Download 2-13 Nomenclature and Strains

Nomenclature
Because of the wealth of mutant strains generated by genetic screens, scientists have developed rules
for naming and referring to genes and their associated gene product, phenotype, and mutations.
Scientists routinely use abbreviations when referring to the protein, mutations, and phenotypes
associated with a given gene. A few simple rules (nomenclature) allow scientists to distinguish between
the gene and its associated protein, phenotype, and known mutations. Abbreviations for C. elegans
genes consist of 3 lower case, italicized letters and a number,. For example, unc-3 is an abbreviation for
uncoordinated-3. Geneticists name genes based on the phenotype observed when the gene in question
is mutated. So, in this example, the loss of function of the gene results in an uncoordinated phenotype. It
is important to remember that mutations in many different genes could result in the same phenotype.
There are hundreds of unc genes that are necessary for normal worm movement, and they could be
involved in such diverse functions as axonal guidance to myosin function. Thus, unc-2 is a different gene
from unc-3, coding for an entirely different gene product. Gene names also do not confer any information
regarding location in the genome. The number associated with the name refers to the order in which the
mutations were discovered with unc-2 being discovered before unc-3 in this example. Alleles (or different
mutations in the same gene) are designated in parentheses following the gene name. For example, unc3(e151) is a specific allele of the unc-3 gene. The 1 to 2 letter prefix in the allele name refers to the
laboratory in which the mutation was isolated. In this example, e is the allele abbreviation for Jonathan
Hodgkin’s laboratory at Oxford University in England.
The protein associated with a gene is written in capitalized, non-italic capital letters. Thus, the gene
product of unc-3 would be written as UNC-3. A simple rule of thumb to remember is that protein names
are always written entirely in nonitalicized capital letters while references to DNA, such as a gene name,
are always written in italicized, lower case letters.
The phenotype associated with a mutated gene is written without italics, with just the first letter of the
gene name capitalized. The phenotype of unc-3 is Unc-3. A generic reference to any unc phenotype
would be written as Unc.
Using this nomenclature system allows scientists to efficiently distinguish between a mutation, protein, or
phenotype associated with a given gene without the need for a long explanation.
Wild-Type Strains Discussed in the BABEC C. elegans Modules
N2 is the most common wild-type worm strain used in C. elegans research. Whenever wild-type worms
are discussed in the accompanying lab activities, the protocol refers to N2 worms (unless otherwise
stated).
Strain CB4856 is a wild-type strain from Hawaii that develops ethanol tolerance more quickly than N2
wild-type worms due to an allelic variation in the npr-1 gene (Davies et al., 2004). npr-1 encodes a Gcoupled protein receptor in the neuropeptide Y (NPY) receptor family (deBono and Bargmann, 2004).
Allelic variation in npr-1 also affects other behaviors such as speed of locomotion on food, social
behavior, and bordering (preference for the thicker parts of the bacterial lawn) (deBono and Bargmann,
1998).
Mutant Strains Discussed in the BABEC C. elegans Modules
The che-2 mutant lacks chemosensory cilia and is therefore unable to detect chemicals in its environment
and has defective chemotaxis.
The che-3 mutant has defective chemosensory cilia – a part of the neuron where odor receptors are
normally located. Therefore, the che-3 mutant cannot detect and chemotax toward many attractant
chemicals.
C. elegans Nomenclature and Strains
BABEC 6/6/10
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The daf-2 mutation causes an increased lifespan. daf-2 mutants make extra enzymes that destroy free
radicals (protein and DNA destroying by-products of metabolism) as well as proteins that help worms
resist stress. The daf-2 gene product, known as the DAF-2 protein, is a receptor that resembles a human
receptor for insulin-like growth factor (IGF-1). Mice that were engineered to produce fewer IGF-1
receptors also lived longer than normal. A functioning daf-2 gene keeps the daf-16 gene in check.
Therefore, when both genes are working, worms live the expected 2-3 weeks.
The daf-6 and daf-10 mutants lack chemosensory cilia and are therefore unable to detect chemicals in
the environment. They also have defective chemotaxis.
The daf-16 gene triggers several genes that promote longevity. Normally, this function is kept in check by
another gene, daf-2. However, when the daf-2 gene is damaged or mutated, the daf-16 gene will set into
motion a cascade of events the lead to a long-lived worm.
The glr-1and eat-4 mutants are defective in the nose touch response.
The him-5 mutant is used in breeding experiments in order to increase the number of male progeny
produced.
The mec-6 mutant is insensitive to gentle prodding and unresponsive to tapping the dish whereas wildtype worms will stop crawling and back up in response to both stimuli.
The odr-3 mutant has defective olfactory neurons. These mutants cannot smell, but they can move and
taste normally. The odr-3 mutant should crawl randomly when in the presence of volatile odorants but still
move normally toward dissolved salts (gustatory chemotaxis).
The odr-10 mutant is unable to produce functional ODR-10 odor receptor proteins. The result is that the
odr-10 mutant cannot recognize the butter-like odorant diacetyl. The odr-10 mutant displays normal
chemotaxis toward other chemical odorants, but cannot recognize diacetyl.
The slo-1 mutant is resistant to the effects of ethanol on locomotion and egg-laying. The slo-1 gene codes
for a homolog of a type of potassium channel that is also found in humans (the BK channel).
The unc-14 mutant is uncoordinated. It is sluggish, almost paralyzed and tends to coil.
The unc-22 mutant twitches. This mutant moves slowly with constant trembling. It has thin, poorly
developed muscle fibers. It is resistant to levamisole (a nematocide and acetylcholine agonist). It is also
likely resistant to nicotine.
The unc-24 mutant is a weak kinker. It also tends to form an omega shape.
The unc-37 mutant is a severe coiler. Rather than moving in the characteristic sine-wave pattern, the unc37 mutant will coil and form ring shapes.
The unc-46/dpy-11 double mutant is a dumpy shrinker, with poor backing and slow forward movement. It
contracts when poked. Physically, it appears dumpy (short and fat, shaped somewhat like a football.)
References
Davies AG, Bettinger JC, Thiele TR, Judy ME, McIntire SL. 2004. Natural variation in the npr-1 gene
modifies ethanol responses of wild strains of C. elegans. Neuron 42(5): 731-743.
deBono and Bargmann. 1998. Natural variation in a neuropeptide Y receptor homolog modifies social
behavior and food response in C. elegans. Cell 94(5): 549-50.
C. elegans Nomenclature and Strains
BABEC 6/6/10
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