racic bristles in Drosophila, then for decreased num- bers). reverse transcriptase RNA-dependent DNA poly- merase (q.v.). reverse transcription DNA synthesis from an RNA template, mediated by reverse transcriptase. Since retroviruses undergo reverse transcription, they have two genomic forms: ssRNA in their viri- ons and dsDNA in their prophages. See RNA-depen- dent DNA polymerase. reverse transcription-polymerase chain reaction (RT-PCR) The most sensitive technique for mRNA detection and quantitation, involving amplification of a reverse transcription product. In this technique, an RNA template is reverse transcribed using an RNA-dependent DNA polymerase (q.v.).
The re- sulting cDNA (q.v.) is then amplified using the poly- merase chain reaction (q.v.). cDNA corresponding to the rarest of transcripts can be detected by this method. RT-PCR products are quantitated using any of a variety of methods, providing information about the expression levels of a particular gene or relative transcription of multiple RNAs. reversion reverse mutation (q.v.). revertant 1. an allele that undergoes reverse muta- tion. 2. an organism bearing such an allele. reverted Bar See Bar. Rf in paper chromatography, a ratio given by the distance traveled by the solute divided by the dis- tance traveled by the solvent. For a given solute mol- ecule the Rf varies with the solvent, and therefore the solvent must be specified for any Rf value. RF 1. replicative form; 2. recombination frequency. R factor resistance factor (q.v.). RFLP pronounced “rif lip.” See restriction fragment length polymorphisms. R genes of maize a family of genes responsible for determining the temporal and spatial pattern of an- thocyanin (q.v.) pigmentation in the corn plant. The gene products are proteins that bind to DNA and activate the transcription of the structural genes that function directly in anthocyanin synthesis. rhabdomere a specialized organelle found in the photoreceptor cells of an ommatidium (q.v.).
In Drosophila each rhabdomere is composed of 60,000 tightly packed microvilli which expand the membrane surface to accommodate hundreds of millions of molecules of rhodopsin (q.v.). Each rhab- domere functions like the discs in the outer seg- ments of the photoreceptor cells of the vertebrate retina (q.v.). See microvillus. rhabdoviridae a family of enveloped viruses (q.v.) with negative-strand RNA genomes. The rabies virus (q.v.) belongs to this family. It binds to a receptor on peripheral nerves and is then transmitted to cells of the central nervous system and salivary glands. rhesus factor See Rh factor. rhesus monkey See Macaca mulatta. rheumatoid factor a distinctive gamma globulin commonly present in the serum of patients with rheumatoid arthritis. Rh factor an antigen occurring on the erythrocytes of certain human beings. The Rh system actually contains several antigens.
The most important one was first found in the Rhesus monkey—hence the name. Persons of genotype r/r produce no antigen and are classified as Rh-negative. R/R and R/r indi- viduals produce the antigen. A pregnant mother who is Rh-negative but is carrying an Rh-positive child may produce antibodies against the child in utero, causing the child to develop a hemolytic dis- ease called erythroblastosis fetalis. However, this oc- curs only if the mother has been previously exposed to the Rh antigen from cells entering her circulation during the birth of a previous Rh-positive baby. The Rh antigens are encoded by two closely linked and highly homologous genes (RHD and RHCE) located at 1p34-36. The most clinically important antigen, D, is encoded by RHD, and the Rh-negative pheno- type results from deletions in the RHD gene. The highest frequency of Rh in the world is seen in Basques (q.v.).
See Appendix C, 1939, Levine and Stetson; 1947, Mourant; RhoGAM. Rhizobium a genus of nitrogen-fixing bacteria that live as symbionts in the root nodules of leguminous plants. The most studied species are R. meliloti and R. trifoli. The genes involved in host specificity, no- dulation, and nitrogen fixation are carried on large plasmids, and restriction maps have been con- structed of those regions carrying symbiotically im- portant genes. See Appendix A, Bacteria, Proteobact- eria; Appendix C, 1981, Hombrecher et al.; Appendix E; bacteroids, nif genes, plasmid, restriction map, sym-plasmid. Rhizopoda the phylum of protoctists containing singled-celled amoebas. See Amoeba proteus, Appen- dix A. rhodoplast the red plastid of red algae.
rhodopsin (RHO) the light-sensitive chromopro- tein found in the rod cells of the retina. Rhodopsin consists of the protein opsin (q.v.) in combination with retinal (q.v.). In the primary event of visual ex- citation, rhodopsin (also called visual purple) is bleached to a yellow compound. In humans, the gene encoding RHO resides at 3q 21.3-24. RHO is a multiple transmembrane domain protein (q.v.). The cone pigment genes (q.v.) show considerable se- quence similarities to RHO. See color blindness, reti- nitis pigmentosum (RP), rhabdomere. rhodamine B a fluorochrome commonly used to tag compounds that bind to specific cell compo- nents. See rhodaminylphalloidin.
rhodaminylphalloidin a fluorescent derivative of phalloidin used to specifically stain actin filaments in whole mounts of cells. See fluorescence microscopy, phallotoxins. rho factor an oligomeric protein in E. coli that at- taches to certain sites on its DNA to assist in termi- nation of transcription. RhoGAM the trade name for anti-Rh gamma glob- ulin used in the prevention of Rh hemolytic disease. See Appendix C, 1964, Gorman et al.; Rh factor. rho( )-independent terminators E. coli DNA se- quences recognized by RNA polymerase as tran- scription termination signals in the absence of rho (ρ) factors.
Rhynchosciara a genus of fungus gnats belonging to the Sciaridae. Two species, R. angelae and R. hol- laenderi, can be reared in the laboratory and have been extensively studied because of the gigantic po- lytene chromosomes found in various larval tissues (such as the salivary glands, Malpighian tubules, and anterior mid gut). RNA puffs occur often, and they are tissue and developmental stage specific. The DNA puffs are rare and were first discovered in Rhynchos- ciara.
They occur in several regions of the polytene chromosomes of the salivary glands of fourth instar larvae. The DNA in each puff undergoes a 16-fold increase, and the mRNAs transcribed from the am- plified genes are translated into salivary proteins.
See Appendix A, Arthropoda, Insecta, Diptera; gene am- plification, Sciara. RIA radioimmunoassay (q.v.). riboflavin vitamin B2, a subunit of flavin adenine dinucleotide and flavin mononucleotide. The struc- ture appears below. riboflavin phosphate flavin mononucleotide (q.v.). ribonuclease the enzyme that hydrolyzes ribo- nucleic acid. ribonuclease A an enzyme made up of 124 amino acids, first isolated from bovine pancreas.
Ribo- nuclease A hydrolyzes pyrimidines at the 3′ phos- phate group and cleaves the 5′ phosphate linkage to the adjacent nucleotide. The end products of diges- tion are pyrimidine 3′ phosphates and oligonucleo- tides with pyrimidine 3′ phosphate termini. Ribo- nuclease A was the first protein to be subjected to reversible chemical modifications that demonstrated that the linear sequence of amino acids determined the unique three-dimensional structure of the pro- tein. See Appendix C, 1961, Anfinsen et al.
ribosomes of organelles
ribonuclease H an endonuclease that specifically degrades the RNA strands of RNA-DNA hybrid molecules. However, the enzyme does not hydro- lyze RNAs complexed with Morpholinos (q.v.). ribonuclease P a universally occurring enzyme which, by removing the tRNA molecules, converts them into their func- tional states. RNase P is a heterodimer made up of one large RNA and one small protein molecule. The protein alone has no catalytic activity. The RNA alone can catalyze the cleavage, although less effi- ciently than the intact enzyme. RNase P was the first RNA found to exhibit the characteristics of a true enzyme.
See Appendix C, 1983, Guerrier-Takada et al.; 1989, Cech and Altmann; ribozyme. ribonuclease T1 cifically attacks the 3′ phosphate groups of guano- sine nucleotides and cleaves the 5′ phosphate linkage to the adjacent nucleotide. The end products of di- gestion are guanosine 3′ phosphates and oligonucle- otides with guanosine 3′ phosphate termini. ribonucleic acid (RNA) any of a family of poly- nucleotides characterized by their component sugar (ribose) and one of their pyrimidines (uracil). RNA molecules are single stranded and have lower molec- ular weights than DNAs. There are three classes of RNAs: (1) messenger RNA (q.v.), (2) ribosomal RNA (see ribosome), and (3) transfer RNA (q.v.). See Appendix C, 1941, Brachet and Caspersson; hy- drogen bonding, plus (+) and minus (−) viral strands. ribonucleoprotein a complex macromolecule con- taining both RNA and protein and symbolized by RNP. ribonucleotide an organic compound that consists of a purine or pyrimidine base bounded to ribose, which in turn is esterified with a phosphate group. ribose a five-carbon sugar. See ribonucleic acid (RNA).
ribosomal binding site See Shine-Dalgarno se- quence. ribosomal DNA See rDNA. ribosomal DNA amplification See rDNA amplifi- cation. ribosomal precursor RNA See preribosomal RNA. ribosomal protein See ribosome. ribosomal RNA (rRNA) See ribonucleic acid (RNA), ribosome. ribosomal RNA genes rRNA genes reside as tan- dem repeating units in the nucleolus organizer re- gions of eukaryotic chromosomes. Each unit is sepa- rated from the next by a nontranscribed spacer.
Each unit contains three cistrons coding for the 28S, 18S, and 5.8S rRNAs. The transcriptional polarity of the unit is 5′-18S-5.8S-28S-3′. Ribosomal RNA genes are often symbolized by rDNA. See Miller trees, preribosomal RNA, rDNA amplification, RNA polymerase. ribosomal stalling See attenuation. ribosome one of the ribonucleoprotein particles, 10-20 nanometers in diameter, that are the sites of translation. Ribosomes consist of two unequal sub- units bound together by magnesium ions. Each sub- unit is made up of roughly equal parts of RNA and protein. Each ribosomal subunit is assembled from one molecule of ribosomal RNA that is noncova- lently bonded to 20 to 30 smaller protein molecules to form a compact, tightly coiled particle. In eukary- otes, the rRNAs of cytoplasmic ribosomes are formed by cistrons localized in the nucleolus orga- nizer region (q.v.) of chromosomes. Animal ribo- somes also contain a 5.8S rRNA, which is hydrogen bonded to the 28S rRNA and is derived from the same intermediate precursor as the 28S rRNA (see table on page 390).
See Appendix C, 1956, Palade and Siekevitz; 1959, McQuillen et al.; 1961, Jacob and Monod, Waller and Harris, Littauer; 1964, Brown and Gurdon; 1965, Sabatini et al.; 1980, Woese et al.; 2001, Yusupov et al.; cyclohexamide, preribosomal RNA, receptor-mediated translocation, ribosomes of organelles, 16S rRNA, translation. ribosomes of organelles ribosomes of chloro- plasts and mitochondria show a variety of sedimen- tation constants. Chloroplast ribosomes are 70S, mi- tochondrial ribosomes from plant cells are 78S, mitochondrial ribosomes from fungal cells are 73S, and mitochondrial ribosomes from mammalian cells are 60S. Both mitochondria and chloroplasts are be- lieved to have arisen from free-living prokaryotes that fused with primitive nucleated cells. The fact that translation starts with N-formylmethionine on
the ribosomes of both mitochondria and chloroplasts supports the theory of their endosymbiotic orgin. See initiator tRNA, serial symbiosis theory, 5S rRNA. riboswitches in prokaryotes and some eukaryotes, genetic control elements found in untranslated re- gions of some messenger RNAs (mRNAs), which di- rectly and selectively bind target metabolites and regulate the transcription or translation of the bound mRNAs. The binding of the metabolite to the RNA usually induces a structural change in the mRNA, which causes either the termination of transcription or inhibition of translation initiation.
Riboswitches may also regulate gene expression at the level of pre- mRNA splicing, or mRNA processing or stability. A number of distinct riboswitches have been identi- fied, which regulate a variety of metabolic pathways. These genetic elements do not require proteins for ligand recognition and regulatory functions and are thought to be of ancient origin, from a time period prior to the emergence of proteins. 5-ribosyluracil pseudouridine. See rare bases. ribothymidine See rare bases. ribotype the RNA complement of a cell. ribozyme an RNA molecule with catalytic activ- ity.
An example is the self-splicing rRNA of Tetrahy- mena thermophila. The gene for the 26S rRNA con- tains an intron 413 base pairs long. The precursor rRNA molecule transcribed from this gene includes a copy of this intervening sequence, which must be deleted by RNA splicing. If the pre-rRNAs are incu- bated in vitro with certain cations and guanosine, the intervening sequences are excised and the mature se- quences are ligated. Ribonuclease P (q.v.) is another example of a ribozyme. Perhaps in the primordial biosphere ribozymes functioned as the first enzymes, and as life evolved proteins began to fine-tune the catalysis and eventually replaced ribozymes as en- zymes. In vitro selection experiments have generated ribozymes that can catalyze self-alkylation reactions. This finding suggests that RNA may be capable of a broad range of catalytic activities. See Appendix C, 1981, Cech et al.; 1989, Cech and Altman; 1995, Wilson and Szostak; hairpin ribozyme, hammerhead ribozyme, in vitro evolution. ribulose-1,5-bisphosphate carboxylase-oxygen- ase (RuBisCO) an enzyme responsible for virtually all photosynthetic CO2 fixation. It is located in the stromal surface of the thylakoid membranes of chlo- roplasts (q.v.). RuBisCO is probably the most abun- dant protein in the biosphere, since it makes up about 40% of the protein in green leaves. RuBisCO catalyzes the reaction:
The enzyme consists of eight large subunits (Mr 56,000 each) and eight small subunits (Mr 14,000 each). See cyanelles, Cyanobacteria, rbc genes.
rice Oryza sativa (q.v.).
Ricinus communis the castor bean. The genetics of sex determination has been extensively studied in this species. rickets a deficiency disease of growing bone due to insufficient vitamin D in the diet. See vitamin D- resistant rickets. Rickettsia a genus of Gram-negative, oval to rod- shaped, nonmotile, obligatory intracellular prokary- otes, placed in the Proteobacteria. All are spread by arthropod vectors (lice, fleas, mites, and ticks). See Appendix A, Prokaryotes, Proteobacteria. Rickettsia prowazeki the bacterium responsible for louse-borne epidemic typhus. Its genome con-
tains 1,111,523 base pairs and only 834 ORFs, com-
pared to the 4,300 ORFs of the free-living bacte- rium E. coli. Because of its parasitic habit, this rickettsia has undergone reductive evolution (q.v.). For example, it has lost genes that encode enzymes that metabolize sugars and synthesize amino acids and nucleotides. Based on the sequences of nucleo- tides in the rRNA of the small subunit of the ribo- somes, these bacteria are closest to the ancestor of mitochondria. See Appendix A, Bacteria, Proteobac- teria; Appendix C, 1998, Anderson et al.; mitochon- drion, serial symbiosis theory. rifampicin the most commonly used of the rifamy- cins (q.v.). rifamycins a group of antibiotic molecules pro- duced by Streptomyces mediterranei that interfere with the beta subunit of prokaryotic RNA polymer- ases and thereby inhibit initiation of transcription.
See RNA polymerase. rift a place where the earth’s surface is cracking apart because of tectonic activity. An example of an undersea rift is the Galapagos rift, about 380 miles north of the Galapagos Islands, where undersea vent communities (q.v.) were first discovered. See Appen- dix C, 1977, Corliss and Ballard. right splicing junction the boundary between the right (3′) end of an intron and the left (5′) end of an adjacent exon in mRNA; also called the acceptor splicing site. ring canals canals connecting sister cystocytes in the Drosophila egg chamber. The rim of each canal is formed by a partially closed contractile ring (q.v.). The canal system is initially plugged by a polyfu- some (q.v.). Once this dissolves, the ring canals allow a stream of cytoplasm to flow from the nurse cells (q.v.) to the oocyte.
As each ring matures, it develops a coating of actin filaments and increases in diameter and thickness. During the growth of the egg chamber, proteins encoded first by the gene hts and later by kel serve to organize the actin filaments by cross-linking them in various ways. This process requires phosphorylation reactions catalyzed by Src protein tyrosine kinases. See cystocyte divisions, hu- li tai shao (hts), kelch (kel), and Src. ring chromosome 1. an aberrant chromosome with no ends. 2. a ring-shaped chromosomal associa- tion seen during diakinesis in normal metacentric tetrads with two terminal chiasmata.
Ringer solution a physiological saline containing sodium, potassium, and calcium chlorides used in physiological experiments for temporarily maintain- ing cells or organs alive in vitro. Ringer solution is sometimes simply designated as “ringer.” RING finger a protein motif that helps add ubiqui- tin (q.v.) to proteins, thereby marking them for de- struction.
The RING finger is an evolutionarily con- served structure found in more than 200 proteins, in which two loops of amino acids are pulled together at their base by eight cysteine or histidine residues that bind two zinc ions. See metaloprotein. ring gland a gland lying above the hemispheres (h) of the brain of the larval Drosophila. Its lateral extremities encircle the aorta (a) like a ring, hence its name. The gland contains three endocrine tissues: the corpus allatum (ca), the prothoracic gland (pg), and the corpus cardiacum (cc). The diagrams here show the ring gland viewed from the side (A) and from above (B).
Other symbols are as follows: n1 = afferent nerve to the corpus cardiacum from the brain; n2 = efferent nerve from the corpus cardi- acum; n3 = nerve from corpus cardiacum to the cor- pus allatum; o = oesophagus; vg = ventral ganglion. See allatum hormones, ecdysone. RIP repeat-induced point mutation (q.v.).
RISC RNA-induced silencing complex. See RNA in- terference (RNAi). RK a symbol used in Drosophila studies to indicate rank or valuation of a given mutant. For example, RK1 indicates the best and most used mutants, with sharp classification, excellent viability, and accurate genetic localization. RK5 mutants show poor pene- trance, low viability, and their chromosomal loci are not accurately determined. R loop during molecular hybridization, the single- stranded sense strand of DNA that is prevented from reannealing because its complementary template strand is base-paired with an mRNA exon as a heter- oduplex. R-loop mapping a technique for visualizing under the electron microscope the complementary regions shared by a specific eukaryotic RNA and a segment of one strand of a DNA duplex.
The RNA-DNA hy- brid segment displaces one of the DNA strands, causing it to form a loop; hence the name of the technique. Double-stranded regions appear thicker than single-stranded regions in electron micrographs. Introns cannot hybridize with mature mRNA (from which introns have been removed); thus, one intron results in two R loops, two introns yield three R loops, etc. See Appendix C, 1977, Chow and Berget. RMRP a gene located on human chromosome 9 at p13. It encodes an RNA component of a Mitochon- drial RNA Processing endoribonuclease (hence the abbreviation). Therefore the RNAs transcribed from the nuclear gene are transferred to mitochondria where they form enzyme components. Mutations of RMRP result in a hereditary disease called cartilage- hair hypoplasia (CHH) (q.v.).
See Appendix C, 2001, Ridanpaa et al. RNA ribonucleic acid (q.v.). RNA amplification a technique that allows the synthesis by T7 RNA polymerase of antisense mole- cules from cDNAs containing a T7 promoter. See Appendix C, 1990, Van Gelder et al. RNAase See RNase. RNA coding triplets See amino acid, start codon, stop codon. RNA-dependent DNA polymerase an enzyme that synthesizes a single strand of DNA from deoxy- ribonucleoside triphosphates, using RNA molecules as templates. Such enzymes occur in oncogenic RNA viruses.
This class of enzymes, also known as reverse transcriptases, can be used experimentally to make complementary DNA (cDNA) from purified RNA. The functioning of these polymerases contra- dicts the central dogma (q.v.) in the sense that the direction of information exchange between DNA and RNA is reversed. See Appendix C, 1970, Balti- more, Temin and Mizutani; Rous sarcoma virus (RSV), telomerase. RNA-dependent RNA polymerase an enzyme that uses an RNA template to synthesize a comple- mentary RNA molecule.
All RNA viruses use such polymerases to replicate their genomes and to tran- scribe mRNAs from their minus strands. See plus (+) and minus (−) viral strands, replicase, RNA replicase. RNA-driven hybridization an in vitro technique that uses an excess of RNA molecules to ensure that all complementary sequences in single-stranded DNA undergo molecular hybridization. See DNA- driven hybridization. RNA editing a mechanism for modifying the nu- cleotide compositions of previously formed mRNAs by adding or deleting uridine molecules at precise sites within the coding regions of mRNAs.