Skip to main content
SpringerLink
Log in

Plastid Gene Transcription: An Update on Promoters and RNA Polymerases

  • Protocol
  • First Online:
Chloroplast Biotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2317))

Abstract

Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Mereschkowsky C (1905) Über die Natur und den Ursprung der Chromatophoren im Pflanzenreiche. Biol Zentralblatt 25(593–604):989–691

    Google Scholar 

  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, pp 73–118

    Chapter  Google Scholar 

  3. Gray MW (1999) Evolution of organellar genomes. Curr Opin Genet Dev 9(6):678–687

    Article  CAS  PubMed  Google Scholar 

  4. Emelyanov VV (2003) Mitochondrial connection to the origin of the eukaryotic cell. Eur J Biochem 270(8):1599–1618

    Article  CAS  PubMed  Google Scholar 

  5. McFadden GI (2001) Chloroplast origin and integration. Plant Physiol 125(1):50–53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19(1):47–56

    Article  CAS  PubMed  Google Scholar 

  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(6):1128–1137

    Article  CAS  PubMed  Google Scholar 

  8. Cline K, Henry R (1996) Import and routing of nucleus-encoded chloroplast proteins. Annu Rev Cell Dev Biol 12:1–26

    Article  CAS  PubMed  Google Scholar 

  9. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  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(19):12246–12251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Palmer JD (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19:325–354

    Article  CAS  PubMed  Google Scholar 

  12. Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19(1):149–168

    Article  CAS  PubMed  Google Scholar 

  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(2):153–158

    Article  CAS  PubMed  Google Scholar 

  14. Allen JF (1993) Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165(4):609–631

    Article  CAS  PubMed  Google Scholar 

  15. 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

    Chapter  Google Scholar 

  16. 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(31):11647–11652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Richter U, Kiessling J, Hedtke B, Decker E, Reski R, Borner T, Weihe A (2002) Two RpoT genes of Physcomitrella patens encode phage-type RNA polymerases with dual targeting to mitochondria and plastids. Gene 290(1–2):95–105

    Article  CAS  PubMed  Google Scholar 

  18. Kabeya Y, Hashimoto K, Sato N (2002) Identification 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(3):245–255

    Article  CAS  PubMed  Google Scholar 

  19. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kusumi K, Yara A, Mitsui N, Tozawa Y, Iba K (2004) Characterization of a rice nuclear-encoded plastid RNA polymerase gene OsRpoTp. Plant Cell Physiol 45(9):1194–1201

    Article  CAS  PubMed  Google Scholar 

  21. 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(3):460–472

    Article  CAS  PubMed  Google Scholar 

  22. Ikeda TM, Gray MW (1999) Identification and characterization of T3/T7 bacteriophage-like RNA polymerase sequences in wheat. Plant Mol Biol 40(4):567–578

    Article  CAS  PubMed  Google Scholar 

  23. 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(5):911–926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hedtke B, Legen J, Weihe A, Herrmann RG, Borner T (2002) Six active phage-type RNA polymerase genes in Nicotiana tabacum. Plant J 30(6):625–637

    Article  CAS  PubMed  Google Scholar 

  25. Kobayashi Y, Dokiya Y, Sugiura M, Niwa Y, Sugita M (2001) Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris. Gene 279(1):33–40

    Article  CAS  PubMed  Google Scholar 

  26. 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(5):1106–1113

    Article  CAS  PubMed  Google Scholar 

  27. Hedtke B, Borner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1(5):435–440

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Clayton DA (1987) Nuclear gene products that function in mitochondrial DNA replication. Philos Trans R Soc Lond Ser B Biol Sci 317(1187):473–482

    CAS  Google Scholar 

  29. 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(22):10348–10351

    Article  CAS  PubMed  Google Scholar 

  30. Kirk JT (1964) Studies on RNA synthesis in chloroplast preparations. Biochem Biophys Res Commun 16(3):233–238

    Article  CAS  PubMed  Google Scholar 

  31. 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(12):4839–4842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 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(4):1531–1535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. 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(9):2043–2049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Bunger W, Feierabend J (1980) Capacity for RNA synthesis in 70S ribosome-deficient plastids of heat-bleached rye leaves. Planta 149(2):163–169

    Article  CAS  PubMed  Google Scholar 

  35. dePamphilis CW, Palmer JD (1990) Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348(6299):337–339

    Article  CAS  PubMed  Google Scholar 

  36. 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-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J 12(2):563–571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15(11):2802–2809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Maliga P (1998) Two plastid RNA polymerases of higher plants: an evolving story. Trends Plant Sci 3:4–6

    Article  Google Scholar 

  39. 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(4):1165–1170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hess WR, Borner T (1999) Organellar RNA polymerases of higher plants. Int Rev Cytol 190:1–59

    Article  CAS  PubMed  Google Scholar 

  41. 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(1):249–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. 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(3):781–791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Allison LA (2000) The role of sigma factors in plastid transcription. Biochimie 82(6–7):537–548

    Article  CAS  PubMed  Google Scholar 

  44. 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

    Article  CAS  PubMed  Google Scholar 

  45. 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(12):940–946

    Article  CAS  PubMed  Google Scholar 

  46. 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(11):3281–3288

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. 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(13):4041–4048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. 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(12):5509–5513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Hedtke B, Borner T, Weihe A (1997) Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277(5327):809–811

    Article  CAS  PubMed  Google Scholar 

  50. 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(3):1159–1165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Silhavy D, Maliga P (1998) Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr Genet 33(5):340–344

    Article  CAS  PubMed  Google Scholar 

  52. Gray MW, Lang BF (1998) Transcription in chloroplasts and mitochondria: a tale of two polymerases. Trends Microbiol 6(1):1–3

    Article  CAS  PubMed  Google Scholar 

  53. Hallick RB, Lipper C, Richards OC, Rutter WJ (1976) Isolation of a transcriptionally active chromosome from chloroplasts of Euglena gracilis. Biochemistry 15(14):3039–3045

    Article  CAS  PubMed  Google Scholar 

  54. Bogorad L, Bedbrook JR, Davidson JN, Hanson MR, Kolodner R (1977) Genes for plastid ribosomal proteins and RNAs. Brookhaven Symp Biol 29:1–15

    CAS  Google Scholar 

  55. 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

    Article  CAS  PubMed  Google Scholar 

  56. Deng XW, Stern DB, Tonkyn JC, Gruissem W (1987) Plastid run-on transcription. Application to determine the transcriptional regulation of spinach plastid genes. J Biol Chem 262(20):9641–9648

    Article  CAS  PubMed  Google Scholar 

  57. Mullet JE, Klein RR (1987) Transcription and RNA stability are important determinants of higher plant chloroplast RNA levels. EMBO J 6(6):1571–1579

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Svab Z, Hajdukiewicz P, Maliga P (1990) Stable transformation of plastids in higher plants. Proc Natl Acad Sci U S A 87(21):8526–8530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. 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(8):3313–3318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. 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(5270):1932–1935

    Article  CAS  PubMed  Google Scholar 

  61. 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(2):181–189

    Article  CAS  PubMed  Google Scholar 

  62. Kim M, Mullet JE (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(9):1445–1457

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 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-specific functions. Eur J Biochem 267(1):253–261

    Article  CAS  PubMed  Google Scholar 

  64. 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(8):1851–1860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kuhn K, Richter U, Meyer EH, Delannoy E, de Longevialle AF, O’Toole N, Borner T, Millar AH, Small ID, Whelan J (2009) Phage-type RNA polymerase RPOTmp performs gene-specific transcription in mitochondria of Arabidopsis thaliana. Plant Cell 21(9):2762–2779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. 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(3):712–721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. 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(3):785–792

    Article  CAS  PubMed  Google Scholar 

  68. 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(3):942–956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Bottomley W, Smith HJ, Bogorad L (1971) RNA polymerases of maize: partial purification and properties of the chloroplast enzyme. Proc Natl Acad Sci U S A 68(10):2412–2416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. McKown RL, Tewari KK (1984) Purification and properties of a pea chloroplast DNA polymerase. Proc Natl Acad Sci U S A 81(8):2354–2358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Lerbs S, Briat JF, Mache R (1983) Chloroplast RNA polymerase from spinach: purification and DNA-binding proteins. Plant Mol Biol 2:67–74

    Article  CAS  PubMed  Google Scholar 

  72. Igloi GL, Kössel H (1992) The transcriptional apparatus of chloroplasts. Crit Rev Plant Sci 10:525–558

    Article  CAS  Google Scholar 

  73. 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(3):185–209

    Article  CAS  PubMed  Google Scholar 

  74. 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(44):27969–27974

    Article  CAS  PubMed  Google Scholar 

  75. 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(4):218–225

    Article  CAS  PubMed  Google Scholar 

  76. Shinozaki K, Sugiura M (1986) Organization of chloroplast genomes. Adv Biophys 21:57–78. doi:0065-227X(86)90014-6 [pii]

    Article  CAS  PubMed  Google Scholar 

  77. 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(18):5324–5331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. 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(4):730–741

    Article  CAS  PubMed  Google Scholar 

  79. Smith AC, Purton S (2002) The principle apparatus of algal plastids. Eur J Phycol 37:301–311

    Article  Google Scholar 

  80. 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(2):155–172

    Article  CAS  PubMed  Google Scholar 

  81. Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ (2010) Organization and expression of organellar genomes. Philos Trans R Soc Lond Ser B Biol Sci 365(1541):785–797

    Article  CAS  Google Scholar 

  82. Burgess RR, Travers AA, Dunn JJ, Bautz EKF (1969) Factor stimulating transcription by RNA polymerase. Nature 221:43–46

    Article  CAS  PubMed  Google Scholar 

  83. 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

    Article  CAS  PubMed  Google Scholar 

  84. 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(6):811–824

    Article  CAS  PubMed  Google Scholar 

  85. Busby S, Ebright RH (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79(5):743–746

    Article  CAS  PubMed  Google Scholar 

  86. 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(7):1661–1666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Bülow S, Link G (1988) Sigma-like activity from mustard (Sinapis alba L) chloroplasts conferring DNA-binding and transcription specificity to E coli core RNA polymerase. Plant Mol Biol 10:349–357

    Article  PubMed  Google Scholar 

  88. 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(1):176–197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Link G (1984) DNA sequence requirements for the accurate transcription of a protein-coding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.). EMBO J 3(8):1697–1704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Orozco EM Jr, Mullet JE, Chua NH (1985) An in vitro system for accurate transcription initiation of chloroplast protein genes. Nucleic Acids Res 13(4):1283–1302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. 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(1):69–81

    Article  CAS  PubMed  Google Scholar 

  92. 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(13):3329–3337

    Article  CAS  PubMed  Google Scholar 

  93. 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(11):2191–2204

    Article  PubMed  CAS  Google Scholar 

  94. Suzuki JY, Ytterberg AJ, Beardslee TA, Allison LA, Wijk KJ, Maliga P (2004) Affinity purification of the tobacco plastid RNA polymerase and in vitro reconstitution of the holoenzyme. Plant J 40(1):164–172

    Article  CAS  PubMed  Google Scholar 

  95. Satoh J, Baba K, Nakahira Y, Tsunoyama Y, Shiina T, Toyoshima Y (1999) Developmental stage-specific multi-subunit plastid RNA polymerases (PEP) in wheat. Plant J 18(4):407–415

    Article  CAS  PubMed  Google Scholar 

  96. Helmann JD, Chamberlin MJ (1988) Structure and function of bacterial sigma factors. Annu Rev Biochem 57:839–872

    Article  CAS  PubMed  Google Scholar 

  97. Wosten MM (1998) Eubacterial sigma-factors. FEMS Microbiol Rev 22(3):127–150

    Article  CAS  PubMed  Google Scholar 

  98. Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning of the bacterial transcription space. Annu Rev Microbiol 57:441–456

    Article  CAS  PubMed  Google Scholar 

  99. Geszvain K, Landick R (2005) The structure of bacterial RNA polymerase. Website Edition (www bact wisc edu/Landick) 1:1–10

    Google Scholar 

  100. Ishihama A (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54:499–518

    Article  CAS  PubMed  Google Scholar 

  101. Malhotra A, Severinova E, Darst SA (1996) Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87(1):127–136

    Article  CAS  PubMed  Google Scholar 

  102. 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(6890):712–719

    Article  CAS  PubMed  Google Scholar 

  103. 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 specificity sigma subunit. Mol Cell 9(3):527–539

    Article  CAS  PubMed  Google Scholar 

  104. Campbell EA, Tupy JL, Gruber TM, Wang S, Sharp MM, Gross CA, Darst SA (2003) Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Mol Cell 11(4):1067–1078

    Article  CAS  PubMed  Google Scholar 

  105. Link G (1994) Plastid differentiation: organelle promoters and transcription factors. Results Probl Cell Differ 20:65–85

    Article  CAS  PubMed  Google Scholar 

  106. 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(2):309–313

    Article  CAS  PubMed  Google Scholar 

  107. Isono K, Niwa Y, Satoh K, Kobayashi H (1997) Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots. Plant Physiol 114(2):623–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Tozawa Y, Tanaka K, Takahashi H, Wakasa K (1998) Nuclear encoding of a plastid sigma factor in rice and its tissue- and light-dependent expression. Nucleic Acids Res 26(2):415–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. 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(11):2747–2753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. 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(9):5316–5321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Morikawa K, Ito S, Tsunoyama Y, Nakahira Y, Shiina T, Toyoshima Y (1999) Circadian-regulated expression of a nuclear-encoded plastid sigma factor gene (sigA) in wheat seedlings. FEBS Lett 451(3):275–278

    Article  CAS  PubMed  Google Scholar 

  112. 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(2):221–228

    Article  CAS  PubMed  Google Scholar 

  113. Schweer J (2010) Plant sigma factors come of age: flexible transcription factor network for regulated plastid gene expression. Endocytobiosis Cell Res 20:1–20

    Google Scholar 

  114. 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(5):333–340

    Article  CAS  PubMed  Google Scholar 

  115. 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 Aarabidopsis thaliana. FEBS Lett 481(1):47–52

    Article  CAS  PubMed  Google Scholar 

  116. 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(8):832–842

    Article  CAS  PubMed  Google Scholar 

  117. Lysenko EA (2007) Plant sigma factors and their role in plastid transcription. Plant Cell Rep 26(7):845–859

    Article  CAS  PubMed  Google Scholar 

  118. 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

    Article  PubMed  CAS  Google Scholar 

  119. Ishizaki Y, Tsunoyama Y, Hatano K, Ando K, Kato K, Shinmyo A, Kobori M, Takeba G, Nakahira Y, Shiina T (2005) A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J 42(2):133–144

    Article  CAS  PubMed  Google Scholar 

  120. 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 deficient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 68(3):694–704

    Article  CAS  PubMed  Google Scholar 

  121. 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(9):3304–3309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. 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(2–3):300–304

    Article  CAS  PubMed  Google Scholar 

  123. Xie YD, Li W, Guo D, Dong J, Zhang Q, Fu Y, Ren D, Peng M, Xia Y (2010) The Arabidopsis gene SIGMA FACTOR-BINDING PROTEIN 1 plays a role in the salicylate- and jasmonate-mediated defence responses. Plant Cell Environ 33(5):828–839

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Kolpack A (2010) Regulatory protein-protein interactions in the plastid transcription. PhD thesis. Ruhr University, Bochum

    Google Scholar 

  125. 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(11):2215–2223

    Article  CAS  PubMed  Google Scholar 

  126. 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(3):385–399

    Article  CAS  PubMed  Google Scholar 

  127. 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 plastid-encoded RNA polymerase, in Arabidopsis thaliana. Nucleic Acids Res 31(24):7090–7098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Favory JJ, Kobayshi M, Tanaka K, Peltier G, Kreis M, Valay JG, Lerbs-Mache S (2005) Specific function of a plastid sigma factor for ndhF gene transcription. Nucleic Acids Res 33(18):5991–5999

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Zghidi W, Merendino L, Cottet A, Mache R, Lerbs-Mache S (2007) Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids. Nucleic Acids Res 35(2):455–464

    Article  CAS  PubMed  Google Scholar 

  130. Yao J, Roy-Chowdhury S, Allison LA (2003) AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. Plant Physiol 132(2):739–747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Loschelder H, Schweer J, Link B, Link G (2006) Dual temporal role of plastid sigma factor 6 in Arabidopsis development. Plant Physiol 142(2):642–650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Schweer J, Loschelder H, Link G (2006) A promoter switch that can rescue a plant sigma factor mutant. FEBS Lett 580(28–29):6617–6622

    Article  CAS  PubMed  Google Scholar 

  133. 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(7):1382–1386

    Article  CAS  PubMed  Google Scholar 

  134. 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(1):14–25

    Article  CAS  PubMed  Google Scholar 

  135. Lahiri SD, Yao J, McCumbers C, Allison LA (1999) Tissue-specific and light-dependent expression within a family of nuclear-encoded sigma-like factors from Zea mays. Mol Cell Biol Res Commun 1(1):14–20

    Article  CAS  PubMed  Google Scholar 

  136. 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-specific and light-responsive gene expression. Plant Cell Physiol 48(1):186–192

    Article  CAS  PubMed  Google Scholar 

  137. 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(6):1288–1300

    Article  CAS  PubMed  Google Scholar 

  138. 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(1–2):87–91

    Article  CAS  PubMed  Google Scholar 

  139. 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(4):4285–4298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Browning DF, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2(1):57–65

    Article  CAS  PubMed  Google Scholar 

  141. Tiller K, Link G (1995) Sigma-like plastid transcription factors. Methods Mol Biol 37:337–348

    CAS  PubMed  Google Scholar 

  142. 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(5):1745–1753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Baginsky S, Tiller K, Pfannschmidt T, Link G (1999) PTK, the chloroplast RNA polymerase-associated protein kinase from mustard (Sinapis alba), mediates redox control of plastid in vitro transcription. Plant Mol Biol 39(5):1013–1023

    Article  CAS  PubMed  Google Scholar 

  144. Meggio F, Pinna LA (2003) One-thousand-and-one substrates of protein kinase CK2? FASEB J 17(3):349–368

    Article  CAS  PubMed  Google Scholar 

  145. 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(6):3229–3237

    Article  CAS  PubMed  Google Scholar 

  146. 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(2):192–202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. 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

    Article  PubMed  CAS  Google Scholar 

  148. 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(23):10760–10764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Kornberg RD (2007) The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A 104(32):12955–12961

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. 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(10):1713–1722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Weihe A, Borner T (1999) Transcription and the architecture of promoters in chloroplasts. Trends Plant Sci 4(5):169–170

    Article  CAS  PubMed  Google Scholar 

  152. Liere K, Maliga P (2001) Plastid RNA polymerases. In: Aro E-M, Andersson B (eds) Regulation of photosynthesis. Kluwer Academic Publishers, Dordrecht, pp 29–49

    Google Scholar 

  153. Kapoor S, Sugiura M (1999) Identification 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(9):1799–1810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Kapoor S, Suzuki JY, Sugiura M (1997) Identification and functional significance of a new class of non-consensus-type plastid promoters. Plant J 11(2):327–337

    Article  CAS  PubMed  Google Scholar 

  155. Sriraman P, Silhavy D, Maliga P (1998) Transcription from heterologous rRNA operon promoters in chloroplasts reveals requirement for specific activating factors. Plant Physiol 117(4):1495–1499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. 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(21):4874–4879

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. 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 of the psbA promoter. EMBO J 9(12):3981–3987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Christopher DA, Kim M, Mullet JE (1992) A novel light-regulated promoter is conserved in cereal and dicot chloroplasts. Plant Cell 4(7):785–798

    CAS  PubMed  PubMed Central  Google Scholar 

  159. 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-specific DNA binding factor. Plant Cell Physiol 37(5):660–666

    Article  PubMed  Google Scholar 

  160. Hoffer PH, Christopher DA (1997) Structure and blue-light-responsive transcription of a chloroplast psbD promoter from Arabidopsis thaliana. Plant Physiol 115(1):213–222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Cheng MC, Wu SP, Chen LF, Chen SC (1997) Identification and purification of a spinach chloroplast DNA-binding protein that interacts specifically with the plastid psaA-psaB-rps14 promoter region. Planta 203(3):373–380

    Article  CAS  PubMed  Google Scholar 

  162. 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(1):195–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. 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(1):35–44

    Article  CAS  PubMed  Google Scholar 

  164. Iratni R, Diederich L, Harrak H, Bligny M, Lerbs-Mache S (1997) Organ-specific transcription of the rrn operon in spinach plastids. J Biol Chem 272(21):13676–13682

    Article  CAS  PubMed  Google Scholar 

  165. Hubschmann T, Borner T (1998) Characterisation of transcript initiation sites in ribosome-deficient barley plastids. Plant Mol Biol 36(3):493–496

    Article  CAS  PubMed  Google Scholar 

  166. Vera A, Sugiura M (1995) Chloroplast rRNA transcription from structurally different tandem promoters: an additional novel-type promoter. Curr Genet 27(3):280–284

    Article  CAS  PubMed  Google Scholar 

  167. 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(13):3577–3581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. 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(8):4684–4692

    Article  CAS  PubMed  Google Scholar 

  169. Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13(12):663–670

    Article  CAS  PubMed  Google Scholar 

  170. Mullet JE (1993) Dynamic regulation of chloroplast transcription. Plant Physiol 103(2):309–313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8(3):185–195

    Article  CAS  PubMed  Google Scholar 

  172. 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(1):123–136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Newell CA, Gray JC (2010) Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation. Nucleic Acids Res 38(14):e145

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  174. 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(19):7541–7546

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Finster S, Eggert E, Zoschke R, Weihe A, Schmitz-Linneweber C (2013) Light-dependent, plastome-wide association of the plastid-encoded RNA polymerase with chloroplast DNA. Plant J 76(5):849–860

    Article  CAS  PubMed  Google Scholar 

  176. Zhong L, Zhou W, Wang H, Ding S, Lu Q, Wen X, Peng L, Zhang L, Lu C (2013) Chloroplast small heat shock protein HSP21 interacts with plastid nucleoid protein pTAC5 and is essential for chloroplast development in Arabidopsis under heat stress. Plant Cell 25(8):2925–2943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Hanaoka M, Kato M, Anma M, Tanaka K (2012) SIG1, a sigma factor for the chloroplast RNA polymerase, differently associates with multiple DNA regions in the chloroplast chromosomes in vivo. Int J Mol Sci 13(10):12182–12194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Noordally ZB, Ishii K, Atkins KA, Wetherill SJ, Kusakina J, Walton EJ, Kato M, Azuma M, Tanaka K, Hanaoka M, Dodd AN (2013) Circadian control of chloroplast transcription by a nuclear-encoded timing signal. Science 339(6125):1316–1319

    Article  CAS  PubMed  Google Scholar 

  179. Steiner S, Schroter Y, Pfalz J, Pfannschmidt T (2011) Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development. Plant Physiol 157(3):1043–1055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Chang SH, Lee S, Um TY, Kim JK, Do Choi Y, Jang G (2017) pTAC10, a key subunit of plastid-encoded RNA polymerase, promotes chloroplast development. Plant Physiol 174(1):435–449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Yu QB, Zhao TT, Ye LS, Cheng L, Wu YQ, Huang C, Yang ZN (2018) pTAC10, an S1-domain-containing component of the transcriptionally active chromosome complex, is essential for plastid gene expression in Arabidopsis thaliana and is phosphorylated by chloroplast-targeted casein kinase II. Photosynth Res 137(1):69–83

    Article  CAS  PubMed  Google Scholar 

  182. Bock S, Ortelt J, Link G (2014) AtSIG6 and other members of the sigma gene family jointly but differentially determine plastid target gene expression in Arabidopsis thaliana. Front Plant Sci 5:667

    Article  PubMed  PubMed Central  Google Scholar 

  183. Liebers M, Chevalier F, Blanvillain R, Pfannschmidt T (2018) PAP genes are tissue- and cell-specific markers of chloroplast development. Planta 248(3):629–646

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank all our colleagues who made possible sharing data and exchange of views for making this review better and we apologize that, because of space limitations, not all important work could be included. Research from our own group was funded by the DFG (LI261/21 and SFB480). Particular thanks are due to Brigitte Link for her strong commitment and expert technical assistance throughout this work.

Author information

Authors and Affiliations

  1. Department of Biology and Biotechnology, University of Bochum, Bochum, Germany

    Jennifer Ortelt & Gerhard Link

Authors
  1. Jennifer Ortelt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gerhard Link .

Editor information

Editors and Affiliations

  1. Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA

    Pal Maliga

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Ortelt, J., Link, G. (2021). Plastid Gene Transcription: An Update on Promoters and RNA Polymerases. In: Maliga, P. (eds) Chloroplast Biotechnology. Methods in Molecular Biology, vol 2317. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1472-3_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1472-3_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1471-6

  • Online ISBN: 978-1-0716-1472-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation