Caenorhabditis elegans

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.

Biology
C. elegans is unsegmented, vermiform, and bilaterally symmetrical, with a cuticle integument, four main epidermal cords and a fluid-filled pseudocoelomate cavity. Members of the species have many of the same organ systems as other animals. In the wild, they feed on bacteria that develop on decaying vegetable matter. 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.

C. elegans eggs are laid by the hermaphrodite. After hatching, they pass through four juvenile 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 (150 sperm per gonadal arm) and then switch over to producing oocytes. The sperm are stored in the same area of the gonad as the oocytes until the first oocyte pushes the sperm into the spermatheca (a chamber where the oocytes become fertilized by the sperm). The male can inseminate the hermaphrodite, which will use male sperm preferentially (both types of sperm are stored in the spermatheca). When self-inseminated, the wild-type worm will lay approximately 300 eggs. When inseminated by a male, the number of progeny can exceed 1,000. 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. Sex in C. elegans is based on an X0 sex-determination system. Hermaphrodite C. elegans have a matched pair of sex chromosomes (XX); the rare males have only one sex chromosome (X0). The sperm of C. elegans is ameboid, lacking flagella and acrosomes.

C. elegans is notable in animal sleep studies as the most primitive organism in which sleep-like states have been observed. In C. elgans, a lethargus phase occurs in short periods preceding each moult.

Ecology
The different Caenorhabditis species occupy various nutrient and bacteria rich environments. They do not form self-sustaining populations in soil, as it lacks enough organic matter. C. elegans can survive on a diet of a variety of kinds of bacteria (not all bacteria, though), but its wild ecology is largely unknown. Most laboratory strains were found in human-made environments such as gardens and compost piles. Recently, however, C. elegans has been found to be abundant in rotting organic matter, particularly rotting fruit. Dauer larvae can be transported by invertebrates including millipedes, insects, isopods, and gastropods. When they reach a desirable location they then get off, and at least in the lab they will also feed on the host if it dies.

Nematodes are capable of surviving desiccation, and in C. elegans the mechanism for this capability has been demonstrated to be Late Embryogenesis Abundant (LEA) proteins.

Laboratory uses
In 1963 Sydney Brenner proposed using Caenorhabditis elegans as a model organism for the investigation of animal development including neural development. Brenner chose it mainly because it is simple, easy to grow in bulk populations, and convenient for genetic analysis.

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. 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 largely invariant between individuals, in contrast to mammals where cell development from the embryo is more largely dependent on cellular cues. 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). This aspect has been thoroughly studied in this organism, specifically because of this "apoptotic predictability", which has contributed to the elucidation of some apoptotic genes, mainly through observation of abnormal, apoptosis-surviving nematodes.



In addition, C. elegans is one of the simplest organisms with a nervous system. In the hermaphrodite, this comprises 302 neurons whose pattern of connectivity, or "connectome", has been completely mapped and shown to be a small-world network. Research has explored the neural mechanisms responsible for several of the more interesting behaviors shown by C. elegans, including chemotaxis, thermotaxis, mechanotransduction, and male mating behavior.

A useful feature of C. elegans is that it is relatively straightforward to disrupt the function of specific genes 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. Alternatively, worms can be fed on genetically transformed bacteria which express the double stranded RNA of interest.

C. elegans has also been useful in the study of meiosis. As sperm and egg nuclei move down the length of the gonad, they undergo a temporal progression through meiotic events. This progression means that every nucleus at a given position in the gonad will be at roughly the same step in meiosis, eliminating the difficulties of heterogeneous populations of cells.

The organism has also been identified as a model for nicotine dependence as it has been found to exhibit behavioral responses to nicotine that parallel those observed in mammals, including acute response, tolerance, withdrawal, and sensitization.

As for most model organisms, there is a dedicated online database for the species that is actively curated by scientists working in this field. The WormBase database attempts to collate all published information on C. elegans and other related nematodes. A reward of $4000 has been advertised on their website, for the finder of a new species of closely related nematode. Such a discovery would broaden research opportunities with the worm.

Genome
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. The adult hermaphrodite has 959 somatic nuclei. Its gene density is about 1 gene/5kb. Introns are 26% of the genome. There are some large intergenic regions containing repetitive DNA sequences. Many genes are arranged in operons: polycistronic series that are transcribed together. C. elegans and other nematodes are among the few eukaryotes currently known to have operons. The C. elegans genome sequence is approximately 100 million base pairs long. The genome consists of 6 chromosomes (named I, II, II, IV, V and X) and a mitochondrion.

The genome contains approximately 20,470 protein-coding genes. The number of known RNA genes in the genome has increased greatly due to the 2006 discovery of a new class of 21U-RNA gene, and the genome is now believed to contain more than 16,000 RNA genes, up from as few as 1,300 in 2005. Scientific curators continue to appraise the set of known genes, such that new gene predictions continue to be added and incorrect ones modified or removed.

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. These newer genome sequences are being determined using the whole genome shotgun technique which means they are likely to be less complete and less accurate than that of C. elegans, which was sequenced using the "hierarchical" or clone-by-clone approach.

The official version of the C. elegans genome sequence continues to change as and when new evidence reveals errors in the original sequencing (DNA sequencing is not an error-free process). Most changes are minor, adding or removing only a few base pairs (bp) of DNA. For example, the WS202 release of WormBase (April 2009) added 2 base pairs to the genome sequence. Occasionally more extensive changes are made, as in the WS197 release of December 2008, which added a region of over 4,600 bp to the sequence.

Evolution
It has been shown that a small number of conserved protein sequences from sponges are more similar to humans than to C. elegans. This suggests that there has been an accelerated rate of evolution in the C. elegans lineage. The same study found that several phylogenetically ancient genes are not present in C. elegans.

RNA interference
RNA interference (RNAi) has been used extensively in C. elegans because it can 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.

Incidentally, RNAi does not work nearly as well in other species of worm in the Caenorhabditis genus. Although injecting RNA into the body cavity of the animal induces silencing in most species, only C. elegans and a few other distantly related nematodes can uptake RNA from the bacteria they eat for RNAi. This ability has been mapped down to a single gene, sid-2, which when inserted as a transgene in other species allows them to uptake RNA for RNAi the way C. elegans does.

Scientific community
In 2002, the Nobel Prize in Physiology or Medicine was awarded to Sydney Brenner, H. Robert Horvitz and John Sulston for their work on the genetics of organ development and programmed cell death in C. elegans. The 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Fire and Craig C. Mello for their discovery of RNA interference in C. elegans. In 2008 Martin Chalfie shared a Nobel Prize in Chemistry for his work on green fluorescent protein in C. elegans.

Because all research into C. elegans essentially started with Sydney Brenner in the 1970s, many scientists working in this field share a close connection to Brenner, having either worked as a post-doctoral or post-graduate researcher in Brenner's lab or in the lab of someone who previously worked with Brenner. Because most people who worked in his lab went on to establish their own worm research labs, there is now a fairly well documented "lineage" of C. elegans scientists. This lineage was recorded in some detail at the 2003 International Worm Meeting and the results were stored in the WormBase database.

Long-term storage
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 at −196°C, the temperature of liquid nitrogen.

In the media
C. elegans made news when it was discovered that specimens had survived the Space Shuttle Columbia disaster in February 2003. Later, in January 2009, it was announced that live samples of C. elegans from the University of Nottingham will spend two weeks on the International Space Station as part of a project to explore the effects of zero gravity on muscle development and its physiology. The emphasis of the research will be on the genetic basis of muscle atrophy. This has relevance to space travel, but also to individuals who are bed-ridden, geriatric or diabetic. Descendants of the worms that were aboard Columbia in 2003 were launched into space on Endeavour for the STS-134 mission.

Publications






Online resources

 * WormBase - an extensive online database covering the biology and genomics of C. elegans and other nematodes
 * WormBook - a free online compendium of all aspects of C. elegans biology, including laboratory protocols
 * Wormatlas - an online database for behavioral and structural anatomy of C. elegans
 * 3D digital atlas of C. elegans - a 3D digital atlas at the single nucleus resolution with searching functions, quantitative analysis and 3D visualization tool for the structural anatomy of C. elegans
 * Wellcome Trust Sanger Institute C. elegans page - half of the genome sequence is maintained by this institute
 * WashU Genome Sequencing Center C. elegans page - the institute maintaining the other half of the genome
 * AceView WormGenes - another genome database for C. elegans, maintained at the NCBI
 * TCNJ Worm Lab - Easy to follow protocols and pictures for C. elegans research. Made by undergrads for undergrads.
 * Worm Classroom - An education portal for C. elegans
 * Textpresso - WormBase search engine
 * C. elegans movies - Timelapse films made by C. elegans researchers worldwide
 * C. elegans II - a free online textbook.
 * Silencing Genomes RNA interference (RNAi) experiments and bioinformatics in C. elegans for education. From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory.
 * C.elegans 3D model by the Ewbank Lab - Videos and photos that explain the basic anatomy of C. elegans
 * C. elegans protein abundance
 * WormWeb.org: Interactive Visualization of the C. elegans Neural Network - Connectivity between all 302 neurons, including a feature to search and find the shortest path between any 2 neurons
 * WormWeb.org: Interactive Visualization of the C. elegans Cell Lineage - The divisions that lead to every cell in the worm

Nobel lectures

 * Brenner S (2002) Nature's Gift to Science. In. http://nobelprize.org/nobel_prizes/medicine/laureates/2002/brenner-lecture.pdf
 * Horvitz HR (2002) Worms, Life and Death. In. http://nobelprize.org/nobel_prizes/medicine/laureates/2002/horvitz-lecture.pdf
 * Sulston JE (2002) The Cell Lineage and Beyond. In. http://nobelprize.org/nobel_prizes/medicine/laureates/2002/sulston-lecture.pdf