Plastid gene transcription: Promoters and RNA polymerases

Methods in Molecular Biology

Volumn 1132, Issue , 2014, Pages 47-72

  Ortelt, Jennifer ^a   Link, Gerhard ^a  

^a NONE

Author keywords

Chloroplast; DNA binding proteins; Gene expression; NEP; PEP; Promoters; RNA polymerase; Sigma factors; Transcriptional regulation

Indexed keywords

MITOCHONDRIAL RNA; PHOSPHOTRANSFERASE; PLANT RNA; RNA POLYMERASE; SIGMA FACTOR; VEGETABLE PROTEIN; ARABIDOPSIS PROTEIN; CHLOROPLAST PROTEIN; DNA BINDING PROTEIN; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; MITOCHONDRIAL PROTEIN; PLANT DNA; RNA POLYMERASE ALPHA SUBUNIT; RPOB PROTEIN, E COLI; RPOTMP PROTEIN, ARABIDOPSIS; RPOTP PROTEIN, ARABIDOPSIS; SIG5 PROTEIN, ARABIDOPSIS; SIG6 PROTEIN, ARABIDOPSIS;

AMINO ACID SEQUENCE; ARABIDOPSIS THALIANA; ARTICLE; BLUE LIGHT; CHLOROPLAST; EUDICOT; GENETIC TRANSCRIPTION; GREEN ALGA; MONOCOT; NONHUMAN; PHYLOGENY; PLANT GENE; PLASTID; PRIORITY JOURNAL; PROMOTER REGION; ARABIDOPSIS; CHLOROPLAST GENOME; GENE EXPRESSION REGULATION; GENETICS; TOBACCO;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHLOROPLAST PROTEINS; CHLOROPLASTS; DNA, PLANT; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, PLANT; GENOME, CHLOROPLAST; MITOCHONDRIAL PROTEINS; PROMOTER REGIONS, GENETIC; SIGMA FACTOR; TOBACCO; TRANSCRIPTION, GENETIC;

EID: 84907817499     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-995-6_3     Document Type: Article

References (173)

1. Mereschkowsky C (1905) Über die Natur und den Ursprung der Chromatophoren im Pfl anzenreiche. Biol Centralbl 25:593–604, 689–691
2. Herrmann RG (1997) Eukaryotism, towards a new interpretation. In: Schenk HEA, Herrmann RG, Jeon KW, Müller NE, Schwemmler W (eds) Eukaryotism and symbiosis. Springer, Berlin Heidelberg, 73–118
3. Gray MW (1999) Evolution of organellar genomes. Curr Opin Genet Dev 9: 678–687
4. Emelyanov VV (2003) Mitochondrial connection to the origin of the eukaryotic cell. Eur J Biochem 270:1599–1618
5. McFadden GI (2001) Chloroplast origin and integration. Plant Physiol 125:50–53
6. Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19:47–56
7. Baginsky S, Siddique A, Gruissem W (2004) Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids. J Proteome Res 3:1128–1137
8. Cline K, Henry R (1996) Import and routing of nucleus-encoded chloroplast proteins. Annu Rev Cell Dev Biol 12:1–26
9. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the fl owering plant Arabidopsis thaliana. Nature 408:796–815
10. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 99:12246–12251
11. Palmer JD (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19:325–354
12. Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19:149–168
13. Tsudzuki J, Ito S, Tsudzuki T, Wakasugi T, Sugiura M (1994) A new gene encoding tRNA(Pro) (GGG) is present in the chloroplast genome of black pine: a compilation of 32 tRNA genes from black pine chloroplasts. Curr Genet 26:153–158
14. Allen JF (1993) Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165:609–631
15. Clayton DA (1987) Nuclear gene products that function in mitochondrial DNA replication. Philos Trans R Soc Lond B Biol Sci 317:473–482
16. Kelly JL, Greenleaf AL, Lehman IR (1986) Isolation of the nuclear gene encoding a subunit of the yeast mitochondrial RNA polymerase. J Biol Chem 261:10348–10351
17. Kirk JT (1964) Studies on RNA synthesis in chloroplast preparations. Biochem Biophys Res Commun 16:233–238
18. Smith HJ, Bogorad L (1974) The polypeptide subunit structure of the DNA-dependent RNA polymerase of Zea mays chloroplasts. Proc Natl Acad Sci U S A 71:4839–4842
19. Hu J, Bogorad L (1990) Maize chloroplast RNA polymerase: the 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes. Proc Natl Acad Sci U S A 87:1531–1535
20. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi- Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049
21. Bunger W, Feierabend J (1980) Capacity for RNA synthesis in 70S ribosome-defi cient plastids of heat-bleached rye leaves. Planta 149:163–169
22. dePamphilis CW, Palmer JD (1990) Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic fl owering plant. Nature 348:337–339
23. Hess WR, Prombona A, Fieder B, Subramanian AR, Borner T (1993) Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome- defi cient plastids: evidence for a functioning non-chloroplastencoded RNA polymerase. EMBO J 12:563–571
24. Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15:2802–2809
25. Maliga P (1998) Two plastid RNA polymerases of higher plants: an evolving story. Trends Plant Sci 3:4–6
26. Serino G, 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
27. Hess WR, Borner T (1999) Organellar RNA polymerases of higher plants. Int Rev Cytol 190:1–59
28. Liere K, Maliga P (1999) In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. EMBO J 18:249–257
29. Baumgartner BJ, Rapp JC, Mullet JE (1993) Plastid genes encoding the transcription/ translation apparatus are differentially transcribed early in barley (Hordeum vulgare) chloroplast development (evidence for selective stabilization of psbA mRNA). Plant Physiol 101:781–791
30. Allison LA (2000) The role of sigma factors in plastid transcription. Biochimie 82: 537–548
31. Shiina T, Tsunoyama Y, Nakahira Y, Khan MS (2005) Plastid RNA polymerases, promoters, and transcription regulators in higher plants. Int Rev Cytol 244:1–68
32. Schweer J, Turkeri H, Kolpack A, Link G (2010) Role and regulation of plastid sigma factors and their functional interactors during chloroplast transcription—recent lessons from Arabidopsis thaliana. Eur J Cell Biol 89:940–946
33. Morden CW, Wolfe KH, dePamphilis CW, Palmer JD (1991) Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. EMBO J 10:3281–3288
34. Hajdukiewicz PT, Allison LA, Maliga P (1997) The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 16:4041–4048
35. 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 Sci U S A 90:5509–5513
36. Ikeda TM, Gray MW (1999) Identifi cation and characterization of T3/T7 bacteriophagelike RNA polymerase sequences in wheat. Plant Mol Biol 40:567–578
37. Hedtke B, Borner T, Weihe A (1997) Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277:809–811
38. Hedtke B, Borner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1:435–440
39. Liere K, Kaden D, Maliga P, Borner T (2004) Overexpression of phage-type RNA polymerase RpoTp in tobacco demonstrates its role in chloroplast transcription by recognizing a distinct promoter type. Nucleic Acids Res 32:1159–1165
40. Emanuel C, Weihe A, Graner A, Hess WR, Borner T (2004) Chloroplast development affects expression of phage-type RNA polymerases in barley leaves. Plant J 38:460–472
41. Silhavy D, Maliga P (1998) Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr Genet 33:340–344
42. Gray MW, Lang BF (1998) Transcription in chloroplasts and mitochondria: a tale of two polymerases. Trends Microbiol 6:1–3
43. Chang CC, Sheen J, Bligny M, Niwa Y, Lerbs-Mache S, Stern DB (1999) Functional analysis of two maize cDNAs encoding T7-like RNA polymerases. Plant Cell 11:911–926
44. Kusumi K, Yara A, Mitsui N, Tozawa Y, Iba K (2004) Characterization of a rice nuclearencoded plastid RNA polymerase gene OsRpoTp. Plant Cell Physiol 45:1194–1201
45. Kobayashi Y, Dokiya Y, Sugiura M, Niwa Y, Sugita M (2001) Genomic organization and organ-specifi c expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris. Gene 279:33–40
46. Kobayashi Y, Dokiya Y, Sugita M (2001) Dual targeting of phage-type RNA polymerase to both mitochondria and plastids is due to alternative translation initiation in single transcripts. Biochem Biophys Res Commun 289:1106–1113
47. Hedtke B, Legen J, Weihe A, Herrmann RG, Borner T (2002) Six active phage-type RNA polymerase genes in Nicotiana tabacum. Plant J 30:625–637
48. Bligny M, Courtois F, Thaminy S, Chang CC, Lagrange T, Baruah-Wolff J, Stern D, Lerbs-Mache S (2000) Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases. EMBO J 19:1851–1860
49. Kuhn K, Richter U, Meyer EH, Delannoy E, de Longevialle AF, O’Toole N, Borner T, Millar AH, Small ID, Whelan J (2009) Phagetype RNA polymerase RPOTmp performs gene-specifi c transcription in mitochondria of Arabidopsis thaliana. Plant Cell 21: 2762–2779
50. Courtois F, Merendino L, Demarsy E, Mache R, Lerbs-Mache S (2007) Phage-type RNA polymerase RPOTmp transcribes the rrn operon from the PC promoter at early developmental stages in Arabidopsis. Plant Physiol 145:712–721
51. Swiatecka-Hagenbruch M, Emanuel C, Hedtke B, Liere K, Borner T (2008) Impaired function of the phage-type RNA polymerase RpoTp in transcription of chloroplast genes is compensated by a second phage-type RNA polymerase. Nucleic Acids Res 36:785–792
52. Hricova A, Quesada V, Micol JL (2006) The SCABRA3 nuclear gene encodes the plastid RpoTp RNA polymerase, which is required for chloroplast biogenesis and mesophyll cell proliferation in Arabidopsis. Plant Physiol 141:942–956
53. Bottomley W, Smith HJ, Bogorad L (1971) RNA polymerases of maize: partial purifi cation and properties of the chloroplast enzyme. Proc Natl Acad Sci U S A 68:2412–2416
54. McKown RL, Tewari KK (1984) Purifi cation and properties of a pea chloroplast DNA polymerase. Proc Natl Acad Sci U S A 81:2354–2358
55. Lerbs S, Briat JF, Mache R (1983) Chloroplast RNA polymerase from spinach: purifi cation and DNA-binding proteins. Plant Mol Biol 2:67–74
56. Igloi GL, Kössel H (1992) The transcriptional apparatus of chloroplasts. Crit Rev Plant Sci 10:525–558
57. 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, Yamada M, Yasuda M, 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 (supplement). DNA Res 3:185–209
58. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A (1996) Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta′ subunits of Escherichia coli RNA polymerase. J Biol Chem 271:27969–27974
59. Suzuki JY, Maliga P (2000) Engineering of the rpl23 gene cluster to replace the plastid RNA polymerase alpha subunit with the Escherichia coli homologue. Curr Genet 38:218–225
60. Shinozaki K, Sugiura M (1986) Organization of chloroplast genomes. Adv Biophys 21:57–78
61. Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (2003) Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res 31:5324–5331
62. Kabeya Y, Kobayashi Y, Suzuki H, Itoh J, Sugita M (2007) Transcription of plastid genes is modulated by two nuclear-encoded alpha subunits of plastid RNA polymerase in the moss Physcomitrella patens. Plant J 52:730–741
63. Smith AC, Purton S (2002) The principle apparatus of algal plastids. Eur J Phycol 37:301–311
64. Wilson RJ, Denny PW, Preiser PR, Rangachari K, Roberts K, Roy A, Whyte A, Strath M, Moore DJ, Moore PW, Williamson DH (1996) Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J Mol Biol 261:155–172
65. Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ (2010) Organization and expression of organellar genomes. Philos Trans R Soc Lond B Biol Sci 365:785–797
66. Burgess RR, Travers AA, Dunn JJ, Bautz EKF (1969) Factor stimulating transcription by RNA polymerase. Nature 221:43–46
67. Darst SA, Polyakov A, Richter C, Zhang G (1998) Structural studies of Escherichia coli RNA polymerase. Cold Spring Harb Symp Quant Biol 63:269–276
68. Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 98: 811–824
69. Busby S, Ebright RH (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79:743–746
70. Lerbs S, Brautigam E, Parthier B (1985) Polypeptides of DNA-dependent RNA polymerase of spinach chloroplasts: characterization by antibody-linked polymerase assay and determination of sites of synthesis. EMBO J 4:1661–1666
71. Bulow S, Link G (1988) Sigma-like activity from mustard (Sinapis alba L) chloroplasts conferring DNA-binding and transcription specifi city to E. coli core RNA polymerase. Plant Mol Biol 10:349–357
72. Liu B, Troxler RF (1996) Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium. Proc Natl Acad Sci U S A 93: 3313–3318
73. Tanaka K, Oikawa K, Ohta N, Kuroiwa H, Kuroiwa T, Takahashi H (1996) Nuclear encoding of a chloroplast RNA polymerase sigma subunit in a red alga. Science 272: 1932–1935
74. Hallick RB, Lipper C, Richards OC, Rutter WJ (1976) Isolation of a transcriptionally active chromosome from chloroplasts of Euglena gracilis. Biochemistry 15:3039–3045
75. Pfalz J, Liere K, Kandlbinder A, Dietz KJ, Oelmuller R (2006) pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell 18:176–197
76. Link G (1984) DNA sequence requirements for the accurate transcription of a proteincoding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.). EMBO J 3: 1697–1704
77. Gruissem W, Greenberg BM, Zurawski G, Prescott DM, Hallick RB (1983) Biosynthesis of chloroplast transfer RNA in a spinach chloroplast transcription system. Cell 35:815–828
78. Orozco EM Jr, Mullet JE, Chua NH (1985) An in vitro system for accurate transcription initiation of chloroplast protein genes. Nucleic Acids Res 13:1283–1302
79. Deng XW, Stern DB, Tonkyn JC, Gruissem W (1987) Plastid run-on transcription. Jennifer Ortelt and Gerhard Link Application to determine the transcriptional regulation of spinach plastid genes. J Biol Chem 262:9641–9648
80. Mullet JE, Klein RR (1987) Transcription and RNA stability are important determinants of higher plant chloroplast RNA levels. EMBO J 6:1571–1579
81. Svab Z, Hajdukiewicz P, Maliga P (1990) Stable transformation of plastids in higher plants. Proc Natl Acad Sci U S A 87: 8526–8530
82. Pfannschmidt T, Link G (1994) Separation of two classes of plastid DNA-dependent RNA polymerases that are differentially expressed in mustard (Sinapis alba L.) seedlings. Plant Mol Biol 25:69–81
83. Pfannschmidt T, Ogrzewalla K, Baginsky S, Sickmann A, Meyer HE, Link G (2000) The multisubunit chloroplast RNA polymerase A from mustard (Sinapis alba L.). Integration of a prokaryotic core into a larger complex with organelle-specifi c functions. Eur J Biochem 267:253–261
84. Ogrzewalla K, Piotrowski M, Reinbothe S, Link G (2002) The plastid transcription kinase from mustard (Sinapis alba L.). A nuclear-encoded CK2-type chloroplast enzyme with redox-sensitive function. Eur J Biochem 269:3329–3337
85. Schroter Y, Steiner S, Matthai K, Pfannschmidt T (2010) Analysis of oligomeric protein complexes in the chloroplast sub-proteome of nucleic acid-binding proteins from mustard reveals potential redox regulators of plastid gene expression. Proteomics 10:2191–2204
86. Suzuki JY, Ytterberg AJ, Beardslee TA, Allison LA, Wijk KJ, Maliga P (2004) Affi nity purifi -cation of the tobacco plastid RNA polymerase and in vitro reconstitution of the holoenzyme. Plant J 40:164–172
87. Satoh J, Baba K, Nakahira Y, Tsunoyama Y, Shiina T, Toyoshima Y (1999) Developmental stage-specifi c multi-subunit plastid RNA polymerases (PEP) in wheat. Plant J 18:407–415
88. Helmann JD, Chamberlin MJ (1988) Structure and function of bacterial sigma factors. Annu Rev Biochem 57:839–872
89. Wosten MM (1998) Eubacterial sigmafactors. FEMS Microbiol Rev 22:127–150
90. Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning of the bacterial transcription space. Annu Rev Microbiol 57:441–456
91. Geszvain K, Landick R (2005) The structure of bacterial RNA polymerase. Website Edition (http://www. bact.wisc.edu/Landick) 1:1–10
92. Ishihama A (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54:499–518
93. Malhotra A, Severinova E, Darst SA (1996) Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87: 127–136
94. Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417:712–719
95. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA (2002) Structure of the bacterial RNA polymerase promoter specifi city sigma subunit. Mol Cell 9:527–539
96. Campbell EA, Tupy JL, Gruber TM, Wang S, Sharp MM, Gross CA, Darst SA (2003) Crystal structure of Escherichia coli sigma E with the cytoplasmic domain of its anti-sigma RseA. Mol Cell 11:1067–1078
97. Link G (1994) Plastid differentiation: organelle promoters and transcription factors. Results Probl Cell Differ 20:65–85
98. Tanaka K, Tozawa Y, Mochizuki N, Shinozaki K, Nagatani A, Wakasa K, 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. FEBS Lett 413:309–313
99. Isono K, Niwa Y, Satoh K, Kobayashi H (1997) Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots. Plant Physiol 114:623–630
100. Tozawa Y, Tanaka K, Takahashi H, Wakasa K (1998) Nuclear encoding of a plastid sigma factor in rice and its tissue- and lightdependent expression. Nucleic Acids Res 26:415–419
101. Kestermann M, Neukirchen S, Kloppstech K, Link G (1998) Sequence and expression characteristics of a nuclear-encoded chloroplast sigma factor from mustard (Sinapis alba). Nucleic Acids Res 26:2747–2753
102. Tan S, Troxler RF (1999) Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: photoregulation and differential expression. Proc Natl Acad Sci U S A 96:5316–5321
103. Morikawa K, Ito S, Tsunoyama Y, Nakahira Y, Shiina T, Toyoshima Y (1999) Circadianregulated expression of a nuclear-encoded plastid sigma factor gene (sigA) in wheat seedlings. FEBS Lett 451:275–278
104. Oikawa K, Fujiwara M, Nakazato E, Tanaka K, Takahashi H (2000) Characterization of two plastid sigma factors, SigA1 and SigA2, that mainly function in matured chloroplasts in Nicotiana tabacum. Gene 261:221–228
105. Schweer J (2010) Plant sigma factors come of age: fl exible transcription factor network for regulated plastid gene expression. Endocytobiosis Cell Res 20:1–20
106. Bohne AV, Irihimovitch V, Weihe A, Stern DB (2006) Chlamydomonas reinhardtii encodes a single sigma70-like factor which likely functions in chloroplast transcription. Curr Genet 49:333–340
107. Fujiwara M, Nagashima A, Kanamaru K, Tanaka K, Takahashi H (2000) Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase sigma factors in Arabidopsis thaliana. FEBS Lett 481:47–52
108. Kanamaru K, Fujiwara M, Seki M, Katagiri T, Nakamura M, Mochizuki N, Nagatani A, Shinozaki K, Tanaka K, Takahashi H (1999) Plastidic RNA polymerase sigma factors in Arabidopsis. Plant Cell Physiol 40:832–842
109. Lysenko EA (2007) Plant sigma factors and their role in plastid transcription. Plant Cell Rep 26:845–859
110. Lerbs-Mache S (2010) Function of plastid sigma factors in higher plants: regulation of gene expression or just preservation of constitutive transcription? Plant Mol Biol 76: 235–249
111. Ishizaki Y, Tsunoyama Y, Hatano K, Ando K, Kato K, Shinmyo A, Kobori M, Takeba G, Nakahira Y, Shiina T (2005) A nuclearencoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J 42:133–144
112. Nagashima A, Hanaoka M, Motohashi R, Seki M, Shinozaki K, Kanamaru K, Takahashi H, Tanaka K (2004) DNA microarray analysis of plastid gene expression in an Arabidopsis mutant defi cient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 68:694–704
113. Tsunoyama Y, Ishizaki Y, Morikawa K, Kobori M, Nakahira Y, Takeba G, Toyoshima Y, Shiina T (2004) Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc Natl Acad Sci U S A 101:3304–3309
114. Morikawa K, Shiina T, Murakami S, Toyoshima Y (2002) Novel nuclear-encoded proteins interacting with a plastid sigma factor, Sig1, in Arabidopsis thaliana. FEBS Lett 514:300–304
115. Xie YD, Li W, Guo D, Dong J, Zhang Q, Fu Y, Ren D, Peng M, Xia Y (2010) The Arabidopsis gene SIGMA FACTORBINDING PROTEIN 1 plays a role in the salicylate- and jasmonate-mediated defence responses. Plant Cell Environ 33:828–839
116. Kolpack A (2010) Regulatory protein-protein interactions in the plastid transcription. PhD thesis, Ruhr University, Bochum
117. Kanamaru K, Tanaka K (2004) Roles of chloroplast RNA polymerase sigma factors in chloroplast development and stress response in higher plants. Biosci Biotechnol Biochem 68:2215–2223
118. Privat I, Hakimi MA, Buhot L, Favory JJ, Mache-Lerbs S (2003) Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3. Plant Mol Biol 51:385–399
119. Hanaoka M, Kanamaru K, Takahashi H, Tanaka K (2003) Molecular genetic analysis of chloroplast gene promoters dependent on SIG2, a nucleus-encoded sigma factor for the plastidencoded RNA polymerase, in Arabidopsis thaliana. Nucleic Acids Res 31:7090–7098
120. Favory JJ, Kobayshi M, Tanaka K, Peltier G, Kreis M, Valay JG, Lerbs-Mache S (2005) Specifi c function of a plastid sigma factor for ndhF gene transcription. Nucleic Acids Res 33:5991–5999
121. Zghidi W, Merendino L, Cottet A, Mache R, Lerbs-Mache S (2007) Nucleus-encoded plastid sigma factor SIG3 transcribes specifi-cally the psbN gene in plastids. Nucleic Acids Res 35:455–464
122. Yao J, Roy-Chowdhury S, Allison LA (2003) AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. Plant Physiol 132:739–747
123. Loschelder H, Schweer J, Link B, Link G (2006) Dual temporal role of plastid sigma factor 6 in Arabidopsis development. Plant Physiol 142:642–650
124. Schweer J, Loschelder H, Link G (2006) A promoter switch that can rescue a plant sigma factor mutant. FEBS Lett 580:6617–6622
125. Schweer J, Geimer S, Meurer J, Link G (2009) Arabidopsis mutants carrying chimeric sigma factor genes reveal regulatory determinants for plastid gene expression. Plant Cell Physiol 50:1382–1386
126. Chi W, Mao J, Li Q, Ji D, Zou M, Lu C, Zhang L (2010) Interaction of the pentatricopeptide- repeat protein DELAYED GREENING 1 with sigma factor SIG6 in the regulation of chloroplast gene expression in Arabidopsis cotyledons. Plant J 64:14–25
127. Lahiri SD, Yao J, McCumbers C, Allison LA (1999) Tissue-specifi c and light-dependent expression within a family of nuclear-encoded sigma-like factors from Zea mays. Mol Cell Biol Res Commun 1:14–20
128. Kubota Y, Miyao A, Hirochika H, Tozawa Y, Yasuda H, Tsunoyama Y, Niwa Y, Imamura S, Shirai M, Asayama M (2007) Two novel nuclear genes, OsSIG5 and OsSIG6, encoding potential plastid sigma factors of RNA polymerase in rice: tissue-specifi c and lightresponsive gene expression. Plant Cell Physiol 48:186–192
129. Homann A, Link G (2003) DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. Eur J Biochem 270:1288–1300
130. Hara K, Morita M, Takahashi R, Sugita M, Kato S, Aoki S (2001) Characterization of two genes, Sig1 and Sig2, encoding distinct plastid sigma factors(1) in the moss Physcomitrella patens: phylogenetic relationships to plastid sigma factors in higher plants. FEBS Lett 499:87–91
131. Ichikawa K, Sugita M, Imaizumi T, Wada M, Aoki S (2004) Differential expression on a daily basis of plastid sigma factor genes from the moss Physcomitrella patens. Regulatory interactions among PpSig5, the circadian clock, and blue light signaling mediated by cryptochromes. Plant Physiol 136:4285–4298
132. Browning DF, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2:57–65
133. Tiller K, Link G (1995) Sigma-like plastid transcription factors. Methods Mol Biol 37:337–348
134. Tiller K, Link G (1993) Phosphorylation and dephosphorylation affect functional characteristics of chloroplast and etioplast transcription systems from mustard (Sinapis alba L.). EMBO J 12:1745–1753
135. Baginsky S, Tiller K, Pfannschmidt T, Link G (1999) PTK, the chloroplast RNA polymeraseassociated protein kinase from mustard (Sinapisalba), mediates redox control of plastid in vitro transcription. Plant Mol Biol 39:1013–1023
136. Baginsky S, Tiller K, Link G (1997) Transcription factor phosphorylation by a protein kinase associated with chloroplast RNA polymerase from mustard (Sinapis alba). Plant Mol Biol 34:181–189
137. Meggio F, Pinna LA (2003) One-thousandand- one substrates of protein kinase CK2? FASEB J 17:349–368
138. Johnson NL, Gardner AM, Diener KM, Lange-Carter CA, Gleavy J, Jarpe MB, Minden A, Karin M, Zon LI, Johnson GL (1996) Signal transduction pathways regulated by mitogen-activated/extracellular response kinase kinase kinase induce cell death. J Biol Chem 271:3229–3237
139. Schweer J, Turkeri H, Link B, Link G (2010) AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact of cpCK2 phosphorylation. Plant J 62:192–202
140. Turkeri H, Schweer J, Link G (2012) Phylogenetic and functional features of the plastid transcription kinase cpCK2 from Arabidopsis signify a role of cysteinyl SH-groups in regulatory phosphorylation of plastid sigma factors. FEBS J 279:395–409
141. Shimizu M, Kato H, Ogawa T, Kurachi A, Nakagawa Y, Kobayashi H (2010) Sigma factor phosphorylation in the photosynthetic control of photosystem stoichiometry. Proc Natl Acad Sci U S A 107:10760–10764
142. Kornberg RD (2007) The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A 104:12955–12961
143. Shiina T, Allison L, Maliga P (1998) rbcL transcript levels in tobacco plastids are independent of light: reduced dark transcription rate is compensated by increased mRNA stability. Plant Cell 10:1713–1722
144. Weihe A, Borner T (1999) Transcription and the architecture of promoters in chloroplasts. Trends Plant Sci 4:169–170
145. Liere K, Maliga P (2001) Plastid RNA polymerases. In: Aro E-M, Andersson B (eds) Regulation of photosynthesis. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 29–49
146. Liere K, Borner T (2007) Transcription and transcriptional regulation in plastids. In: Bock R (ed) Topics in current genetics: cell and molecular biology of plastids. Springer, Berlin, pp 121–174
147. Kapoor S, Sugiura M (1999) Identifi cation of two essential sequence elements in the nonconsensus type II PatpB-290 plastid promoter by using plastid transcription extracts from cultured tobacco BY-2 cells. Plant Cell 11:1799–1810
148. Kapoor S, Suzuki JY, Sugiura M (1997) Identifi cation and functional signifi cance of a new class of non-consensus-type plastid promoters. Plant J 11:327–337
149. Sriraman P, Silhavy D, Maliga P (1998) Transcription from heterologous rRNA operon promoters in chloroplasts reveals requirement for specifi c activating factors. Plant Physiol 117:1495–1499
150. Sriraman P, Silhavy D, Maliga P (1998) The phage-type PclpP-53 plastid promoter comprises sequences downstream of the transcription initiation site. Nucleic Acids Res 26: 4874–4879
151. Eisermann A, Tiller K, Link G (1990) In vitro transcription and DNA binding characteristics of chloroplast and etioplast extracts from mustard (Sinapis alba) indicate differential usage ofthe psbA promoter. EMBO J 9:3981–3987
152. Christopher DA, Kim M, Mullet JE (1992) A novel light-regulated promoter is conserved in cereal and dicot chloroplasts. Plant Cell 4:785–798
153. To KY, Cheng MC, Suen DF, Mon DP, Chen LF, Chen SC (1996) Characterization of the light-responsive promoter of rice chloroplast psbD-C operon and the sequence-specifi c DNA binding factor. Plant Cell Physiol 37:660–666
154. Hoffer PH, Christopher DA (1997) Structure and blue-light-responsive transcription of a chloroplast psbD promoter from Arabidopsis thaliana. Plant Physiol 115:213–222
155. Cheng MC, Wu SP, Chen LF, Chen SC (1997) Identifi cation and purifi cation of a spinach chloroplast DNA-binding protein that interacts specifi cally with the plastid psaA-psaB-rps14 promoter region. Planta 203:373–380
156. Suzuki JY, Sriraman P, Svab Z, Maliga P (2003) Unique architecture of the plastid ribosomal RNA operon promoter recognized by the multisubunit RNA polymerase in tobacco and other higher plants. Plant Cell 15:195–205
157. Pfannschmidt T, 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
158. Iratni R, Diederich L, Harrak H, Bligny M, Lerbs-Mache S (1997) Organ-specifi c transcription of the rrn operon in spinach plastids. J Biol Chem 272:13676–13682
159. Hubschmann T, Borner T (1998) Characterisation of transcript initiation sites in ribosome-defi cient barley plastids. Plant Mol Biol 36:493–496
160. Vera A, Sugiura M (1995) Chloroplast rRNA transcription from structurally different tandem promoters: an additional novel-type promoter. Curr Genet 27:280–284
161. Baeza L, Bertrand A, Mache R, 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
162. Kim M, Thum KE, Morishige DT, Mullet JE (1999) Detailed architecture of the barley chloroplast psbD-psbC blue light-responsive promoter. J Biol Chem 274:4684–4692
163. Kim M, Mullet JE (1995) Identifi cation of a sequence-specifi c DNA binding factor required for transcription of the barley chloroplast blue light-responsive psbD-psbC promoter. Plant Cell 7:1445–1457
164. Bogorad L, Bedbrook JR, Davidson JN, Hanson MR, Kolodner R (1977) Genes for plastid ribosomal proteins and RNAs. Brookhaven Symp Biol 1–15
165. Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13:663–670
166. Mullet JE (1993) Dynamic regulation of chloroplast transcription. Plant Physiol 103: 309–313
167. Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8:185–195
168. Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y, Moreau H (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A 103:11647–11652
169. Richter U, Kiessling J, Hedtke B, Decker E, Reski R, Borner T, Weihe A (2002) Two RpoT genes of Physcomitrella patens encode phagetype RNA polymerases with dual targeting to mitochondria and plastids. Gene 290:95–105
170. Kabeya Y, Hashimoto K, Sato N (2002) Identifi cation and characterization of two phage-type RNA polymerase cDNAs in the moss Physcomitrella patens: implication of recent evolution of nuclear-encoded RNA polymerase of plastids in plants. Plant Cell Physiol 43:245–255
171. Yin C, Richter U, Borner T, Weihe A (2010) Evolution of plant phage-type RNA polymerases: the genome of the basal angiosperm Nuphar advena encodes two mitochondrial and one plastid phage-type RNA polymerases. BMC Evol Biol 10:379
172. Yagi Y, Ishizaki Y, Nakahira Y, Tozawa Y, Shiina T (2012) Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase. Proc Natl Acad Sci U S A 109:7541–7546
173. Zhelyazkova P, Sharma CM, Forstner KU, Liere K, Vogel J, Borner T (2012) The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell 24:123–136.