Xenopus (//) (Gk., ξενος, xenos=strange, πους, pous=foot, commonly known as the clawed frog) is a genus of highly aquatic frogs native to sub-Saharan Africa. Twenty species are currently described in the Xenopus genus. The two best-known species of this genus are Xenopus laevis and Xenopus tropicalis, which are commonly studied as model organisms for developmental biology, cell biology, toxicology, neuroscience and for modelling human disease and birth defects.
- 1 Characteristics
- 2 Species
- 3 Xenopus as a model organism for biomedical research
- 4 Investigations of human disease genes using Xenopus
- 5 Investigation of fundamental biological processes using Xenopus
- 6 Use of Xenopus for small molecule screens to develop novel therapeutics
- 7 Use of Xenopus tropicalis for genetic studies
- 8 Use of Morpholino knockdown techniques for gene knockdown in Xenopus
- 9 References
- 10 External links
All species of Xenopus have flattened, somewhat egg-shaped and streamlined bodies, and very slippery skin (because of a protective mucus covering). The frog's skin is smooth, but with a lateral line sensory organ that has a stitch-like appearance. The frogs are all excellent swimmers and have powerful, fully webbed toes, though the fingers lack webbing. Three of the toes on each foot have conspicuous black claws.
The frog's eyes are on top of the head, looking upwards. The pupils are circular. They have no moveable eyelids, tongues (rather it is completely attached to the floor of the mouth) or eardrums (similarly to Pipa pipa, the common Suriname toad).
Xenopus species are entirely aquatic, though they have been observed migrating on land to nearby bodies of water during times of drought or in heavy rain. They are usually found in lakes, rivers, swamps, potholes in streams, and man-made reservoirs.
Adult frogs are usually both predators and scavengers, and since their tongues are unusable, the frogs use their small fore limbs to aid in the feeding process. Since they also lack vocal sacs, they make clicks (brief pulses of sound) underwater (again similar to Pipa pipa). Males establish a hierarchy of social dominance in which primarily one male has the right to make the advertisement call. The females of many species produce a release call, and "Xenopus laevis" females produce an additional call when sexually receptive and soon to lay eggs. The Xenopus species are also active during the twilight (or crepuscular) hours.
During breeding season, the males develop ridge-like nuptial pads (black in color) on their fingers to aid in grasping the female. The frogs' mating embrace is inguinal, meaning the male grasps the female around her waist.
- X. amieti (volcano clawed frog)
- X. andrei (Andre's clawed frog)
- X. borealis (Marsabit clawed frog)
- X. boumbaensis (Mawa clawed frog)
- X. clivii (Eritrea clawed frog)
- X. fraseri (Fraser's clawed frog or Fraser's platanna)
- X. gilli (Cape platanna)
- X. itombwensis (Itombwe Massif clawed frog)
- X. laevis (African clawed frog or common platanna)
- X. largeni (Largen's clawed frog)
- X. lenduensis (Lendu Plateau clawed frog)
- X. longipes (Lake Oku clawed frog)
- X. muelleri (Müller's platanna)
- X. petersii (Peters' platanna)
- X. pygmaeus (Bouchia clawed frog)
- X. ruwenzoriensis (Uganda clawed frog)
- X. tropicalis (western clawed frog)
- X. vestitus (Kivu clawed frog)
- X. victorianus (Lake Victoria clawed frog)
- X. wittei (De Witte's clawed frog)
Xenopus as a model organism for biomedical research
Like many other anurans, they are often used in laboratory as research subjects. Xenopus embryos and eggs are a popular model system for a wide variety of biological studies. This animal is used because of its powerful combination of experimental tractability and close evolutionary relationship with humans, at least compared to many model organisms.
Xenopus has long been an important tool for in vivo studies in molecular, cell, and developmental biology of vertebrate animals. However, the wide breadth of Xenopus research stems from the additional fact that cell-free extracts made from Xenopus are a premier in vitro system for studies of fundamental aspects of cell and molecular biology. Thus, Xenopus is the only vertebrate model system that allows for high-throughput in vivo analyses of gene function and high-throughput biochemistry. Finally, Xenopus oocytes are a leading system for studies of ion transport and channel physiology.
Model Organism Database for Xenopus
Investigations of human disease genes using Xenopus
All modes of Xenopus research (embryos, cell-free extracts, and oocytes) are commonly used in direct studies of human disease genes. Xenopus embryos for in vivo studies of human disease gene function: Xenopus embryos are large and easily manipulated, and moreover, thousands of embryos can be obtained in a single day. Indeed, Xenopus was the first vertebrate animal for which methods were developed to allow rapid analysis of gene function using misexpression (by mRNA injection ). Injection of mRNA in Xenopus that led to the cloning of interferon. Moreover, the use of morpholino-antisense oligonucleotides for gene knockdowns in vertebrates, which is now widely used, was first developed by Janet Heasman using Xenopus.
In recent years, these approaches have played in important role in studies of human disease genes. The mechanism of action for several genes mutated in human cystic kidney disorders (e.g. nephronophthisis) have been extensively studied in Xenopus embryos, shedding new light on the link between these disorders, ciliogenesis and Wnt signaling. Xenopus embryos have also provided a rapid test bed for validating newly discovered disease genes. For example, studies in Xenopus confirmed and elucidated the role of PYCR1 in cutis laxa with progeroid features.
Transgenic Xenopus for studying transcriptional regulation of human disease genes: Xenopus embryos develop rapidly, so transgenesis in Xenopus is a rapid and effective method for analyzing genomic regulatory sequences. In a recent study, mutations in the SMAD7 locus were revealed to associate with human colorectal cancer. Interestingly, the mutations lay in conserved, but noncoding sequences, suggesting these mutations impacted the patterns of SMAD7 transcription. To test this hypothesis, the authors used Xenopus transgenesis, and revealed this genomic region drove expression of GFP in the hindgut. Moreover, transgenics made with the mutant version of this region displayed substantially less expression in the hindgut.
Xenopus cell-free extracts for biochemical studies of proteins encoded by human disease genes: A unique advantage of the Xenopus system is that cytosolic extracts contain both soluble cytoplasmic and nuclear proteins (including chromatin proteins). This is in contrast to cellular extracts prepared from somatic cells with already distinct cellular compartments. Xenopus egg extracts have provided numerous insights into the basic biology of cells with particular impact on cell division and the DNA transactions associated with it (see below).
Studies in Xenopus egg extracts have also yielded critical insights into the mechanism of action of human disease genes associated with genetic instability and elevated cancer risk, such as ataxia telangiectasia, BRCA1 inherited breast and ovarian cancer, Nbs1 Nijmegen breakage syndrome, RecQL4 Rothmund-Thomson syndrome, c-Myc oncogene and FANC proteins (Fanconi anemia). 
Xenopus oocytes for studies of gene expression and channel activity related to human disease: Yet another strength of Xenopus is the ability to rapidly and easily assay the activity of channel and transporter proteins using expression in oocytes. This application has also led to important insights into human disease, including studies related to trypanosome transmission, Epilepsy with ataxia and sensorineural deafness Catastrophic cardiac arrhythmia (Long-QT syndrome) and Megalencephalic leukoencephalopathy.
Investigation of fundamental biological processes using Xenopus
Signal transduction: Xenopus embryos and cell-free extracts are widely used for basic research in signal transduction. In just the last few years, Xenopus embryos have provided crucial insights into the mechanisms of TGF-beta and Wnt signal transduction. For example, Xenopus embryos were used to identify the enzymes that control ubiquitination of Smad4, and to demonstrate direct links between TGF-beta superfamily signaling pathways and other important networks, such as the MAP kinase pathway and the Wnt pathway. Moreover, new methods using egg extracts revealed novel, important targets of the Wnt/GSK3 destruction complex.
Cell division: Xenopus egg extracts have allowed the study of many complicated cellular events in vitro. Because egg cytosol can support successive cycling between mitosis and interphase in vitro, it has been critical to diverse studies of cell division. For example, the small GTPase Ran was first found to regulate interphase nuclear transport, but Xenopus egg extracts revealed the critical role of Ran GTPase in mitosis independent of its role in interphase nuclear transport. Similarly, the cell-free extracts were used to model nuclear envelope assembly from chromatin, revealing the function of RanGTPase in regulating nuclear envelope reassembly after mitosis. More recently, using Xenopus egg extracts, it was possible to demonstrate the mitosis-specific function of the nuclear lamin B in regulating spindle morphogenesis and to identify new proteins that mediate kinetochore attachment to microtubules.
Embryonic development: Xenopus embryos are widely used in developmental biology. A summary of recent advances made by Xenopus research in recent years would include:
- Epigenetics of cell fate specification
- microRNA in germ layer patterning and eye development
- Link between Wnt signaling and telomerase
- Development of the vasculature
- Gut morphogenesis
- Contact inhibition and neural crest cell migration
DNA replication: Xenopus cell-free extracts also support the synchronous assembly and the activation of origins of DNA replication. They have been instrumental in characterizing the biochemical function of the prereplicative complex, including MCM proteins.
DNA damage response: Cell-free extracts have been instrumental to unravel the signaling pathways activated in response to DNA double-strand breaks (ATM), replication fork stalling (ATR) or DNA interstrand crosslinks (FA proteins and ATR). Notably, several mechanisms and components of these signal transduction pathways were first identified in Xenopus.
Apoptosis: Xenopus oocytes provide a tractable model for biochemical studies of apoptosis. Recently, oocytes were used recently to study the biochemical mechanisms of caspase-2 activation; importantly, this mechanism turns out to be conserved in mammals.
Regenerative medicine: In recent years, tremendous interest in developmental biology has been stoked by the promise of regenerative medicine. Xenopus has played a role here, as well. For example, expression of seven transcription factors in pluripotent Xenopus cells rendered those cells able to develop into functional eyes when implanted into Xenopus embryos, providing potential insights into the repair of retinal degeneration or damage. In a vastly different study, Xenopus embryos was used to study the effects of tissue tension on morphogenesis, an issue that will be critical for in vitro tissue engineering.
Physiology: The directional beating of multiciliated cells is essential to development and homeostasis in the central nervous system, the airway, and the oviduct. Interestingly, the multiciliated cells of the Xenopus epidermis have recently been developed as the first in vivo test-bed for live-cell studies of such ciliated tissues, and these studies have provided important insights into the biomechanical and molecular control of directional beating.
Use of Xenopus for small molecule screens to develop novel therapeutics
Because huge amounts of material are easily obtained, all modalities of Xenopus research are now being used for small-molecule based screens.
Chemical genetics of vascular growth in Xenopus tadpoles: Given the important role of neovascularization in cancer progression, Xenopus embryos were recently used to identify new small molecules inhibitors of blood vessel growth. Notably, compounds identified in Xenopus were effective in mice. Notably, frog embryos figured prominently in a study that used evolutionary principles to identify a novel vascular disrupting agent that may have chemotherapeutic potential. That work was featured in the New York Times Science Times 
In vivo testing of potential endocrine disruptors in transgenic Xenopus embryos: Endocrine disrupting chemicals released into the environment pose a potential public health risk, but our ability to identify such compounds in vitro vastly outstrips our ability to monitor the in vivo effects of such chemicals. A high-throughput assay for thyroid disruption has recently been developed using transgenic Xenopus embryos.
Small molecule screens in Xenopus egg extracts: Egg extracts provide ready analysis of molecular biological processes and can rapidly screened. This approach was used to identify novel inhibitors of proteasome-mediated protein degradation and DNA repair enzymes.
Use of Xenopus tropicalis for genetic studies
While Xenopus laevis is the most commonly used species for developmental biology studies, genetic studies, especially forward genetic studies, can be complicated by their pseudotetraploid genome. Xenopus tropicalis provides a simpler model for genetic studies, having a diploid genome.
Use of Morpholino knockdown techniques for gene knockdown in Xenopus
Morpholino oligos are also used in both X. laevis and X. tropicalis to probe the function of a protein by observing the results of eliminating the protein's activity, for example, as was done to screen a set of X. tropicalis genes, published in 2006.
Morpholino oligos (MOs) are short, antisense oligos made of modified nucleotides. MOs can knock down gene expression by inhibiting mRNA translation, blocking RNA splicing, or inhibiting miRNA activity and maturation. MOs have proven to be effective knockdown tools in developmental biology experiments and RNA-blocking reagents for cells in culture. MOs do not degrade their RNA targets, but instead act via a steric blocking mechanism RNAse H-independent manner. They remain stable in cells and do not induce immune responses. Microinjection of MOs in early Xenopus embryos can suppress gene expression in a targeted manner.
Like all antisense approaches, different MOs can have different efficacy, and may cause off-target, non-specific effects. Often, several MOs need to be tested to find an effective target sequence. Rigorous controls are used to demonstrate specificity, including:
- Phenocopy of genetic mutation
- Verification of reduced protein by western or immunostaining
- mRNA rescue by adding back a mRNA immune to the MO
- use of 2 different MOs (translation blocking and splice blocking)
- injection of control MOs
Xenbase provides a searchable catalog of over 2000 MOs that have been specifically used in Xenopus research. The data is searchable via sequence, gene symbol and various synonyms (as used in different publications). See: http://www.xenbase.org/reagents/morpholino.doXenbase maps the MOs to the latest Xenopus genomes in GBrowse, predicts 'off-target' hits, and lists all Xenopus literature in which the morpholino has been published.
- Wallingford, J., Liu, K., and Zheng, Y. 2010. Current Biology v. 20, p. R263-4
- Harland, R.M. and Grainger, R.M. 2011. Trends in Genetics v. 27, p 507-15
- "IACUC Learning Module — Xenopus laevis". University of Arizona. Retrieved 2009-10-11.
- Roots, Clive. Nocturnal animals. Greenwood Press. p. 19. ISBN 0-313-33546-X.
- Passmore, N. I. & Carruthers, V. C. (1979). South African Frogs, p.42-43. Witwatersrand University Press, Johannesburg. ISBN 0-85494-525-3.
- Tobias, Martha; Corke, A; Korsh, J; Yin, D; Kelley, DB (2010). "Vocal competition in male Xenopus laevis frogs". Behavioral Ecology and Sociobiology 64: 1791–1803.
- Tobias, ML; Viswanathan, SS; Kelley, DB (1998). "Rapping, a female receptive call, initiates male-female duets in the South African clawed frog". Proc Natl Acad Sci USA 95: 1870–1875.
- Gurdon, J. B.; Lane, C. D.; Woodland, H. R.; Marbaix, G. (17 September 1971). "Use of Frog Eggs and Oocytes for the Study of Messenger RNA and its Translation in Living Cells". Nature 233 (5316): 177–182. doi:10.1038/233177a0. PMID 4939175.
- Reynolds, F. H.; Premkumar, E.; Pitha, P. M. (1 December 1975). "Interferon activity produced by translation of human interferon messenger RNA in cell-free ribosomal systems and in Xenopus oocytes.". Proceedings of the National Academy of Sciences 72 (12): 4881–4885. doi:10.1073/pnas.72.12.4881.
- Heasman, J; Kofron, M; Wylie, C (Jun 1, 2000). "Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach.". Developmental biology 222 (1): 124–34. doi:10.1006/dbio.2000.9720. PMID 10885751.
- Schäfer, T; Pütz, M; Lienkamp, S; Ganner, A; Bergbreiter, A; Ramachandran, H; Gieloff, V; Gerner, M; Mattonet, C; Czarnecki, PG; Sayer, JA; Otto, EA; Hildebrandt, F; Kramer-Zucker, A; Walz, G (Dec 1, 2008). "Genetic and physical interaction between the NPHP5 and NPHP6 gene products.". Human Molecular Genetics 17 (23): 3655–62. doi:10.1093/hmg/ddn260. PMID 18723859.
- Reversade, B; Escande-Beillard, N; Dimopoulou, A; Fischer, B; Chng, SC; Li, Y; Shboul, M; Tham, PY; Kayserili, H; Al-Gazali, L; Shahwan, M; Brancati, F; Lee, H; O'Connor, BD; Schmidt-von Kegler, M; Merriman, B; Nelson, SF; Masri, A; Alkazaleh, F; Guerra, D; Ferrari, P; Nanda, A; Rajab, A; Markie, D; Gray, M; Nelson, J; Grix, A; Sommer, A; Savarirayan, R; Janecke, AR; Steichen, E; Sillence, D; Hausser, I; Budde, B; Nürnberg, G; Nürnberg, P; Seemann, P; Kunkel, D; Zambruno, G; Dallapiccola, B; Schuelke, M; Robertson, S; Hamamy, H; Wollnik, B; Van Maldergem, L; Mundlos, S; Kornak, U (Sep 2009). "Mutations in PYCR1 cause cutis laxa with progeroid features.". Nature Genetics 41 (9): 1016–21. doi:10.1038/ng.413. PMID 19648921.
- Pittman, AM; Naranjo, S; Webb, E; Broderick, P; Lips, EH; van Wezel, T; Morreau, H; Sullivan, K; Fielding, S; Twiss, P; Vijayakrishnan, J; Casares, F; Qureshi, M; Gómez-Skarmeta, JL; Houlston, RS (Jun 2009). "The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression.". Genome Research 19 (6): 987–93. doi:10.1101/gr.092668.109. PMC 2694486. PMID 19395656.
- Joukov, V; Groen, AC; Prokhorova, T; Gerson, R; White, E; Rodriguez, A; Walter, JC; Livingston, DM (Nov 3, 2006). "The BRCA1/BARD1 heterodimer modulates ran-dependent mitotic spindle assembly.". Cell 127 (3): 539–52. doi:10.1016/j.cell.2006.08.053. PMID 17081976.
- You, Z; Bailis, JM; Johnson, SA; Dilworth, SM; Hunter, T (Nov 2007). "Rapid activation of ATM on DNA flanking double-strand breaks.". Nature Cell Biology 9 (11): 1311–8. doi:10.1038/ncb1651. PMID 17952060.
- Ben-Yehoyada, M; Wang, LC; Kozekov, ID; Rizzo, CJ; Gottesman, ME; Gautier, J (Sep 11, 2009). "Checkpoint signaling from a single DNA interstrand crosslink.". Molecular Cell 35 (5): 704–15. doi:10.1016/j.molcel.2009.08.014. PMC 2756577. PMID 19748363.
- Sobeck, A; Stone, S; Landais, I; de Graaf, B; Hoatlin, ME (Sep 18, 2009). "The Fanconi anemia protein FANCM is controlled by FANCD2 and the ATR/ATM pathways.". The Journal of Biological Chemistry 284 (38): 25560–8. doi:10.1074/jbc.M109.007690. PMC 2757957. PMID 19633289.
- Dominguez-Sola, D; Ying, CY; Grandori, C; Ruggiero, L; Chen, B; Li, M; Galloway, DA; Gu, W; Gautier, J; Dalla-Favera, R (Jul 26, 2007). "Non-transcriptional control of DNA replication by c-Myc.". Nature 448 (7152): 445–51. doi:10.1038/nature05953. PMID 17597761.
- Dean, S; Marchetti, R; Kirk, K; Matthews, KR (May 14, 2009). "A surface transporter family conveys the trypanosome differentiation signal.". Nature 459 (7244): 213–7. doi:10.1038/nature07997. PMC 2685892. PMID 19444208.
- Bockenhauer, D; Feather, S; Stanescu, HC; Bandulik, S; Zdebik, AA; Reichold, M; Tobin, J; Lieberer, E; Sterner, C; Landoure, G; Arora, R; Sirimanna, T; Thompson, D; Cross, JH; van't Hoff, W; Al Masri, O; Tullus, K; Yeung, S; Anikster, Y; Klootwijk, E; Hubank, M; Dillon, MJ; Heitzmann, D; Arcos-Burgos, M; Knepper, MA; Dobbie, A; Gahl, WA; Warth, R; Sheridan, E; Kleta, R (May 7, 2009). "Epilepsy, ataxia, sensorineural deafness, tubulopathy, and KCNJ10 mutations.". The New England Journal of Medicine 360 (19): 1960–70. doi:10.1056/NEJMoa0810276. PMC 3398803. PMID 19420365.
- Gustina, AS; Trudeau, MC (Aug 4, 2009). "A recombinant N-terminal domain fully restores deactivation gating in N-truncated and long QT syndrome mutant hERG potassium channels.". Proceedings of the National Academy of Sciences of the United States of America 106 (31): 13082–7. doi:10.1073/pnas.0900180106. PMC 2722319. PMID 19651618.
- Duarri, A; Teijido, O; López-Hernández, T; Scheper, GC; Barriere, H; Boor, I; Aguado, F; Zorzano, A; Palacín, M; Martínez, A; Lukacs, GL; van der Knaap, MS; Nunes, V; Estévez, R (Dec 1, 2008). "Molecular pathogenesis of megalencephalic leukoencephalopathy with subcortical cysts: mutations in MLC1 cause folding defects.". Human Molecular Genetics 17 (23): 3728–39. doi:10.1093/hmg/ddn269. PMC 2581428. PMID 18757878.
- Cell. 2009. 136,123-35
- Science. 2007. 315, 840-3
- Cell. 2007. 131, 980-993
- PNAS. 2009. 106, 5165-5170
- Nature. 2006 440, 697-701
- Science 2006 311, 1887-1893
- Nat. Cell Biol. 2009. 11, 247-256
- Cell. 2007. 130, 893-905
- Dev. Cell. 2009. 17, 425-434
- Dev. Cell. 2009. 16, 517-527; Genes & Dev. 2009. 23, 1046-1051
- Nature. 2009. 460, 66-72
- Cell. 2008.135, 1053-64
- Genes & Dev. 2008. 22, 3050-3063
- Nature. 2008. 146, 957-961
- Mol. Cell. 2008. 32, 862-9; EMBO J. 2009. 28, 3005-14
- Mol Cell. 2009. 35,704-15; Cell. 2008. 134, 969-80; Genes Dev. 2007. 21, 898-903
- Dev Cell. 2009. 16, 856-66
- PLoS Biology. 2009. 7, e1000174
- Dev Cell. 2009. 16, 421-432
- Nat Genet. 2008. 40, 871-9; Nature. 2007. 447, 97-101
- Blood. 2009. 114, 1110-22; Blood. 2008. 112, 1740-9
- PloS Biol. 2012. V. 10, P e1001379
- "Gene Tests in Yeast Aid Work on Cancer".
- Environ. Sci. Technol. 2007. 41, 5908-14
- Nat Chem Biol. 2008. 4, 119-25; Int. J. Cancer. 2009. 124, 783-92
- Rana AA, Collart C, Gilchrist MJ, Smith JC (November 2006). "Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides". PLoS Genet. 2 (11): e193. doi:10.1371/journal.pgen.0020193. PMC 1636699. PMID 17112317.
"A Xenopus tropicalis antisense morpholino screen". Gurdon Institute.
- Xenbase ~ A Xenopus laevis and tropicalis Web Resource