled by odr-4 and odr -8 which direct expression to cilia • GPCRs whose expression are regulated by odr-7 • GPCRs expressed by strains with unique response to odorants • Test candidates by knockout or knockdown techniques

Additional Studies • Identify novel receptor/odorant pairs – Similar to SPRI’s Orphan GPCR Program • Chemoreceptor evolution/diversity – Explore “flatliner” chemoreceptor phenomenon

“Flatliner” Chemoreceptors Stewart et al (2005) Genetics 169: 1985 -1996 • str family of chemoreceptors – 321 members, 93 apparent pseudogenes • srh family of chemoreceptors – 305 members, 89 apparent pseudogenes • 102/182 apparent pseudogenes have a single defect, either single stop codon or deletion • 31 apparent pseudogenes (12 str, 19 srh) (14 stops, 17 deletions) examined against 22 wild isolates • Remarkably 10/31 putative functional alleles identified – 5 stop codons converted to sense codons – 5 insertions

Summary • C. elegans is an attractive model organism to investigate a multitude of biological processes accommodating a wide range of student interests • Laboratory resources are relatively modest • Chemoreception provides interesting project to establish the laboratory while still offering significant challenges/opportunities to make scientific contributions.

RNAi Libraries • Ahringer lab – 16, 757 clones, made by cloning gene-specific genomic fragments between two inverted T 7 promoters – Chromosome V 4712 clones • Vidal lab – 11, 511 clones, made by the Gateway cloning of full-length open reading frame (ORF) c. DNAs into a double T 7 vector • Both libraries use the HT 115 bacterial strain as a host for the plasmid RNAi clones; HT 115 has IPTG inducible T 7 polymerase and a disruption of the RNAse III gene (a ds. RNAse)

LIFE CYCLE 3/6/2021 Kavya Leo 32