Biology, genome, life cycle and why c. elegans are referred to as model organism

1. C. elegans genome and its
life cycle
SUBHRADEEP SARKAR
M.Sc IN APPLIED GENETICS

2. Model organisms
 A model organism is a non-human species that is extensively studied to understand
particular biological phenomena, with the expectation that discoveries made in the
organism model will provide insight into the workings of other organisms.
 Model organisms are in vivo models and are widely used to research
human disease when human experimentation would be unfeasible or unethical.
 Most model organisms share a set of common features that make them amenable to
study in the laboratory: They are generally small, easy, and inexpensive to rear in the
lab, and reproduce quickly and prodigiously.
 In addition, the best genetic model organisms have small genome sizes, and many can
reproduce sexually, allowing researchers to cross-breed individuals of different
genotypes.
 Beyond these common traits, most model organisms have one or several unique
attributes that make them ideal for a particular line of research.
 For instance, zebrafish readily produce many large, transparent embryos, and are
therefore a favorite research subject for developmental biologists.
 The roundworm,Caenorhabditis elegans, has a simple but nonetheless sophisticated
nervous system, and displays simple behaviors, such as movement, feeding, and
mating. These properties make it well suited for neurobiology and behavioral genetics.


3. Caenorhabditis elegans: Biology and Genome
• Caenorhabditis elegans is a free-living, transparent nematode
(roundworm), about 1 mm in length, which lives in temperate
soil environments.
• Research into the molecular and developmental biology of C.
elegans was begun in 1974 by Sydney Brenner and it has since
been used extensively as a model organism.
• The organism is transparent and easy for manipulation and
observation , feeds on bacteria ,cheaply housed and cultivated in
large number (1000 worms / petridish) in the laboratory .
• Most investigators grow C.elegans on agar-filled petridishes
that are covered with a lawn of bacteria.

4. Biology of c. elegans
• C.elegans is unsegmented, vermiform, and bilaterally symmetrical, with
a cuticle integument, four main epidermal cords and a fluid-filled
pseudocoelomate cavity.
• C. elegans has two sexes: hermaphrodites and males.
• Individuals are almost all hermaphrodite, with males comprising just
0.05% of the total population on average.
• The basic anatomy of C. elegans includes a mouth, pharynx, intestine,
gonad, and collagenous cuticle.
• Males have a single-lobed gonad, vas deferens, and a tail specialized for
mating.
• Hermaphrodites have two ovaries, oviducts, spermatheca, and a single
uterus.
• Eggs are laid by the hermaphrodite and development is completed
externally.
• Eggs are fertilized internally , either from sperm produced by
hermaphrodite or from sperm contributed by by a male.

5. Biology of c. elegans
• When self-inseminated the wild type worm lay about 300 eggs. When
inseminated by by a male , the number of eggs may exceed 1000.
• Hermaphrodites which self fertilize produce only hermaphrodites. When
hermaphrodites mate with males , 50% of the progeny will be male s and
50% will be hermaphrodites.
• After hatching (about 14 hrs. after fertilization ), they pass through four
Larval stages (L1–L4).
• When crowded or in the absence of food, C. elegans can enter an
alternative third larval stage called the dauer state.
• Dauer larvae are stress-resistant and do not age.
• Hermaphrodites produce all their sperm in the L4 stage and then switch
over to producing oocytes.
• At 20 °C, the laboratory strain of C. elegans has an average life span of
approximately 2–3 weeks and a generation time of approximately 4 days.
• C. elegans has five pairs of autosomes and one pair of sex chromosomes.
• Hermaphrodite C. elegans have a pair of sex chromosomes (XX); the
rare males have only one sex chromosome (X0).

8. C.elegans as a model organism
• C. elegans is studied as a model organism for a variety of reasons.
• It is a multicellular eukaryotic organism that is simple enough to be
studied in great detail.
• Strains are cheap to breed and can be frozen. When subsequently
thawed they remain viable, allowing long-term storage.
• In addition, C. elegans is transparent, facilitating the study of cellular
differentiation and other developmental processes in the intact
organism.
• Nematodes have a fixed, genetically determined number of cells, a
phenomenon known as eutely..The developmental fate of every single
somatic cell (959 in the adult hermaphrodite; 1031 in the adult male) has
been mapped out.
• These patterns of cell lineage are invariant between individuals, in
contrast to mammals where cell development from the embryo is more
largely dependent on cellular cues.

9. C.elegans as a model organism
• In both sexes, a large number of additional cells (131 in the hermaphrodite, most
of which would otherwise become neurons), are eliminated by programmed cell
death (apoptosis).
• Researchers who study apoptosis (programmed cell death) use C. elegans as an
experimental organism in the hope of finding treatments for certain types of
human cancers, such as leukemia. By studying apoptosis in C. elegans,
researchers hope to identify genes that switch-on cell death in cancer cells.
• C. elegans is one of the simplest organisms with a nervous system.
• In the hermaphrodite, this comprises 302 neurons whose pattern of connectivity
has been completely mapped out.
• Researchers have explored the neural mechanisms responsible for several
interesting behaviors shown by C. elegans, including chemotaxis,
thermotaxis,mechanotransduction, and male mating behavior.

10. C.elegans as a model organism
• A useful feature of C. elegans is that the function of specific genes can be
disrupted by by RNA interference (RNAi).
• Silencing the function of a gene in this way can sometimes allow a researcher to
infer what the function of that gene may be.
• The nematode can either be soaked in or injected with a solution of double
stranded RNA , the sequence of which is complementary to the sequence of the
gene that the researcher wishes to disable.
• RNA interference (RNAi) in C. elegans can also be done by simply feeding the
worms transgenic bacteria expressing RNA complementary to the gene of
interest.
• This strategy for gene loss of function experiments is the easiest of all animal
models, and thus, scientists were able to knock down 86% of the ~20,000 genes
in the worm, establishing a functional role for 9% of the genome

11. • C.elegans can be stored for a long term in the laboratory.
• A 15% glycerol solution is used for the freezing of C. elegans.
• Samples are cooled at 1°C per minute. Freshly starved young
larvae survive freezing best.
• About 35 to 45% of the worms stored in liquid nitrogen survive.
• The worms can also be stored at −80°C for over ten years, but
survival is not as great as for worms stored in liquid nitrogen at
−196°C.
•

12. Genome of C.elegans
• C. elegans was the first multicellular organism to have its genome
completely sequenced.
• The sequence was published in 1998 although a number of small gaps were
present; the last gap was finished by October 2002.
• C. elegans genome was sequenced using the clone-by-clone approach.
• The C. elegans genome size is l (9.7 x 107
base pairs or 97 Megabases)
• This is approximately 20 x bigger than that of E. coli and about 1/30 of that
of human
• The adult hermaphrodite has 959 somatic nuclei. Its gene density is about 1
gene/5kb.
• Introns are 26% of the genome.
• About 35% of C. elegans genes have human homologs.
• Remarkably, it has been shown repeatedly that human genes replace their C.
elegans homologs when introduced into C. elegans. Conversely, many C.
elegans genes can function similarly to mammalian genes.
• There are some large intergenic regions containing repetitive DNA
sequences.
• Many genes are arranged in operons. C. elegans and other nematodes are the
only eukaryotes currently known to have operons.

13. Genome of C.elegans
• There are 19,735 protein coding genes with 2685 alternative splice forms,
bringing the predicted protein count to 22,420 .
• The genome contains more than 16,000 RNA genes.
• In 2003, the genome sequence of the related nematode C. briggsae was also
determined, allowing researchers to study the comparative genomics of these
two organisms.
• Work is now ongoing to determine the genome sequences of more
nematodes from the same genus such as C. remanei, C. japonica and C.
brenneri.
• The official version of the C. elegans genome sequence continues to change
as new evidence reveals errors in the original sequencing .
• Most changes are minor, adding or removing only a few base pairs (bp) of
DNA.
• For example, the WS169 release of WormBase (December 2006) lists a net
gain of 6 base pairs to the genome sequence.
• Occasionally more extensive changes are made, as in the WS159 release of
May 2006, which added over 300 bp to the sequence.