Organellar RNA polymerases of higher plants

International Review of Cytology

Volumn 190, Issue , 1999, Pages 1-59

  Hess, Wolfgang R ^a   Börner, Thomas ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Gene regulation; Linear plasmids; Mitochondria; Plastids; Promoter; Sigma factor; Transcription

Indexed keywords

CORE PROTEIN; MITOCHONDRIAL ENZYME; NUCLEAR RNA; PROTEIN SUBUNIT; RNA POLYMERASE; SIGMA FACTOR;

ARABIDOPSIS; BACTERIOPHAGE; CHLOROPLAST; EUBACTERIUM; GENE ACTIVITY; GENE CONTROL; GENE SEQUENCE; GENETIC TRANSCRIPTION; HIGHER PLANT; MITOCHONDRION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASTID; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TRANSCRIPTION INITIATION;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); EMBRYOPHYTA;

EID: 0032903448     PISSN: 00747696     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0074-7696(08)62145-2     Document Type: Review

References (298)

1. Allen, C. A., Hakanson, G., and Allen, J. F. (1995). Redox conditions specify the proteins synthesised by isolated chloroplasts and mitochondria. Redox Rep. 1, 119-123.
2. Allison, L. A., Levine, S. J., and Maliga, P. (1995). Multiple mechanisms regulate transcription in plastids of higher plants. In "Photosynthesis: From Light to Biosphere" (P. Mathis, ed.), Vol. Ill, pp. 551-556. Kluwer, Dordrecht.
3. Allison, L. A., Simon, L. D., and Maliga, P. (1996). Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J. 15, 2802-2809.
4. Antoshechkin, L, and Bogenhagen, D. F. (1995). Distinct roles for two purified factors in transcription of Xenopus mitochondrial DNA. Mol. Cell. Biol. 15, 7032-7042.
5. Antoshechkin, I., Bogenhagen, D. F., and Mastrangelo, I. A. (1997). The HMG-box mitochondrial transcription factor xl-mtTFA binds DNA as a tetramer to activate bidirectional transcription. EMBO J. 16, 3198-3206.
6. Baeza, L., Bertrand, A., Mache, R., and Lerbs-Mache, S. (1991). Characterization of a protein binding sequence in the promoter region of the 16S rRNA gene of the spinach chloroplast genome. Nucleic Acids Res. 19, 3577-3581.
7. Baginsky, S., Tiller, K., and Link, G. (1997). Transcription factor phosphorylation by a protein kinase associated with the chloroplast RNA polymerase from mustard (Sinapis alba). Plant Mol. Biol. 34, 181-189.
8. Baumgartner, B. J., Rapp, J. C., and Mullet, J. E. (1993). Plastid genes encoding the transcription/translation apparatus are differentially transcribed early in barley (Hordewn vulgare) chloroplast development. Plant Physiol. 101, 781-791.
9. Bergsland, K. J., and Haselkorn, R. (1991). Evolutionary relationships among eubacteria, cyanobacteria, and chloroplasts: Evidence from the rpoCl gene oiAnabaena sp. strain PCC 7120. J. Bacterial. 173, 3446-3455.
10. Bertrand, H., and Griffiths, A. J. F. (1989). Linear plasmids that integrate into mitochondrial DNA in Neurospora. Genome 31, 155-159.
11. Binder, S., and Brennicke, A. (1993a). Transcription initiation sites in mitochondria of Oenothera berteriana. J. Biol. Chem. 268, 7849-7855.
12. Binder, S., and Brennicke, A. (1993b). A tRNA gene transcription initiation site is similar to mRNA and rRNA promoters in plant mitochondria. Nucleic Acids Res. 21, 5012-5019.
13. Binder, S., Thalheim, C, and Brennicke, A. (1994). Transcription of potato mitochondrial 26S rRNA is initiated at its mature 5′ end. Curr. Genet. 26, 519-523.
14. Binder, S., Hatzack, F., and Brennicke, A. (1995). A novel pea mitochondrial m vitro transcription system recognizes homologous and heterologous mRNA and tRNA promoters. J. Biol. Client. 270, 22182-22189.
15. Binder, S., Marchfelder, A., and Brennicke, A. (1996). Regulation of gene expression in plant mitochondria. Plant Mol. Biol. 32, 303-314.
16. Bogorad, L. (1991). Replication and transcription of plastid DNA. In "The Molecular Biology of Plastids, Vol. 7A, Cell Culture and Somatic Cell Genetics of Plants" (L. Bogorad and I. K. Vasil, eds.), pp. 93-124. Academic Press, San Diego.
17. Bogorad, L., and Woodcock, C. L. F. (1970). Rifamycins: The inhibition of plastid RNA synthesis in vivo and variable effects on chlorophyll formation in maize leaves. In "Autonomy and Biogenesis of Mitochondria and Chloroplasts," pp. 92-97. North-Holland, Amsterdam.
18. Borner, T., and Hess, W. R. (1993). Altered nuclear, mitochondrial and plastid gene expression in white barley cells containing ribosome-deficient plastids. In "Plant Mitochondria" (U. Kück and A. Brennicke, eds.), pp. 207-220. Verlag Chemie, Weinheim.
19. Börner, T., Hedtke, B., Hess, W. R., Legen, J., and Weihe, A. (1999). Phage-type RNA polymerases in higher plants. In "The Chloroplast: From Molecular Biology to Biotechnology" (J. Argyroudi-Akoyunoglou, ed.). Kluwer, Dordrecht, in press.
20. Bottomley, W., Smith, H. J., and Bogorad, L. (1971). RNA polymerases of maize. I. The partial purification and properties of the chloroplast enzyme. Proc. Natl. Acad. Sei. USA 68, 2412-2416.
21. Boyer, S. K., and Mullet, J. (1986). Characterization of Pisum sativum chloroplast psbA transcript produced in vivo, in vitro, and in E. coli. Plant Mol. Biol. 6, 229-243.
22. Bradley, D., and Gatenby, A. A. (1985). Mutational analysis of the maize chloroplast ATPase-beta subunit gene promoter: The isolation of promoter mutants in E. coli and their characterization in a chloroplast in vitro transcription system. EMBO J. 4, 3641-3648.
23. Briat, J. F., Laulhere, J. P., and Mache, R. (1979). Transcription activity of a DNA-protein complex isolated from spinach plastids. Ear. J. Biochem. 98, 285-292.
24. Briat, J. F., Dron, M., Loiseaux, S., and Mache, R. (1982). Structure and transcription of the spinach chloroplast rDNA leader region. Nucleic Acids Res. 10, 6865-6878.
25. Briat, J. F., Bisanz-Seyer, C., and Lescure, A. M. (1987). In vitro transcription initiation of the rDNA operon of spinach chloroplast by a highly purified soluble homologous RNA polymerase. Curr. Genet. 11, 259-263.
26. Brown, G. G., Auchincloss, A. H., Covello, P. S., Gray, M. W., Menassa, R., and Singh, M. (1991). Characterization of transcription initiation sites on the soybean mitochondrial genome allows identification of a transcription-associated sequence motif. Mol. Gen. Genet. 228, 345-355.
27. Bülow, S., and Link, G. (1988). Sigma-like activity from mustard (Sinapis alba L.) chloroplasts confering DNA-binding and transcription specificity to E. coli core RNA polymerase. Plant Mol. Biol. 10, 349-357.
28. Bünger, W., and Feierabend, J. (1980). Capacity for RNA synthesis in 70S ribosome-deficient plastids of heat-bleached rye leaves. Planta 149,163-169.
29. Caoile, A. G., and Stern, D. B. (1997). A conserved core element is functionally important for maize mitochondrial promoter activity in vitro. Nucleic Acids Res. 25, 4055-4060.
30. Carrodeguas, J. A., Yun, S., Shadel, G. S., Clayton, D. A., and Bogenhagen, D. F. (1997). Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Exp. 6, 219-230.
31. Caslake, L. F., and Bryant, D. A. (1996). The sigA gene encoding the major sigma factor of RNA polymerase from the marine cyanobacterium Synechococcus sp. strain PCC 7002: Cloning and characterization. Microbiology 142, 347-357.
32. Caslake, L. F., Gruber, T. M., and Bryant, D. A. (1997). Expression of two alternative sigma factors of Synechococcus sp. strain PCC 7002 is modulated by carbon and nitrogen stress. Microbiology 143, 3807-3818.
33. Cermakian, N., Ikeda, T. M., Cedergren, R., and Gray, M. W. (1996). Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage. Nucleic Acids Res. 24, 648-654.
34. Cermakian, N., Ikeda, T. M., Miramontes, P., Lang, B. F., Gray, M. W., and Cedergren, R. (1997). On the evolution of the single-subunit RNA polymerases. J. Mol. Evol. 45,671-681.
35. Chan, B. S., Court, D. A., Vierula, P. J., and Bertrand, H. (1991). The kalilo linear senescence-inducing plasmid of Neurospora is an invertron and encodes DNA and RNA polymerases. Curr. Genet. 20, 225-237.
36. Chase, C. D., and Pring, D. R. (1985). Circular plasmid DNAs from mitochondria of Sorghum bicolor. Plant Mol. Biol. 5, 303-311.
37. Chen, B., Kubelik, A. R., Mohr, S., and Breitenberger, C. A. (1996). Cloning and characterization of the Neurospora crassa cyt-5 gene. A nuclear-coded mitochondrial RNA polymerase with a polyglutamine repeat. J. Biol. Chem. 271, 6537-6544.
38. Chen, L. J., and Orozco, E. M., Jr. (1988). Recognition of prokaryotic transcription terminators by spinach chloroplast RNA polymerase. Nucleic Acids Res. 16, 8411-8431.
39. Chen, Z., Muthukrishnan, S., Liang, G. H., Schertz, K. F., and Hart, G. E. (1993). A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum. Mol. Gen. Genet. 236, 251-259.
40. Chen, Z., Schertz, K. F., Mullet, J. E., DuBell, A., and Hart, G. E. (1995). Characterization and expression of rpoC2 in CMS and fertile lines of sorghum. Plant Mol. Biol. 28,799-809.
41. Chow, K. S., Singh, D. P., Roper, J. M., and Smith, A. G. (1997). A single precursor protein for ferrochelatase-I from Arabidopsis is imported in vitro into both chloroplasts and mitochondria. J. Biol. Chem. 272, 27565-27571.
42. Christopher, D. A. and Hoffer, P. H. (1998). DETI represses a chloroplast blue light responsive promoter in a developmental and tissue-specific manner in Arabidopsis tlialiana. Plant J. 14, 1-11.
43. Christopher, D. A., Kim, M., and Mullet, J. E. (1992). A novel light-regulated promoter is conserved in cereal and dicot chloroplasts. Plant Cell 4, 785-798.
44. Christopher, D. A., Li, X., Kim, M., and Mullet, J. E. (1997). Involvement of protein kinase and extraplastidic serine/threonine protein phosphatases in signaling pathways regulating plastid transcription and the psbD blue light-responsive promoter in barley. Plant Physiol. 113, 1273-1282.
45. Clayton, D. A. (1991). Replication and transcription of vertebrate mitochondrial DNA. Anna. Rev. Cell Biol. 7, 453-478.
46. Clayton, D. A. (1992). Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol. 141, 217-232.
47. Cliften, P. F., Park, J. Y., Davis, B. P., Jang, S. H., and Jaehning, J. A. (1997). Identification of three regions essential for interaction between a sigma-like factor and core RN A polymerase. Genes Dev. 11, 2897-2909.
48. Covello, P. S., and Gray, M. W. (1991). Sequence analysis of wheat mitochondrial transcripts capped in vitro: Definitive identification of transcription initiation sites. Curr. Genet. 20, 245-251.
49. Cozens, A. L., and Walker, J. E. (1986). Pea chloroplast DNA encodes homologues of Escherichia coli ribosomal subunit S2 and the beta'-subunit of RNA polymerase. Biochem. J. 236, 453-460.
50. Delaroque, N., Fontaine, J. K., Kloareg, B., and Loiseaux de Goër, S. (1996). Putative σ-70-like promoters in a brown algal mitochondrial genome. C.R. Acad. Sei. 319, 763-767.
51. Denovan-Wright, E. M., Nedelcu, A. M., and Lee, R. W. (1998). Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. Plant Mol. Biol. 36, 285-295.
52. DePamphilis, C. W., and Palmer, J. D. (1990). Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348, 337-339.
53. Diffiey, J. F. X., and Stillman, B. (1991). A close relative of the nuclear chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc. Natl. Acad. Sei. USA 88,7864-7868.
54. Diffley, J. F. X., and Stillman, B. (1992). DNA-binding properties of an HMGl-related protein from yeast mitochondria. J. Biol. Chem. 267, 3368-3374.
55. Dohmen, G., and Tudzynski, P. (1994). A DNA-polymerase-related reading frame (pol-r) in the mtDNA of Secale cereale. Curr. Genet. 25, 59-65.
56. Edwards, J. C., Levens, D., and Rabinowitz, M. (1982). Analysis of transcriptional initiation of yeast mitochondrial DNA in a homologous in vitro transcription system. Cell 31,337-346.
57. Ems, S., Morden, C. \V., Dixon, C, Wolfe, K. H., de Pamphilis, C. W., and Palmer, J. D. (1995). Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Mol. Biol. 29, 721-733.
58. Falk, J., Schmidt, A., and Krupinska, K. (1993). Characterization of plastid DNA transcription in ribosome deficient plastids of heat-bleached barley leaves. J. Plant Physiol. 141,176-181.
59. Finnegan, P. M., and Brown, G. G. (1987). In organello transcription in maize mitochondria and its sensitivity to inhibitors of RNA synthesis. Plant Pliysiol. 85, 304-309.
60. Finnegan, P. M., and Brown, G. G. (1990). Transcriptional and post-transcriptional regulation of RNA levels in maize mitochondria. Plant Cell 2, 71-83.
61. Fischer, N., Stampacchia, O., Redding, K., and Rochaix, J. D. (1996). Selectable marker recycling in the chloroplast. Mol. Gen. Genet. 251, 373-380.
62. Fisher, R. P., and Clayton, D. A. (1988). Purification and characterization of human mitochondrial transcription factor 1. Mol. Cell. Biol. 8, 3496-3509.
63. Fisher, R. P., Lisowsky, T., Breen, G. A. M., and Clayton, D. A. (1991). A rapid, efficient method for purifying DNA-binding proteins. J. Biol. Chem. 266, 9153-9160.
64. Fisher, R. P., Lisowsky, T., Parisi, M. A., and Clayton, D. A. (1992). DNA wrapping and bending by a mitochondrial high-mobility group-like transcriptional activator protein. J. Biol. Chem. 267, 3358-3367.
65. Galli, G., Hofstetter, H., and Birnstiel, M. L. (1981). Two conserved sequence blocks within eukaryotic tRNA genes are major promotor elements. Nature 294, 626-631.
66. Gardner, M. J., Williamson, D. H., and Wilson, R. J. (1991). A circular DNA in malaria parasites encodes an RNA polymerase like that of prokaryotes and chloroplasts. Mol. Biochem. Parasitai. 44, 115-123.
67. Gardner, M. J., Goldman, N., Barnett, P., Moore, P. W., Rangachari, K., Strath, M., Whyte, A., Williamson, D. H., and Wilson, R. J. (1994). Phylogenetic analysis of the rpoB gene from the plastid-like DNA of Plasmodium falciparum. Mol Biochem. Parasitai. 66,221-231.
68. Gatenby, A. A., Castleton, J. A., and Saul, M. W. (1981). Expression in E. coli of Z. mays and wheat chloroplast genes for large subunit of ribulose biphosphate carboxylase. Nature 291, 117-121.
69. Gauly, A., and Kössel, H. (1989). Evidence for tissue-specific cytosine-methylation of plastid DNA from Zea mays. Curr. Genet. 15, 371-376.
70. Gessner-Ulrich, K., and Tudzynski, P. (1992). Transcripts and translation products of a mitochondrial plasmid of Claviceps pitrpurea. Curr. Genet. 21, 249-254.
71. Giese, A., Thalheim, C., Brennicke, A., and Binder, S. (1996). Correlation of nonanucleotide motifs with transcript initiation of 18S rRNA genes in mitochondria of pea, potato and Arabidopsis. Mol. Gen. Genet. 252, 429-436.
72. Grace, K. S., Allen, J. O., and Newton, K. J. (1994). R-type plasmids in the mitochondria from a single source of Zea luxurious teosinte. Curr. Genet. 25, 258-264.
73. Gray, M. W. (1992). The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141, 233-357.
74. Gray, M. W. (1993). Origin and evolution of organellar genomes. Curr. Opin. Genet. Dev. 3, 884-890.
75. Gray, M. W., and Lang, B. F. (1998). Transcription in chloroplasts and mitochondria: A tale of two polymerases. Trends Microbiol. 6,1-3.
76. Gray, M. W., Hanic-Joyce, P. J., and Covello, P. S. (1992). Transcription, processing and editing in plant mitochondria. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43, 145-175.
77. Greenberg, B. M., Narita, J. O., DeLuca-Flaherty, C., Gruissem, W., Rushlow, K. A., and Hallick, R. B. (1984). Evidence for two RNA polymerase activities in Euglena gracilis chloroplasts. J. Biol. Chem. 259, 14880-14887.
78. Greenleaf, A. L., Kelly, J. L., and Lehman, I. R. (1986). Yeast RPO41 gene product is required for transcription and maintenance of the mitochondrial genome. Proc. Natl. Acad. Sei. USA 83, 3391-3394.
79. Griffiths, A. J. F. (1995). Natural plasmids of filamentous fungi Microbiol. Rev. 59, 673-685.
80. Gruber, T. M., and Bryant, D. A. (1997). Molecular systematic studies of eubacteria using sigma70-type sigma factors of group 1 and group 2. J. Bacterial. 179, 1734-1747.
81. Gruber, T. M., and Bryant, D. A. (1998). Characterization of alternative sigma-factors SigD and SigE in Synechococcus sp. strain PCC 7002. SigE is implicated in transcription of post-exponential-phase-specific genes. Arch. Microbiol. 169, 211-219.
82. Gruissem, W., and Tonkyn, J. C. (1993). Control mechanisms of plastid gene expression. Crit. Rev. Plant Sei. 12, 19-55.
83. Gruissem, W., and Zurawski, G. (1985). Identification and mutational analysis of the promoter for a spinach chloroplast transfer RNA gene. EMBO J. 4,1637-1644.
84. Gruissem, W., Greenberg, B. M., Zurawski, G., Prescott, D. M., and Hallick, R. B. (1983a). Biosynthesis of chloroplast transfer RNA in a spinach chloroplast transcription system. Cell 35, 815-828.
85. Gruissem, W., Narita, J. O., Greenberg, B. M., Prescott, D. M., and Hallick, R. B. (1983b). Selective m vitro transcription of chloroplast genes. J. Cell Biochem. 22, 31-46.
86. Gruissem, W., Elsner-Menzel, C., Latshaw, S., Narita, J. O., Schaffer, M. A., and Zurawski, G. (1986a). A subpopulation of spinach chloroplast tRNA genes does not require upstream promotor elements for transcription. Nucleic Acids Res. 14, 7541-7556.
87. Gruissem, W., Greenberg, B. M, Zurawski, G., and Hallick, R. B. (1986b). Chloroplast gene expression and promoter identification in chloroplast extracts. Methods Enzymol. 118, 253-270.
88. Guilfoyle, T., Ulmasov, T., and Larkin, R. (1994). RNA polymerase genes. Plant Mol. Biol. Rep. 12, 63-66.
89. Gutierres, S., Lelandais, C, Paepe, R. D., Vedel, F., and Chetrit, P. (1997). A mitochondrial sub-stoichiometric orf87-nad3-nad1 exonA co-transcription unit present in Solanaceae was amplified in the genus Nicotiana. Curr. Genet. 31, 55-62.
90. Hajdukiewicz, P. T. J., Allison, L. A., and Maliga, P. (1997). The two RNA polymerases encoded by the nuclear and plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J. 13, 4041-4048.
91. Hallick, R. B., Lipper, C., Richards, O. C, and Rutter, W. J. (1976). Isolation of a transcriptionally active chromosome from chloroplasts of Euglena gracilis. Biochemistry 15, 3039-3045.
92. Hallick, R. B., Hong, L., Drager, R. B., Favreau, M. R., Monfort, A., Orsat B., Spielmann, A., and Stutz, E. (1993). Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids. Res. 21, 3537-3544.
93. Han, C. D., Patrie, W., Polacco, M., and Coe, E. H. (1993). Abberations in plastid transcripts and deficiency of plastid DNA in striped and albino mutants in maize. Planta 191,552-563.
94. Hanic-Joyce, P. J., and Gray, M. W. (1991). Accurate transcription of a plant mitochondrial gene in vitro. Mol. Cell. Biol. 11, 2035-2039.
95. Hatzack, F., Dombrowski, S., Brennicke, A., and Binder, S. (1998). Characterization of DNA-binding proteins from pea mitochondria. Plant Physiol. 116, 519-528.
96. Hawley, D. K., and McClure, W. R. (1983). Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11, 2237-2255.
97. Hedtke, B., Borner, T., and Weihe, A. (1997). Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277, 809-811.
98. Hedtke, B., Meixner, M., Gillandt, S., Richter, E., Borner, T., and Weihe, A. (1999). Green fluorescent protein as a marker to investigate targeting of organellar RNA polymerases of higher plants in vivo. Plant J., in press.
99. Herrmann, R. G. (1997). Eukaryotism, towards a new interpretation. In "Eukaryotism and Symbiosis" (H. E. A. Schenk, R. G. Herrmann, K. W. Jeon, N. E. Müller, and W. Schwemmler, eds.), pp. 73-118. Springer-Verlag, Berlin.
100. Herrmann, R. G., Westhoff, P., and Link, G. (1992). Biogenesis of plastids in higher plants. In "Cell Organelles" (R. G. Herrmann, ed.), 275-349. Springer-Verlag, Vienna.
101. Hess, W. R., Prombona, A., Fieder, B., Subramanian, A. R., and Borner, T. (1993). Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: Evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J. 12, 563-571.
102. Hess, W. R., Hoch, B., Zeltz, P., Hübschmann, T., Kessel, H., and Borner, T. (1994). Inefficient rpl2 splicing in barley mutants with ribosome-deficient plastids. Plant Cell 6, 1455-1465.
103. Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M., Mori, M., Kondo, C., Honji, Y., Sun, C. R., Meng, B. Y., Li, Y. Q., Kanno, A., Nishizawa, Y., Hirai, A., Shinozaki, K., and Sugiura, M. (1989). The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217,185-194.
104. Hoffer, P. A., and Christopher, D. A. (1997). Structure and blue-light-responsive transcription of a chloroplast psbD promoter from Arabidopsis thaliana. Plant Physiol. 115, 213-222.
105. Houchins, J. P., Dale, R. M. K., Ginsburg, H., Hodge, T. P Lonsdale, D. M., Rohrbaugh, M., and Schardl, C. L. (1986). DNA sequence analysis of a 5.27 kb direct repeat occurring adjacent to the regions of S episome homology in maize mitochondria. EMBO J. 5,2781-1788.
106. Howe, C. J. (1996). RNA polymerases and plastid evolution. Trends Plant Sei. 1, 323-324.
107. Howe, C. J., Beanland, T. J., Larkum, A. W. D., and Lockhart, P. J. (1992). Plastid origins. Trends Ecol. Evol. 7, 378-383.
108. Hu, J., and Bogorad, L. (1990). Maize chloroplast RNA polymerase: The 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes. Proc. Natl. Acad. Sei. USA 87, 1531-1535.
109. Hu, J., Troxler, R. F., and Bogorad, L. (1991). Maize chloroplast RNA polymerase: The 78-kilodalton polypeptide is encoded by the plastic rpoCl gene. Nucleic Acids Res. 19,3431-3434.
110. Hübschmann, T., and Borner, T. (1998). Characterisation of transcript initiation sites in ribosome-deficient barley plastids. Plant Mol. Biol. 36, 493-496.
111. Hübschmann, T., Hess, W. R., and Borner, T. (1996). Impaired splicing of the rpsl2 transcripts in ribosome-deficient plastids. Plant Mol. Biol. 30,109-123.
112. Hudson, G. S., Holton, T. A., Whitfield, P. R., and Bottomley, W. (1988). Spinach chloroplast rpoBC genes encode three subunits of the chloroplast RNA polymerase. J. Mol. Biol. 200, 639-654.
113. Hughes, J. E., and Link, G. (1988). Photoregulation of psbA transcript levels in mustard cotyledons. Plant Mol. Biol. 17, 57-73.
114. Igloi, G. L., and Kössel, H. (1992). The transcriptional apparatus of chloroplasts. Crit. Rev. Plant Sei. 10, 525-558.
115. Igloi, G. L., Meinke, A., Dory, I., and Kössel, H. (1990). Nucleotide sequence of the maize chloroplast rpoB/C1/C2 operon: Comparison between the derived protein primary structures from various organisms with respect to functional domains. Mol. Gen. Genet. 221, 379-394.
116. Inada, H., Kusumi, K., Nishimura, M., and Iba, K. (1996). Specific expression of the chloroplast gene for RNA polymerase (rpoB) at an early stage of leaf development in rice. Plant Cell Physiol. 37, 229-232.
117. Inada, H., Seki, M., Morikawa, H., Nishimura, M., and Iba, K. (1997). Existence of three regulatory regions each containing a highly conserved motif in the promoter of plastidencoded RNA polymerase gene (rpoB). Plant J. 11, 883-890.
118. Iratni, R., Baeza, L., Andreeva, A., Mache, R., and Lerbs-Mache, S. (1994). Regulation of rDNA transcription in chloroplasts: Promoter exclusion by constitutive repression. Genes Dev. 8, 2928-2938.
119. Iratni, R., Diederich, L., Harrak, H., Bligny, M., and Lerbs-Mache, S. (1997). Organ-specific transcription of the mi operon in spinach plastids. J. Biol. Client. 272, 13676-13682.
120. Isono, K., Shimizu, M., Yoshimoto, K., Niwa, Y., Satoh, K., Yokota, A., and Kobayashi, H. (1997). Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of £-70 factors of bacterial RNA polymerases in Arabidopsis thaliana. Proc. Natl. Acad. Sei. USA 94, 14948-14953.
121. Jang, S. H., and Jaehning, J. A. (1991). The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J. Biol. Chein. 266, 22671-22677.
122. Jeruzalmi, D., and Steitz, T. A. (1998). Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17, 4101-4113.
123. Joyce, C. M., and Steitz, T. A. (1994). Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63, 777-822.
124. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C, Wada, T., Watanabe, A., Yaraada, M., Yasuda, M., and Tabata, S. (1996). Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3,109-136.
125. Kapoor, S., Suzuki, J. Y., and Sugiura, M. (1997). Identification and functional significance of a new class of non-consensus-type plastid promoters. Plant J. 11, 327-337.
126. Kelly, J. L., Greenleaf, A. L., and Lehman, I. R. (1986). Isolation of the nuclear gene encoding a subunit of the yeast mitochondrial RNA polymerase. J. Biol. Chem. 261,10348-10351.
127. Kempken, F. (1995). Plasmid DNA in mycelial fungi. In "The Mycota" (U. Kuck, ed.), Vol. II, pp. 169-187. Springer-Verlag, Heidelberg.
128. Kempken, F., Hermanns, J., and Osiewacz, H. D. (1992). Evolution of linear plasmids. J. Mol. Evol. 35, 502-513.
129. Kestermann, M., Neukirchen, S., Kloppstech, K., and Link, G. (1998). Sequence and expression characteristics of a nuclear-encoded chloroplast sigma factor from mustard (Sinapis alba). Nucleic Acids Res. 26, 2747-2753.
130. Kidd, G. H., and Bogorad, L. (1980). A facile procedure for purifying maize chloroplast RNA polymerase from whole cell homogenates. Biochim. Biophys. Acta 609, 14-30.
131. Kim, M., and Mullet, J. E. (1995). Identification of a sequence-specific DNA binding factor required for transcription of the barley chloroplast blue light-responsive psbD-psbC promoter. Plant Cell 7, 1445-1457.
132. Klement, J. F., Moorefield, M. B., Jorgensen, E., Brown, J. E., Risman, S., and McAllister, W. T. (1990). Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site. J. Mol. Biol. 215, 21-29.
133. Kobayashi, H., Ngernprasirtsiri, J., and Akazawa, T. (1990). Transcriptional regulation and DNA methylation in plastids during transitional conversion of chloroplasts to chromoplasts. EMBO J. 9, 307-313.
134. Kowallik, K. V., Stoebe, B., Schaffran, I., Kroth-Pancic, P., and Freier, U. (1995). The chloroplast genome of a chlorophyl a + c containing alga, Odontella s'mensis. Plant Mol. Biol. Rep. 13, 336-342.
135. Kusumi, K., Mizutaki, A., Nishimura, M., and Iba, K. (1997). A virescent gene VI determines the expression timing of plastid genes for transcription/translation apparatus during leaf development in rice. Plant J. 12,1241-1250.
136. Kuzmin, E. V., Levchenko, I. V., and Zaitseva, G. (1988). S2 plasmid from cms-maize mitochondria potentially encodes a specific RNA polymerase. Nucleic Acids Res. 16, 4177.
137. Lam, E., Hanley-Bowdoin, L., and Chua, N. H. (1988). Characterization of a chloroplast sequence-specific DNA binding factor. J. Biol. Chem. 263, 8288-8293.
138. Lang, B. F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Tunnel, M., and Gray, M. W. (1997). An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387, 493-497.
139. Larsson, N. G., Garman, J. D., Oldfors, A., Barsh, G. S., and Clayton, D. A. (1996). A single mouse gene encodes the mitochondrial transcription factor A and a testis-specific nuclear HMG-box protein. Nature Genet. 13, 296-302.
140. Leblanc, C., Boyen, C., Richard, O., Bonnard, G., Grienenberger, J. M., and Kloareg, B. (1995). Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization. J. Mol. Biol. 250, 484-495.
141. Lelandais, C., Gutierres, S., Mathieu, C, Vedel, F., Remade, C, Marechal-Drouard, L., Brennicke, A., Binder, S., and Chetrit, P. (1996). A promoter element active in run-off
142. transcription controls the expression of two cistrons of nad and rps genes in Nicotiana sylvestris mitochondria. Nucleic Acids Res. 24, 4798-4804.
143. Leon, P., Walbot, V., and Bedinger, P. (1989). Molecular analysis of the linear 2.3 kb plasmid of maize mitochondria: Apparent capture of tRNA genes. Nucleic Acids Res. 17,4089-4099.
144. Lerbs, S., Briat, J. F., and Mache, R. (1983a). Chloroplast RNA polymerase from spinach: Purification and DNA-binding proteins. Plant Mol. Biol. 2, 67-74.
145. Lerbs, S., Bräutigam, E., and Mache, R. (1983b). DN A-dependent RNA polymerase of spinach chloroplasts: Characterization of sigma-like and alpha-like polypeptides. Mol. Gen. Genet. 211, 459-464.
146. Lerbs, S., Bräutigam, E., and Parthier, B. (1985). Polypeptides in DNA-dependent RNA polymerase of spinach chloroplasts: Characterization by anti-body-linked polymerase assay and determination of sites of synthesis. EMBO J. 4, 1661-1666.
147. Lerbs-Mache, S. (1988). Quantification of DNA-dependent RNA polymerase subunits and initiation factor(s) by antibody-linked polymerase assays. FEBS Lett. 234, 392-394.
148. Lerbs-Mache, S. (1993). The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymerase: Single-subunit enzyme or catalytic core of multimeric enzyme complexes? Proc. Natl. Acad. Sei. USA 90, 5509-5513.
149. Lescure, A.-M., Bisanz-Seyer, C, Pesey, H., and Mache, R. (1985). In vitro transcription initiation of the spinach chloroplast 16S rRNA at two tandem promoters. Nucleic Acids Res. 13, 8787-8796.
150. Levings, C. S., III, and Sederoff, R. (1983). Nucleotide sequence of the S-2 mitochondrial DNA from the S-cyoplasm of maize. Proc. Natl. Acad. Sei. USA 80, 4055-4059.
151. Levings, C. S., III, and Siedow, J. N. (1995). Regulation by redox poise in chloroplasts. Science 268, 695-696.
152. Li, X. Q., Zhang, M., and Brown, G. G. (1996). Cell-specific expression of mitochondrial transcripts in maize seedlings. Plant Cell 8,1961-1975.
153. Liere, K., and Link, G. (1997). Chloroplast endoribonuclease p54 involved in RNA 3′-end processing is regulated by phosphorylation and redox state. Nucleic Acids Res. 25,2403-2408.
154. Liere, K., and Maliga, P. (1999). In vitro characterization of the tobacco rpoB promoter reveals conserved promoter architecture for the phage-type plastid and mitochondrial RNA polymerases. EMBO J., in press.
155. Lindahl, L., Archer, R., and Zengel, J. M. (1983). Transcription of the S10 ribosomal protein operon is regulated by an attenuator in the leader. Cell 33, 241-248.
156. Link, G. (1994). Plastid differentiation: Organelle promoters and transcription factors. In "Results and Problems in Cell Differentiation: Vol. 20, Plant Promoters and Transcription Factors" (L. Nover, ed.), pp. 65-85. Springer-Verlag, Berlin.
157. Link, G. (1996). Green life: Control of chloroplast gene transcription. BioEssays 18,465-471.
158. Link, G., Tiller, K., and Baginsky, S. (1997). Glutathione, a regulator of chloroplast transcription. In "Regulation of Enzymatic Systems Detoxifying Xenobiotics in Plants" (K. K. Hatzios, ed.), pp. 125-137. Kluwer, Dordrecht.
159. Lisowsky, T., and Michaelis, G. (1988). A nuclear gene essential for mitochondrial replication suppresses a defect of mitochondrial transcription in Saccharomyces cerevisiae. Mol. Gen. Genet. 214, 218-223.
160. Little, M. C, and Hallick, R. B. (1988). Chloroplast rpoA, rpoB and rpoC genes specify at least three components of a chloroplast DNA-dependent RNA polymerase active in tRNA and mRNA transcription. J. Biol. Chem. 263, 14302-14307.
161. Liu, B., and Troxler, R. F. (1996). Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium. Proc. Natl. Acad. Sei. USA 93, 3313-3318.
162. Lizama, L., Holuigue, L., and Jordana, X. (1994). Transcription initiation sites for the potato mitochondrial gene coding for subunit 9 of ATP synthase (atp9). FEBS Lett. 349,243-248.
163. Maier, R. M., Neckermann, K., Igloi, G., and Kossel, H. (1995). Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251, 614-628.
164. Maliga, P. (1998). Two plastid RNA polymerases in higher plants: An evolving story. Trends Plant Sei. 3, 4-6.
165. Mangus, D. A., Jang, S. H., and Jaehning, J. A. (1994). Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J. Biol. Chem. 269,26568-26574.
166. Martin, M., Echeverria, M., Litvak, S., and Araya, A. (1987). Studies of transcription in isolated wheat mitochondria and organelle extracts. Plant Sei. 49, 199-207.
167. Masters, B. S., Stohl, L. L., and Clayton, D. A. (1987). Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51, 89-99.
168. Mathews, D. E., and Durbin, R. D. (1990). Tagetitoxin' inhibits RNA synthesis directed by RNA polymerases from chloroplasts and Escherichia coli. J. Biol. Chem. 265, 493-498.
169. Mayfield, S. P., Yohn, C. B., Cohen, A., and Danon, A. (1995). Regulation of chloroplast gene expression. Annii. Rev. Plant Physiol. Plant Mol. Biol. 46, 167-188.
170. Meinhardt, F., Kempken, F., Kämper, J., and Esser, K. (1990). Linear plasmids among eukaryotes: Fundamentals and application. Curr. Genet. 17, 89-95.
171. Miyagi, T., Kapoor, S., Sugita, M., and Sugiura, M. (1998). Transcript analysis of the tobacco plastid operon rps2/atpI/H/F/A reveals the existence of a non-consensus type II (NCII) promoter upstream of the atpl coding sequence. Mot. Gen. Genet. 257, 299-307.
172. Montoya, J., Perez-Martos, A., Garstka, H. L., and Wiesner, R. J. (1997). Regulation of mitochondrial transcription by mitochondrial transcription factor A. Mol. Cell. Biochem. 174, 227-230.
173. Morden, C. W., Wolfe, K. H., dePamphilis, C. W., and Palmer, J. D. (1991). Plastid translation and transcription genes in a non-photosynthetic plant: Intact, missing and pseudogenes. EMBO J. 10, 3281-3288.
174. Morris, C. E., McGraw, N. J., Joho, K., Brown, J. E., Klement, J. F., Ling, M. L., and McAllister, W. T. (1987). In "RNA Polymerase and Regulation of Transcription" (W. S. Reznikoff, R. R. Burgess, J. E. Dahlberg, C. A. Gross, M. T. Record, and M. P. Wickens, eds.), pp. 47-58. Elsevier, New York.
175. Mullet, J. E. (1988). Chloroplast development and gene expression. Anntt. Rev. Plant Physiol. Plant Mol. Biol. 39, 475-502.
176. Mullet, J. E. (1993). Dynamic regulation of chloroplast transcription. Plant Physiol. 103, 309-313.
177. Mulligan, R. M., Maloney, A. P., and Walbot, V. (1988a). RNA processing and multiple transcription initiation sites result in transcript size heterogeneity in maize mitochondria. Mol. Gen. Genet. 211, 373-380.
178. Mulligan, R. M., Lau, G. T., and Walbot, V. (1988b). Numerous transcription initiation sites exist for the maize mitochondrial genes for subunit 9 of the ATP synthase and subunit 3 of cytochrome oxidase. Proc. Natl. Acad. Sei. USA 85, 7998-8002.
179. Mulligan, R. M., Leon, P., and Walbot, V. (1991). Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression. Mol. Cell. Biol. 11, 533-543.
180. Narita, J. O., Rushlow, K. E., and Hallick, R. B. (1985). Characterization of a Euglena gracilis chloroplast RNA polymerase specific for ribosomal RNA genes. J. Biol. Chem. 260, 11194-11199.
181. Neuhaus, H., Scholz, A., and Link, G. (1989). Structure and expression of a split chloroplast gene from mustard (Sinapis alba): Ribosomal protein rps16 reveals unusual transcriptional features and complex RNA maturation. Curr. Genet. 15, 63-70.
182. Neuhaus, H., Pfannschmidt, T., and Link, G. (1990). Nucleotide sequence of the chloroplast psbl and trnS-GCU genes from mustard (Sinapis alba). Nucleic Acids Res. 18, 368.
183. Newton, K. J., Winberg, B., Yamato, K., Lupold, S., and Stern, D. B. (1995). Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes. EMBO J. 14, 585-593.
184. Ngernprasirtsiri, J., Kobayashi, H., and Akazawa, T. (1988). DNA methylation as a mechanism of transcriptional regulation in nonphotosynthetic plastids in plant cells. Proc. Natl. Acad. Sei. USA 85, 4750-4754.
185. Ngernprasirtsiri, J., Chollet, R., Kobayashi, H., Sugiyama, T., and Akazawa, T. (1989). DNA methylation and the differential expression of C4 photosynthesis genes in mesophyll and bundle sheath cells of greening maize leaves. J. Biol. Chem. 264, 8241-8248.
186. Nickelsen, J., and Link, G. (1990). Nucleotide sequence of the mustard chloroplast genes trnH and rps19′. Nucleic Acids Res. 18,1051.
187. Nielsen, B. L., Rajasekhar, V. K., and Tewari, K. K. (1991). Pea chloroplast DNA primase: Characterization and role in initiation of replication. Plant Mol. Biol. 16, 1019-1034.
188. Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Kohchi, T., Ogura, Y., Kanegae, T., Akashi, K., and Ohyama, K. (1992). Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J. Mol. Biol. 223, 1-7.
189. Oeser, B. (1988). S2 plasmid from Zea mays probably encodes a specific RNA polymerase: An alternative alignment. Nucleic Acids Res. 16, 8729.
190. Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T.,- Sano, S., Umesono, K., Shiki, Y., Takeuchi, M, Chang, Z., Aota, S., Inokuchi, H., and Ozeki, H. (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322, 572-574.
191. Ohyama, K., Fukuzawa, H., Kohchi, T., Sano, T., Sano, S., Shirai, H., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., and Ozeki, H. (1988). Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification. J. Mol. Biol. 203, 281-298.
192. Osinga, K. A., Haan, M. D., Christianson, T., and Tabak, H. F. (1982). A nonanucleotide sequence involved in promotion of ribosomal RNA synthesis and RNA priming of DNA replication in yeast mitochondria. Nucleic Acids Res. 10, 7993-8006.
193. Palmer, J. D., Cohen, D. B., Orton, T. J., and Shields, C. R. (1983). An unusual mitochondrial DNA plasmid in the genus Brassica. Nature 301, 725-728.
194. Parisi, M. A., and Clayton, D. A. (1991). Similarity of human mitochondrial transcription factor 1 to high mobility group proteins. Science 252, 965-969.
195. Parisi, M. A., Xu, B., and Clayton, D. A. (1993). A human mitochondrial transcriptional activator can functionally replace a yeast HMG-box protein both in vivo and in vitro. Mol. Cell. Biol. 13, 1951-1961.
196. Patra, D., Lafer, E. M., and Sousa, R. (1992). Isolation and characterization of mutant bacteriophage T7 RNA polymerases. J. Mol. Biol. 224, 307-318.
197. Pfannschmidt, T., and Link, G. (1994). Separation of two classes of plastid DNA-dependent RNA polymerase that are differentially expressed in mustard (Sinapis alba L.) seedlings. Plant Mol. Biol. 25, 69-81.
198. Pfannschmidt, T., and Link, G. (1997). The A and B forms of plastid DNA-dependent RNA polymerase from mustard (Sinapis alba L.) transcribe the same genes in a different developmental context. Mol. Gen. Genet. 257, 35-44.
199. Purton, S., and Gray, J. C. (1989). The plastid rpoA gene encoding a protein homologous to the bacterial RNA polymerase alpha subunit is expressed in pea chloroplasts. Mol. Gen. Genet. 217, 77-84.
200. Rajasekhar, V. K., Sun, E., Meeker, R., Wu, B. W., and Tewari, K. K. (1991). Highly purified pea chloroplast RNA polymerase transcribes both rRNA and mRNA genes. Eur. J. Biochem. 195, 215-228.
201. Rapp, W. D., and Stern, D. B. (1992). A conserved 11 nucleotide sequence contains an essential promoter element of the maize mitochondrial atpl gene. EMBOJ. 11,1065-1073.
202. Rapp, W. D., Lupold, D. S., Mack, S., and Stern, D. (1993). Architecture of the maize mitochondrial atpl promoter as determined by linker-scanning and point mutagenesis. Mol. Cell. Biol. 13, 2732-2738.
203. Raskin, C. A., Diaz, G., Joho, K., and McAllister, W. T. (1992). Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity. J. Mol. Biol. 228, 506-515.
204. Reiss, T., and Link, G. (1985). Characterization of transcriptionally active DNA-protein complexes from chloroplasts and etioplasts of mustard (Sinapis alba L.). Eur. J. Biochem. 148, 207-212.
205. Reith, M., and Munholland, J. (1993). A high-resolution gene map of the chloroplast genome of the red alga Porphyra purpiirea. Plant Cell 5, 465-475.
206. Reith, M., and Munholland, J. (1995). Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol. Biol. Rep. 13, 333-335.
207. Remacle, C., and Marechal-Drouard, L. (1996). Characterization of the potato mitochondrial transcription unit containing "native" trnS (GCU), trnF (GAA) and trnP (UGG). Plant Mot. Biol. 30, 553-563.
208. Rochaix, J. D. (1995). Chlamydomonas reinhardtii as the photosynthetic yeast. Annu. Rev. Genet. 29, 209-230.
209. Rohe, M., Schrunder, J., Tudzynski, P., and Meinhardt, F. (1992). Phylogenetic relationships of linear, protein-primed replicating genomes. Citrr. Genet. 21, 173-176.
210. Romano, L. J., Tamanoi, F., and Richardson, C. C. (1981). Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins: Requirement for T7 RNA polymerase. Proc. Nail. Acad. Sei. USA 78, 4107-4111.
211. Rong, M., He, B., McAllister, W. T., and Durbin, R. K. (1998). Promoter specificity determinants of T7 RNA polymerase. Proc. Natt. Acad. Sei. USA 95, 515-519.
212. Rousvoal, S., Oudot, M. P., Fontaine, J. M., Kloareg, B., and Loiseaux-de Goer, S. (1998). Witnessing the evolution of transcription in mitochondria: The mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. encodes a T7-Iike RNA polymerase. J. Mol. Biol. 277,1047-1057.
213. Ruf, M., and Kössel, H. (1988). Structure and expression of the gene coding for the α-subunit of DNA-dependent RNA-polymerase from the chloroplast genome of Zea mays. Nucleic Acids. Res. 16, 5714-5754.
214. Sane, A. P., Jaiswal, P., Nath, P., Dabholkar, A. R., and Sane, P. V. (1994). Mitochondrial plasmids in Sorghum: Presence of linear plasmids in Indian male sterile and milo 296 lines. J. Plant Biochem. Biotechnol. 3, 121-124.
215. Saumitou-Laprade, P., Pannenbecker, G., Maggouta, F., Jean, R., and Michaelis, G. (1989). A linear 10.4 kb plasmid in the mitochondria of Beta maritima. Curr. Genet. 16, 181-186.
216. Schardl, C. L., Lonsdale, D. M., Pring, D. R., and Rose, K. R. (1984). Linearization of maize mitochondrial chromosomes by recombination with linear episomes. Nature 310,292-296.
217. Schardl, C. L., Pring, D. R., and Lonsdale, D. M. (1985). Mitochondrial DNA rearrangements associated with fertile revertants of S-type male sterile maize. Cell 43, 361-368.
218. Schinkel, A. H., and Tabak, H. F. (1989). Mitochondrial RNA polymerase: Dual role in transcription and replication. Trends Genet. 5, 149-154.
219. Schinkel, A. H., Groot Koerkamp, M. J. A., Touw, E. P. W., and Tabak, H. F. (1987). Specificity factor of yeast mitochondrial RNA polymerase. Purification and interaction with core RNA polymerase. J. Biol. Chem. 262, 12785-12791.
220. Schinkel, A. H., Groot Koerkamp, M. J. A., and Tabak, H. F. (1988). Mitochondrial RNA polymerase of Saccharomyces cerevisiae: Composition and mechanism of promoter recognition. EMBO J. 7, 3255-3262.
221. Schneider-Poetsch, H. A. W., Kolukisaoglu, u., Clapham, D. H., Hughes, J., and Lamparter, T. (1998). Non-angiosperm phytochromes and the evolution of vascular plants. Physlol. Plant. 102, 612-622.
222. Serino, G., and Maliga, P. (1998). RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol. 117,1165-1170.
223. Severinov, K., Mustaev, A., Kukarin, A., Muzzin, O., Bass, I., Darst, S. A., and Goldfarb, A. (1996). Structural modules of the large subunits of RN A polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. J. Biol. Cliem. 271, 27969-27974.
224. Sexton, T. B., Jones, J. T., and Mullet, J. E. (1990a). Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI and trnS(GCU). Curr. Genet. 17, 445-454.
225. Sexton, T. B., Christopher, D. A., and Mullet, J. E. (1990b). Light-induced switch in barley psbD-psb C promoter utilization: A novel mechanism regulating chloroplast gene expression. EMBO J. 9, 4485-4494.
226. Sha, Y., Lindahl, L., and Zengel, J. M. (1995). Role of NusA in L4-mediated attenuation control of the S10 r-protein operon of Escherichia coll. J. Mol. Biol. 245, 474-485.
227. Shadel, G. S., and Clayton, D. A. (1993). Mitochondrial transcription initiation. Variation and conservation. J. Biol. Cliem. 268,16083-16086.
228. Shadel, G. S., and Clayton, D. A. (1995). A Saccharomyces cerevisiae mitochondrial transcription factor, sc-mtTFB, shares features with sigma factors but is functionally distinct. Mol. Cell. Biol. 15, 2101-2108.
229. Shimada, H., Fukuta, M., Ishikawa, M., and Sugiura, M. (1990). Rice chloroplast RNA polymerase genes: The absence of an intron in rpoCl and the presence of an extra sequence in rpoC2. Mol. Gen. Genet. 221, 395-402.
230. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohio, C., Torazawa, K., Meng, B. Y., Sugita, M., Deno, H., Kamogashira, H., Yamada, K., Kusuda, J., Takaiwa, F., Kalo, A., Shimada, A., and Sugiura, M. (1986). The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO J. 5, 2043-2049.
231. Siemenroth, A., Wollgiehn, R., Neumann, D., and Borner, T. (1981). Synthesis of ribosomal RNA in ribosome-deficient plastids of the mutant "albostrians" of Hordeum vulgare L. Planta 153, 547-555.
232. Sijben-Müller, G., Hallick, R. B., Alt, J., Westhoff, P., and Hermann, R. G. (1986). Spinach plastid genes coding for initiation factor IF-1, ribosomal protein Sll and RNA polymerase α-subunit. Nucleic Acids Res. 14, 1029-1044.
233. Silhavy, D., and Maliga, P. (1998a). Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr. Genet. 33, 340-344.
234. Silhavy, D., and Maliga, P. (1998b). Plastid promoter utilization in a rice embryogenic cell culture. Curr. Genet. 34, 67-70.
235. Smith, H. J., and Bogorad, L. (1974). The polymerase of Zea mays chloroplasts. Proc. Natl. Acad. Sei. USA 71, 4839-4842.
236. Sousa, R. (1996). Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sei. 21, 186-190.
237. Sousa, R., Chung, Y. J., Rose, J. P., and Wang, B. C. (1993). Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution. Nature 364, 593-599.
238. Sriraman, P., Silhavy, D., and Maliga, P. (1998a). Transcription from heterologous ribosomal RNA operon promoters in chloroplasts reveals requirement for specific activating factors. Plant Physiol. 117,1495-1499.
239. Sriraman, P., Silhavy, D., and Maliga, P. (1998b). The phage-type PclpP-53 plastid promoter comprises sequences downstream of the transcription initiation site. Nucleic Acids Res. 26, 4874-4879.
240. Stern, D. B., Higgs, D. C., and Yang, J. (1997). Transcription and translation in chloroplasts. Trends Plant Sei. 2, 308-315.
241. Stirdivant, S. M., Crossland, L. D., and Bogorad, L. (1985). DNA supercoiling affects in vitro transcription of two maize chloroplast genes differently. Proc. Natl. Acad. Sei. USA 82, 4886-4890.
242. Stirewalt, V., Michalowski, C. B., Löffelhardt, W., Bohnert, H. J., and Bryant, D. B. (1995). Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol. Biol. Rep. 13, 327-332.
243. Strimmer, K., and von Haeseler, A. (1996). Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
244. Strimmer, K., and von Haeseler, A. (1997). Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc. Nail. Acad. Sei. USA 94, 6815-6819.
245. Strittmatter, G., Godzicka-Josefiak, A., and Kossel, H. (1985). Identification of an rRNA operon promoter from Zea mays chloroplast which excludes the proximal tRNAVal from the primary transcript. EMBO J. 4, 599-604.
246. Suck, R., Zeltz, P., Falk, J., Acker, A., Kossel, H., and Krupinska, K. (1996). Transcriptionally active chromosomes (TACs) of barley chloroplasts contain the α-subunit of plastome-encoded RNA polymerase. Curr. Genet. 30, 515-521.
247. Sugita, M., and Sugiura, M. (1996). Regulation of gene expression in chloroplasts of higher plants. Plant Mol. Biol. 32, 315-326.
248. Sugiura, M. (1992). The chloroplast genome. Plant Mol. Biol. 19, 149-168.
249. Sun, E., Wu, B. W., and Tewari, K. K. (1989). In vitro analysis of the pea chloroplast 16S rRNA gene promoter. Mol. Cell. Biol. 9, 5650-5659.
250. Surzycki, S. J. (1969). Genetic functions of the chloroplast of Chlamydomonas reinhardi: Effect of rifampin on chloroplast DNA-dependent RNA polymerase. Proc. Natt. Acad. Sci. USA 63, 1327-1334.
251. Surzycki, S. J., and Shellenbarger, D. L. (1976). Purification and characterization of a putative sigma factor from Chlamydomonas reinhardtii. Proc. Nail. Acad. Sei. USA 73, 3961-3965.
252. Surzycki, S. J., Goodenough, U. W., Levine, R. P., and Armstrong, J. J. (1970). Nuclear and chloroplast control of chloroplast structure and function in Chlamydomonas reinhardi. Symp. Soc. Exp. Biol. 23, 13-37.
253. Tanaka, K., Oikawa, K., Ohta, N., Kuroiwa, H., Kuroiwa, T., and Takahashi, H. (1996). Nuclear encoding of a chloroplast RNA polymerase sigma subunit in a red alga. Science 272, 1932-1935.
254. Tanaka, K., Tozawa, Y., Mochizuki, N., Shinozaki, K., Nagatani, A., Wakasa, K., and Takahashi, H. (1997). Characterization of three cDNA species encoding plastid RNA polymerase sigma factors in Arabidopsis thaliana: Evidence for the sigma factor heterogeneity in higher plant plastids. FEES Lett. 413, 309-313.
255. Tewari, K. K., and Goel, A. (1983). Solubilization and partial purification of RNA polymerase from pea chloroplasts. Biochemistry 22, 2142-2148.
256. Tiller, K., and Link, G. (1993a). Sigma-Iike transcription factors from mustard (Sinapsis alba L.) etioplast are similar in size to, but functionally distinct from, their chloroplast counterparts. Plant Mol. Biol. 21, 503-513.
257. Tiller, K., and Link, G. (1993b). Phosphorylation and dephosphorylation affect functional characteristics of chloroplast and etioplast transcription systems from mustard (Sinapis alba L.). EMBO J. 12, 1745-1753.
258. Tiller, K., Eisermann, A., and Link, G. (1991). The chloroplast transcription apparatus from mustard (Sinapis alba L.). Evidence for three different transcription factors which resemble bacterial sigma factors. Eur. J. Biochem. 198, 93-99.
259. Timothy, D. H., Goodman, M., Hu, W. W. L., and Levings, C. S., III (1983). Plasmid-like mitochondrial DNAs in diploperenial teosinte. Maydica 28, 139-149.
260. Tiranti, V., Savoia, A., Forti, F., D'Apolito, M. F., Centra, M., Rocchi, M., and Zeviani, M. (1997). Identification of the gene encoding the human mitochondrial RNA polymerase (hmtRPOL) by cyberscreening of the Expressed Sequence Tags database. Hum. Mol. Genet. 6, 615-625.
261. To, K. Y., Cheng, M. C., Suen, D. F., Mon, D. P., Chen, L. F., and Chen, S. C. (1996). Characterization of the light-responsive promoter of rice chloroplast psbD-C operon and the sequence-specific DNA binding factor. Plant Cell Physiol. 37, 660-666.
262. Topping, J. F., and Leaver, C. J. (1990). Mitochondrial gene expression during wheat leaf development. Planta 182, 399-407.
263. Tozawa, Y., Tanaka, K., Takahashi, H., and Wakasa, K. (1998). Nuclear encoding of a plastid sigma factor in rice and its tissue- and light-dependent expression. Nucleic Acids Res. 26, 415-419.
264. Tracy, R. L., and Stern, D. B. (1995). Mitochondrial transcription initiation: Promoter structures and RNA polymerases. Curr. Genet. 28, 205-216.
265. Trifa, Y., Privat, I., Gagnon, J., Baeza, L., and Lerbs-Mache, S. (1998). The nuclear RPL4 gene encodes a chloroplast protein that co-purifies with the T7-like transcription complex as well plastid ribosomes. J. Biol Chem. 273, 3980-3985.
266. Troxler, R. F., Zhang, F., Hu, J., and Bogorad, L. (1994). Evidence that sigma factors are components of chloroplast RNA polymerase. Plant Pliysiol. 104, 753-759.
267. Unseld, M., Marienfeld, J. R., Brandt, P., and Brennicke, A. (1997). The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet. 15, 57-61.
268. Vera, A., and Sugiura, M. (1995). Chloroplast rRNA transcription from structurally different tandem promoters: An additional novel-type promoter. Curr. Genet. 27, 280-284.
269. Vera, A., Matsubayashi, T., and Sugiura, M. (1992). Active transcription from a promoter positioned within the coding region of a divergently oriented gene: The tobacco chloroplast rpl32 gene. Mol. Gen. Genet. 233,151-156.
270. Vera, A., Hirose, T., and Sugiura, M. (1996). A ribosomal protein gene (rpl32) from tobacco chloroplast DNA is transcribed from alternative promoters: Similarities in promoter region organization plastid housekeeping genes. Mol. Gen. Genet. 251, 518-525.
271. Vickery, D. B., and Griffiths, A. J. (1993). Transcription of the kalilo linear senescence plasmid from Neurospora intermedia. Plasmid 29, 180-192.
272. Vlcek, C., Paces, V., Maltsev, N., Paces, J., Haselkorn, R., and Fonstein, M. (1997). Sequence of a 189-kb segment of the chromosome of Rhodobacter capsulants SB1003. Proc. Natl. Acad. Sei. USA 94, 9384-9388.
273. Vogel, J., Hübschmann, T., Borner, T., and Hess, W. R. (1997). Intron-internal RNA editing and splicing of trnK-matK precursor transcripts in barley plastids: Support for MatK as an essential splice factor. J. Mol. Biol. 270,179-187.
274. Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Tsudzuki, T., and Sugiura, M. (1994). Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pima thunbergii. Proc. Natl. Acad. Sei. USA 91, 9794-9798.
275. Wakasugi, T., Nagai, T., Kapoor, M., Sugita, M., Ito, M., Ito, S., Tsudzuki, J., Nakashima, K., Tsudzuki, T., Suzuki, Y., Hamda, A., Ohta, T., Inamura, A., Yoshinaga, K., and Sugiura, M, (1997). Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vttlgaris: The existence of genes possibly involved in chloroplast division. Proc. Natl. Acad. Sei. USA 94, 5967-5972.
276. Walter, G., Müller, A., Hoffmann, P., and Borner, T. (1995). Tetrapyrrole synthesis in leaves and roots of a barley albina mutant with extremely low amount of plastid glutamyl-tRNA. In "Photosynthesis: From Light to Biosphere" (P. Mathis, ed.), Vol. Ill, pp. 937-940. Kluwer, Dordrecht.
277. Weber, B. (1994). DNA-Abschnitte des mitochondrialen Genoms von Beta vulgaris mit Homologie zu Polymerase-Genen und ihr Zusammenhang mit der cytoplasmatischen männlichen Sterilität. Doctoral thesis, Humboldt University, Berlin.
278. Weber, B., Borner, T., and Weihe, A. (1995). Remnants of a DNA polymerase gene in the mitochondrial DNA of Marcliantia polymorpha. Curr. Genet. 27, 488-490.
279. Weihe, A., Hedtke, B., and Borner, T. (1997). Cloning and characterization of a cDNA encoding a bacteriophage-type RNA polymerase from the higher plant Chenopodium album. Nucleic Acids Res. 25, 2319-2325.
280. Weissinger, A., Goodman, M., Hu, W., Levings, C. S., and Timothy, D. (1982). Unique plasmid-like mitochondrial DNAs from indigenous maize races of Latin-America. Proc. Natl. Acad. Sei. USA 79,1-5.
281. Whatley, J. M. (1993). The endosymbiotic origin of chloroplasts. Int. Rev. Cytol. 144,259-299.
282. Wilson, R. J., and Williamson, D. H. (1997). Extrachromosomal DNA in the Apicomplexa. MicrobioL Mol. Biol. Rev. 61, 1-16.
283. Wilson, R. J. M., Denny, P. W., Preiser, P. R., Rangachari, K., Roberts, K., Roy, A., Whyte, A., Strath, M., Moore, P. W., and Williamson, D. H. (1996). Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J. Mol. Biol. 261,155-172.
284. Wolfe, K. H., Gouy, M., Yang, Y. W., Sharp, P. M., and Li, W. H. (1989). Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sei. USA 86, 6201-6205.
285. Wolfe, K. H., Katz-Downie, D. S., Morden, C. W., and Palmer, J. D. (1992a). Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: Accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes. Plant Mol. Biol. 18,1037-1048.
286. Wolfe, K. H., Morden, C. W., Ems, S. C., and Palmer, J. D. (1992b). Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: Loss or accelerated sequence evolution of tRNA and ribosomal protein genes. J. Mol. Evol. 35, 304-317.
287. Wolff, G., Plante, I., Lang, B. F., Kuck, U., and Burger, G. (1994). Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. Gene content and genome organization. J. Mol. Biol. 237, 75-86.
288. Woody, A. Y. M., Eaton, S. S., Osumi-Davis, P. A., and Woody, R. W. (1996). Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription. Biochemistry 35, 144-152.
289. Xu, B., and Clayton, D. A. (1992). Assignment of a yeast protein necessary for mitochondrial transcription initiation. Nucleic Acids Res. 20, 1053-1059.
290. Yan, B., and Pring, D. R. (1997). Transcriptional initiation sites in sorghum mitochondrial DNA indicate conserved and variable features. Curr. Genet. 32, 287-295.
291. Yepiz-Plascencia, G. M., Radebaugh, C. A., and Hallick, R. B. (1990). The Etiglena gracilis chloroplast rpoB gene. Novel gene organization and transcription of the RNA polymerase subunit operon. Nucleic Acids Res. 18, 1869-1878.
292. Young, D. A., and Lonsdale, D. M. (1997). Evidence that plant mitochondrial transcription requires promoter-specific factors. Maize Genet. Coop. News 71, 69-71.
293. Young, D. A., Allen, R. L., Harvey, A. J., and Lonsdale, D. M. (1998). Characterization of a gene encoding a single-subunit bacteriophage-type RNA polymerase from maize which is alternatively spliced. Mol. Gen. Genet. 260, 30-37.
294. Zaitlin, D., Hu, J., and Bogorad, L. (1989). Binding and transcription of relaxed DNA templates by fractions of maize chloroplast extracts. Proc. Natl. Acad. Sei. USA 86, 876-880.
295. Zeltz, P., Hess, W. R., Neckermann, K., Borner, T., and Kössel, H. (1993). Editing of the rpoB transcript is independent of chloroplast translation and shows different patterns in barley and maize. EMBO J 12, 4291-4296.
296. Zengel, J. M., and Lindahl, L. (1990). Ribosomal protein L4 stimulates in vitro termination of transcription at a NusA-dependent terminator in the S10 operon leader. Proc. Natl. Acad. Sei. USA 87, 2675-2679.
297. Zengel, J. M., and Lindahl, L. (1992). Ribosomal protein L4 and transcription factor NusA have separable roles in mediating terminating of transcription within the leader of the S10 operon of Escherichia coli. Genes Dev. 12, 2655-2662.
298. Zengel, J. M., and Lindahl, L. (1993). Domain I of 23S rRNA competes with a paused transcription complex for ribosomal protein L4 of Escherichia coli. Nucleic Acids Res. 21, 2419-2435.