: Gene map of the Drosophila yakuba mitochondrial genome pro- vided by Wolstenholme. The circular molecule of 16,019 nucleotide pairs has been completely sequenced. The 13 pro- tein genes are COI, COII, and COIII (subunits 1, 2, and 3 of cytochrome c oxidase), Cyt b (cytochrome b), ATPase 6 and 8 (subunits 6 and 8 of the Fo ATPase complex), and ND1-ND6 and ND4L (components 1-6 and 4L of the respiratory chain NADH dehydrogenase). Each tRNA gene (hatched) is identified by the one letter amino acid code, and serine and leucine tRNA genes are also identified by the codon family (in parenthesis) that the corresponding tRNAs recognize. s-rRNA and l-rRNA indicate the small and large rRNA genes, respectively. Arrows within and outside the molecule indicate the direction of transcrip- tion of each gene. The numbers of apparently non-coding nucleotides that occur between the genes are shown at the gene boundaries on the inner side of the map. Negative numbers indicate overlapping nucleotides of adjacent genes. Asterisks identify possible incomplete termination codons (T or TA). The location of the origin of replication (O) within the A+T- rich region (dotted) and the direction of replication (R) were determined by electron microscope studies (Goddard and Wol- stenholme, 1980, Nucleic Acids Research 8: 741-757). This map is a modification of that given by Clary and Wolstenholme (1985, J. Mol. Evol. 22: 252-27). NONCHROMOSOMAL INHERITANCE ____________________________________________________________________ # mitochondria Mitochondrial DNA (mtDNA) is a covalently closed duplex cir- cle of about 19,500 base pairs. Contained within Drosophila mtDNA is a region exceptionally rich in adenine + thymine. This A+T-rich region comprises 5-6 kb in D. melanogaster, but is shorter in related species (Fauron and Wolstenholme, 1980, Nucleic Acids Res. 8: 2439-52); some intraspecific variation in the length of this region is recorded; e.g., 5.9, 5.5, and 5.1 kb in three strains of D. melanogaster; these differences used to confirm maternal inheritance of Drosophila mitochon- dria (Fauron and Wolstenholme, 1980, Nucleic Acids Res. 8: 5391-5410). Mitochondria of D. melanogaster replaced by those of D. mauritiana by embryo injection (Niki, Chigusa, and Matsuura, 1989, Nature 341: 551-52). The origin of replica- tion is located within the A+T-rich segment and proceeds uni- directionally around the circle, with the first strand becom- ing as much as 100% completed before the second strand ini- tiates. Extensive sequencing of mtDNA of both D. yakuba and D. melanogaster has shown the two molecules to be highly homolo- gous and to encode thirteen hydrophobic polypeptides, which have been identified as subunits of enzyme complexes associ- ated with the inner mitochondrial membrane, a large and a small ribosomal RNA and 22 transfer RNA's. The polypeptides include cytochrome b, two subunits (6 and 8) of the ATPase, three subunits of the cytochrome c oxidase, and seven subunits of the NADH reductase complex (Chomyn, Marioeeini, Cleeter, Ragan, Matsuno-Yagi, Hatefi, Doolittle, and Attardi, 1985, Nature 314: 592-97). These coding regions are densely packed, with few if any nucleotides separating them and in a few cases overlapping, and none of them containing introns (de Bruijn, 1983, Nature 304: 234-41; Wolstenholme and Clary, 1985, Genetics 109: 725-44; Garesse, 1988, Genetics 118: 649-63). The direction of replication and the order and directions of transcription of these mitochondrial genes are indicated on the diagram of the Drosophila yakuba mitochondria at the beginning of this section; the A+T-rich region of D. yakuba is considerably shorter than that of D. melanogaster. Mouse mitochondrial DNA contains the same genes, but the order differs from that of Drosophila by three inversions, and there has been some shuffling of tRNA-encoding sequences [Wol- stenholme, Clary, Macfarlane, Wahleithner, and Wilcox, 1985, Orgainzation and Evolution of Invertebrate Mitochondrial Genomes (Quagliariello, Slater, Palmieri, Saccone, and Kroon, eds.). Elsevier, Amsterdam, New York, Oxford, Vol. 2: pp. 61-70]. The polypeptide encoding genes use ATA, ATT, or ATG as initiation codons; ATC appears only as an internal codon. TAA is the most frequently used termination codon with ATG found in one case; some genes end in T or TA, and the stop codon is generated by polyadenylation (Garesse). UGA -> tryptophan instead of stop; AUA -> methionine instead of isoleucine; unlike mammalian mitochondria, AGA -> serine instead of arginine as in chromosomally derived messages or stop as in mammalian mitochondria. Overall codon usage reflects the rela- tively high ratio of AT/CG in mitochondrial vis-a-vis chromo- somal DNA. # picornaviruses Three small RNA viruses known as picornaviruses are found in Drosophila melanogaster but only two of these viruses, DAV and DPV are transmitted from females to their offspring in the egg. The third DCV, is transmitted by contamination of the surface of the egg. origin: Transmitted vertically in eggs of young, naturally- infected females of both natural and lab populations (old naturally-infected females and artificially-infected females cannot transmit DAV or DPV in this way); viruses also transmitted by contact, ingestion and inoculation. references: Plus and Duthoit, 1969, C.R. Acad. Sci., Paris 268: 2313. David and Plus, 1971, Ann. Inst. Pasteur, 120: 107-119. Jousset, Plus, Croizier, and Thomas, 1972, C.R. Acad. Sci. Paris 275: 3043-46. Teninges and Plus, 1972, J. Gen. Virol. 16: 103-17. Brun and Plus, 1980, The Genetics and Biology of Drosophila (Ashburner and Wright, eds.). Academic Press, London, New York, San Francisco, Vol. 2d, pp. 625-702. Ashburner, 1989, Drosophila, a Laboratory Handbook, Cold Spring Harbor Press, Cold Spring Harbor, New York, pp. 101- 02. phenotype: Both DAV and DPV are ribosomal viruses of 625-702 nm that are resistant to ether, ethanol, and low pH treatment. Eggs infected with these viruses can be cured by dechorionat- ing them using sodium hypochlorite and transferring them to fresh medium. Unlike DCV, which kills the flies a few days after injection, the viruses DAV and DPV are not immediately pathogenic to their hosts; however, they reduce the longevity and female fertility of the infected flies. No carbon dioxide sensitivity is observed in Drosophila as a result of these viruses. DAV and DPV multiply in the gut, Malpighian tubules, and ovaries of Drosophila melanogaster and are only found in the cytoplasm (not the nucleus) of the infected cells. Molecu- lar weights of major capsid polypeptides of the viruses are: DAV 31,600, 41,200, 72,900 DPV 26,000, 19,400, 48,000. # sigma: sensitivity to carbon dioxide references: L'Heritier and Teissier, 1937, Comp. Rend. 20665: 1099-1101. 1938, Comp. Rend. 206: 1193-9, 1683. 1945, Publ. Lab. Ecole Norm. Super. Biol. (Paris) 1: 35-74. L'Heritier, 1948, Heredity 2: 325-48. 1951, Cold Spring Harbor Symp. Quant. Biol. 16: 99-112. 1958, Advances in Virus Research (K.M. Smith and M.A. Lauffer, eds.). Academic Press, London, New York, San Francisco, pp. 195-245. L'Heritier, and Plus, 1963, Biological Organization at the Cellular and Supercellular level (R.J.C. Harris, ed.). Academic Press, London, New York, San Francisco, pp. 59-71. Gay, 1978, Mol. Gen. Genet. 159: 269-83. L'Heritier, 1979, Handbook of Genetics (King, ed.). Plenum Press, New York and London, Vol. 3, pp. 813-18. Brun and Plus, 1980, The Genetics and Biology of Drosophila (Ashburner and Wright, eds.). Academic Press, London, New York, San Francisco, Vol. 2d, pp. 625-702. Fleuriet, 1980a, Genetics 95: 459-65. 1980b, DIS 55: 43. Teninges and Bras-Herreng, 1987, J. Gen. Virol. 68: 2625-38. Fleuriet, 1988, Evol. Biol. 23: 1-30. Ashburner, 1989, Drosophila, a Laboratory Handbook, 1989, Cold Spring Harbor Press, Cold Spring Harbor, New York. pp. 101- 116, 1192. phenotype: Whereas normal Drosophila melanogaster recover in a short time after carbon dioxide anesthesia, flies belonging to certain strains suffer paralysis eventually followed by death after a short exposure to carbon dioxide. These strains were found to carry the rhabdovirus sigma (L'Heritier and Teissier, 1937). This RNA virus resembles vesicular stomatitis virus (VSV) of horses both in size (70 nm wide and 180 nm long) and shape (bullet-like); VSV and the fish rhabdoviruses PFR and SVC can multiply and produce carbon dioxide sensitivity in Drosophila (Brun and Plus, 1980; Teninges and Bras-Herreng, 1987). The sigma virus, however, does not multiply in any ver- tebrate host and normally is transmitted from Drosophila females to their offspring by way of the egg. The expression of sigma is correlated with the presence of the virus in nerve centers. The virus grows well in Drosophila tissue culture cells (Richard-Molard, Blondel, Wyers, and Dezelee, 1984, J. Gen. Virol. 65: 91-99). Carbon dioxide-sensitive sigma strains may be divided into two types: stabilized and nonstabilized. Artificial inocula- tion regularly leads to the nonstabilized condition. In this state, males do not transmit sensitivity to progeny but females do transmit it to part of their progeny, indicating the presence of the sigma virus in some of the eggs of infected individuals. Some flies of a nonstabilized strain achieve the stabilized state. In the stabilized state, the females transmit the virus and the stabilized condition to approximately 100% of their offspring (Fleuriet, 1980a, 1988). The stabilized males transmit the virus but not the stabilized condition to part of their progeny; electron micrographs show the virus in male germ cells (Brun and Plus, 1980). The ref (refractory) mutants, found on Drosophila chromo- somes X, 2, and 3, prevent flies from being infected by sigma. Some of the virus strains are defective and do not produce carbon dioxide-sensitivity in stabilized flies. Other mutant strains of sigma are heat sensitive and unable to infect flies at 30 (Contamine, 1973, Mol. Gen. Genet. 124: 233-46). Flies stabilized for one of these temperature-sensitive mutants lose their sensitivity to carbon dioxide at the restrictive tem- perature but can transmit the virus to their offspring. molecular biology: Sigma virus from a Drosophila cell line was used to prepare genomic RNA (Teninges and Bras-Herreng, 1987). The sigma strain used gave a high yield of virus but was unable to establish a persistent stabilized-type infection when inoculated into Drosophila tissue culture cells. After preparation, the genomic RNA was purified, labelled with 32P, and used to probe for mRNA in sigma-infected cells. A cDNA copy of the complete coding region of the mRNA was cloned and its nucleotide sequence and deduced amino acid sequence deter- mined (Teninges and Bras-Herreng, 1987). There is a long open reading frame (ORF) in the nucleotide sequence starting at position 47 and ending at position 1624. The putative amino acid sequence consists of a chain of 526 amino acids. Within the long ORF is a short frame-shifted ORF (starting at posi- tion 643 and ending at position 763) which could encode a pep- tide of 40 amino acids. About 20% amino acid sequence iden- tity has been established between the glycoprotein precursor of this strain of sigma virus and that of VSV (New Jersey strain). # SR: Sex Ratio origin: Artificially inoculated into D. melanogaster from SR- bearing D. willistoni and D. nebulosa. references: Poulson and Sakaguchi, 1961, Genetics 46: 890-91. 1962, Ann. Rep. Nat. Inst. Genetics (Misima, Japan) 12: 18- 19; 19-21. Poulson, 1963, Methodology in Basic Genetics (W.J. Burdette, ed.). Holden-Day Inc., pp. 404-24. Sakaguchi and Poulson, 1963, Genetics 48: 841-61. Ikeda, 1965, Science 147: 1147-48. Oishi and Poulson, 1970, Proc. Nat. Acad. Sci. USA 67: 1565- 72. Sakaguchi, 1970, DIS 45: 145. Oishi, 1971, Genet. Res. 18: 45-56. Tsuchiyama and Sakaguchi, 1972, DIS 48: 29. Miyamoto and Oishi, 1975, Genetics 79: 55-61. Watanabe and Yamada, 1977, Jpn. J. Genet. 52: 9-14. Tsuchiyama, Sakaguchi, and Oishi, 1978, Genetics 89: 711-21. Williamson and Poulson, 1979, The Mycoplasmas (Whitcomb and Tully, eds.). Academic Press, London, New York, San Fran- cisco, Vol. III, pp. 175-208. Lauge, 1980, The Genetics and Biology of Drosophila (Ashburner and Wright, eds.). Academic Press, London, New York, San Francisco, Vol. 2d, pp. 33-106. Niki, 1988, Jpn. J. Genet. 63: 11-21. Ashburner, 1989, Drosophila, a Laboratory Handbook, 1989, Cold Spring Harbor Press, Cold Spring Harbor, New York. p. 1193. phenotype: The SR or Sex Ratio phenotype found in several groups of Drosophila carrying spirochaete-like microorganisms now classified as spiroplasmas in their hemolymph (Williamson and Whitcomb, 1975, Science 188: 1018-20) and is character- ized by a failure on the part of females to produce male offspring (Williamson and Poulson, 1979). Spiroplasmas are normally transmitted from female to offspring in the egg (Nikki, 1988). The SR agent can be extracted from D. willis- toni, D. nebulosa, D. paulistorum, or D. equinoxialis and can be transferred by inoculation into D. melanogaster, and D. simulans (Poulson, 1963; Sakaguchi and Poulson, 1963; Ikeda, 1965; Oishi and Poulson, 1970; Watanabe and Yamada, 1977; Tsuchiyama et al., 1978). Two strains of SR microorganisms, WSR from D. willistoni and NSR from D. nebulosa, are quite stable in D. melanogaster, the degree of stability of the infection differing among D. melanogaster strains. XY male offspring of females carrying the infection die as embryos. A few infected gynandromorphs with small areas of X0 tissue sur- vive, but the majority do not survive when X0 cells carry the infection (Tsuchiyama et al., 1978). Triploid intersexes are not killed by the SR agent, nor are females transformed by tra, traD, ix, or dsx (Sakaguchi and Poulson, 1963; Miyamoto and Oishi, 1975). The spiroplasmas of each species of Droso- phila carry their own viruses and these viruses can clump and lyse the spiroplasmas of related species of Drosophila (Oishi, 1971; Poulson and Oishi, 1973, Genetics 74: s216). other information: The name SR was proposed by Magni (1953, Nature 172: 81) for D. bifasciata females (inseminated before capture) that produced only female offspring (Lauge, 1980) and was used by Poulson and colleagues for these maternally- transmitted cytological factors (spiroplasmas) found naturally or by infection in Drosophila.