Restriction endonuclease

1 Apr

Restriction endonuclease

resistance genes genes in plants that confer resis- tance to specific strains of pathogens. The first such gene to be cloned was the R gene in the tomato, which encodes a protein kinase (q.v.). This produces a resistance to certain species of Pseudomonas (q.v.). resistance transfer factor (RTF) See R plasmid. resolvase an enzyme catalyzing the site-specific recombination (q.v.) between two transposons pres- ent as direct repeats in a cointegrate structure (q.v.). The term also refers to a family of site-specific re- combinases. See site-specific recombinase. resolving power the ability of any magnifying sys- tem to reveal fine detail. This ability is often mea- sured as the minimum distance between two lines or points at which they are resolved as two rather than as a single blurred object.

The maximum re- solving power of the light microscope is about 0.2 micrometer; that of the electron microscope, about 0.5 nanometer. resource tracking a hypothesis involving host-par- asite coevolution according to which ectoparasites track a particular resource, such as a type of skin, hair, or feathers. If in addition there is opportunity for a given species of parasite to disperse to unre- lated host species, then there will be no direct paral- lel relationship between the taxonomy of the hosts and that of their parasites (contrast with Fahrenholz’s rule). In birds, for example, the same species of mite may be found on birds from different orders, and a single species of bird may be parasitized by different lice species. Thus, birds and their parasites show lit- tle phylogenetic parallelism. respiration the aerobic, oxidative breakdown and release of energy from fuel molecules. respiratory pigment a substance that combines reversibly with oxygen, thus acting as a carrier of it (hemoglobin, for example).

The color of respiratory pigments is due to their prosthetic groups. In red proteins like hemoglobin or cytochrome c, the pros- thetic group is heme (q.v.). responder in immunology, an animal capable of mounting an immunological response to a particular antigen. resting cell (nucleus) any cell (nucleus) not un- dergoing division. The cell (nucleus) is nevertheless very active metabolically. See cell cycle. restitution the spontaneous rejoining of experi- mentally induced, broken chromsomes to produce the original configuration. restitution nucleus 1. a nucleus containing double the expected number of chromosomes owing to a failure of the mitotic apparatus to function properly. 2. an unreduced product of meiosis. A diploid nu- cleus, resulting from the failure of the first or second meiotic division. See meiosis. restricted transduction See transduction. restriction ability of a bacteriophage to infect bac- teria belonging to certain strains but not others.

See DNA restriction enzyme. restriction allele See DNA restriction enzyme. restriction and modification model a theory pro- posed by W. Arber to explain host-controlled re- striction of bacteriophage growth. According to this model, the DNA of the bacterium contains specific nucleotide sequences that are recognized and cleaved by the restriction endonucleases carried by that cell. The bacterium also contains methylases that methyl- ate these sequences. This chemical modification thus protects the DNA of the bacterium from its own en- donucleases. However, these serve to degrade for- eign DNA introduced by phages.

See Appendix C, 1962, Arber; 1972, Kuhnlein and Arber. restriction endonuclease any one of many en- zymes that cleave foreign DNA molecules at specific recognition sites. Restriction endonucleases are coded for by genes called restriction alleles. The enzymes are named by a symbol that indicates the bacterial species from which they were isolated, followed by a Roman numeral that gives the chronological order of discovery when more than one enzyme came from the same source. Some restriction endonucle- ases, the organisms from which they were isolated, and their target nucleotide sequences are illustrated on page 384.

The arrows indicate the cleavage sites. Note that BamHI and EcoRI cleave the strands of DNA at specific sites four nucleotides apart. Such staggered cleavage yields DNA fragments with pro- truding 5′ termini. Such ends are said to be “sticky” or “cohesive” because they will hydrogen bond to complementary 3′ ends. As a result, the end of any DNA fragment produced by an enzyme, such as EcoRI, can anneal with any other fragment produced by that enzyme. This property allows splicing of for- eign genes into E. coli plasmids. Enzymes like HindII produce flush or blunt-ended fragments. Restriction endonucleases are used extensively to map DNA re- gions of interest. See Appendix C, 1962, Arber; 1968, Smith et al.; 1970, Smith and Wilcox; 1971, Danna and Nathans; 1972, Mertz and Davis, Hedgpeth et al.; Appendix E, Individual Databases; Alu family, po- lylinker site.

Restriction fragment

restriction fragment a fragment of a longer DNA molecule digested by a restriction endonuclease. restriction fragment length polymorphisms (RFLPs) variations occurring within a species in the length of DNA fragments generated by a specific endonuclease. Such variations are generated by mu- tations that create or abolish recognition sites for these enzymes. For example, restriction endonucle- ase mapping of human structural genes for beta he- moglobin chains has shown that patients with the sickle cell mutation produce abnormal restriction fragments. Since restriction enzyme analyses can be performed on DNA from amniotic fluid cells, RFLPs are now used in the prenatal diagnosis of genetic de- fects. A human mutant gene can be mapped, even when the nature of its product is unknown, by searching through DNA samples in a pedigree that contains the mutation, and looking for RFLPs that also segregate with the mutation. See Appendix C, 1978, Kan and Dozy; 1980, Botstein et al.; alphoid sequences, DNA fingerprint technique, variable num- bers of tandem repeats locus. restriction map a diagram portraying a linear array of sites on a DNA segment at which one or more restriction endonucleases (q.v.) cleave the molecule. restriction site a deoxyribonucleotide sequence at which a specific restriction endonuclease cleaves the molecule. restrictive conditions any environmental condi- tion (e.g., temperature or type of host) under which a conditional mutation either cannot grow or ex- presses the mutant phenotype. See temperature sen- sitive mutation. restrictive transduction See transduction. reticulate evolution the netlike lineage relation seen for a series of related allopolyploid species. The cross-links represent places where hybridization has occurred and allotetraploid species have arisen.

Re- ticulate evolution is common in plants. See dendritic evolution. reticulocyte an immature erythrocyte at an active stage in the synthesis of hemoglobin. reticuloendothelial system a network of phago- cytic cells residing in the bone marrow, spleen, and liver of vertebrates, where they free the blood or lymph of foreign particles. retina a delicate, multilayered, light-sensitive mem- brane that lines the inner eyeball and is connected to the brain by the optic nerve. The deepest layer of retinal cells contains melanin (q.v.). This pigment functions to absorb light that might scatter among the photoreceptors that lie above it and create con- fusing neural signals. Photoreceptor cells are con- tained in the visual epithelium, which overlies the pigmented layer.

The photoreceptor cells are modi- fied cilia that contain, in their outer segments, hun- dreds of thin membranes arranged like stacks of coins (see page 385). The photosensitive pigments are attached to these membranes. There are two morphologically distinct types of photoreceptors. The rod cells make up 95% of all photoreceptors and are responsible for perceiving light, particularly when it is at low intensity. Cone cells respond to different wavelengths of light and are responsible for color vision. The supply of photopigments and the outer segment discs themselves are continually re- plenished. As new discs are generated at the proxi- mal end of the outer segment, distal worn-out discs are phagocytosed by cells of the pigmented layer. See


color blindness, cone pigment genes, ocular albinism, opsin, retinitis pigmentosum (RP), rhodopsin (RHO). retinal a light-absorbing, carotenoid pigment that is derived from vitamin A (q.v.). Upon absorbing a photon of light, this chromophore (q.v.) undergoes a change in shape that involves the rotation of the starred carbon atom and the four carbon chain attached to it. This is the primary event in visual ex- citation that eventually leads to a nerve impulse. See opsin.

retinitis pigmentosum (RP) a pathological condi- tion where the retina, when viewed through an oph- thalmoscope, is seen dotted with jet-black pigment spicules. These represent dying photoreceptor cells. There are at least seven autosomal dominant, one autosomal recessive, and three X-linked recessive forms of the disease. One mutant autosomal gene for RP maps at the site (on 3p) of the gene that en- codes rhodopsin (q.v.). Another gene (at 6p) en- codes a glycoprotein called peripherin. This is an ad- hesion molecule localized in the rim of each disc. It joins adjacent discs and maintains their integrity as they lie stacked together in the outer segment of the photoreceptor cells. The most common RP muta- tion in American patients is P23H, a missense muta- tion in the rhodopsin gene.

The mutated rhodopsin forms high molecular weight aggregates which im- pair the ubiquitin-proteasome pathway (q.v.) of pro- tein degradation. See retina, rhabdomere. retinoblastoma a malignant neoplasm composed of primitive retinal cells usually occurring in children less than three years old. Retinoblastoma occurs in hereditary and non-hereditary forms. In the case of hereditary retinoblastoma, patients are generally af- fected bilaterally. The gene involved (RB) is located on the long arm of chromosome 13 at band 14. The normal gene contains 27 exons. The RB gene prod- uct is a nuclear phosphoprotein (pRB). The phos- phates are usually attached to serine and threonine residues. The DNA binding of pRB depends on its degree of phosphorylation (only the underphosphor- ylated molecule binds). Mutant alleles of the RB gene have been found in other types of human can- cers besides retinoblastomas. Such mutations often involve deletions in exons 13-17. Introduction of

retinoic acid

the wild-type RB gene into these tumor cells sup- presses their uncontrolled growth. See Appendix C, 1971, Knudson; 1989, Hong et al.; 1990, Bookstein et al.; anti-oncogenes, Knudson model, retina. retinoic acid a morphologically active compound that exists in a concentration gradient along the limb bud of tetrapods and stimulates the development of limbs and digits. Retinoic acid is vitamin A (q.v.) with the terminal CH2OH replaced by a COOH group. retinol synonymous with vitamin A (q.v.). retrodiction the act of predicting the yet undis- covered results of past events. Useful theories of evolution should allow retrodictions that can be vali- dated by looking in the right places within the fossil record. retrogene See processed gene. retrogression evolution toward a less complex state; characteristic of some parasitic groups. For ex- ample, tapeworms, having no digestive system, are thought to have evolved from free-living flatworms with a digestive system.

retroposons transposable elements (q.v.) that mo- bilize via an RNA intermediate. Each DNA segment in the host chromosome is transcribed into RNA and then reverse-transcribed via a reverse transcriptase (q.v.) into a DNA segment. This is reinserted into the host genome, usually at a new site. Retroposons are the most abundant transposons in plants. These elements account for 70% of the nuclear DNA in maize. The best-understood retroposons are retrovi- ruses (q.v.) such as HIV (q.v.). Retroposon is a short- ened form of retrotransposon, which also appears in the literature. See Appendix C, 1985, Boeke et al.; 1990, Biessmann et al.; centromere, copia elements, repetitious DNA, telomere, Ty elements. retroregulation the ability of downstream DNA sequences to regulate translation of an mRNA. retrotransposon See retroposon. retroviruses RNA viruses that utilize reverse tran- scriptase (q.v.) during their life cycle.

This enzyme allows the viral genome to be transcribed into DNA. The name retrovirus alludes to this “backward” tran- scription. The transcribed viral DNA is integrated into the genome of the host cell where it replicates in unison with the genes of the host chromosome. Therefore retroviruses violate the central dogma (q.v.) during their replication. Most retrovirions carry two copies of a linear, positive sense, ssRNA held together by hydrogen bonds. Most retroviruses carry the genes gag, pol, and env. The gag gene en- codes the structural proteins of the capsid, and env codes for the glycoproteins that form spikes on the envelope of the viral membrane. The pol region en- codes a protease, a reverse transcriptase, and an in- tegrase (q.v.). The transcription of the retroviral ge- nome results in the production of a polycistronic mRNA. This is translated to yield a polyprotein that is subsequently cleaved by the viral protease into the functional subunits. The retroviruses are assigned to three groups: the Lentivirinae, the Oncovirinea, and the Spumavirinae. HIV viruses I and II (q.v.) belong to the Lentivirinae.

The Oncovirinae contain viruses that attack birds, such as the Rous sarcoma virus, ro- dents (the Friend, Moloney, and Rauscher leukemia viruses and the mammary tumor virus), carnivores (the feline leukemia and sarcoma viruses), and pri- mates (the simian sarcoma virus) (all of which see). Also see enveloped viruses, reverse transcription, virus. reversals situations in phylogenetic analysis in which a derived character state changes (reverses) to a preexisting character state. For example, among the vertebrates, limbs are considered to be derived from a limbless state; but snakes are thought to have evolved from tetrapod (four-legged) ancestors and in the process have lost their limbs. reverse genetics an experimental approach for determining gene function in which the sequence of a gene of unknown function is deliberately altered in vitro (q.v.) and introduced back into the cell or the organism, or the expression of the gene is disrupted in order to determine its phenotypic effect. Gene modification or knockout (q.v.) is achieved by such means as chemical and transposon-induced muta- genesis, gene targeting (q.v.), and RNA interference (RNAi) (q.v.). With the availability of tools for ge- nome manipulation and whole-genome sequence data, reverse genetics has gained prominence in ge- netic analysis in a variety of organisms, including bacteria, yeast, the nematode, the fruit fly, the mouse, and many plant species.

This approach is the reverse of the regular or forward genetics approach, in which one begins with a mutant allele or phenotype and then identifies the wild-type gene and its biolog- ical effect. See functional cloning, gene targeting, knockout, positional cloning, transgenic animals. reverse loop pairing See inversion. reverse mutation a change in a mutant gene which restores its ability to produce a functional protein. Compare with forward mutation. reverse selection selection in an experimental sit- uation for a trait opposite to the one selected earlier (e.g., selection first for increased numbers of tho-

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