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. 1999 Sep;11(9):1799–1810. doi: 10.1105/tpc.11.9.1799

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.

S Kapoor 1, M Sugiura 1
PMCID: PMC144303  PMID: 10488244

Abstract

In higher plants, plastid genes are transcribed by at least two types of DNA-dependent RNA polymerases. One of them is the well-known plastid-encoded prokaryotic type of polymerase that recognizes sigma(70)-type promoters consisting of -35 and -10 consensus elements. The other recently recognized RNA polymerase has been found to be encoded entirely in the nucleus, and it recognizes a completely different set of promoters, designated previously as nonconsensus type II (NCII) promoters. Here, we report the development of an in vitro transcription system using nonphotosynthetic plastids of cultured tobacco BY-2 cells. This system preferentially and accurately initiates transcription from NCII promoters. The conditions for in vitro transcription were optimized by using the tobacco PatpB-290 promoter, which has been found to be the most highly expressed NCII promoter in vivo. Analysis of in vitro transcription initiation in a series of PatpB-290 5' deletion constructs revealed that sequences upstream of nucleotide -41 do not influence the transcriptional activity of this promoter. A 43-bp region (nucleotides -35 to +8) was further analyzed by introducing single or multiple nucleotide substitutions into two regions (box I and box II) of high sequence conservation. We report here that the ATAGAA sequence comprising box II and the -11 to +4 region (relative to transcription initiation) in box I significantly influence the activity of this NCII promoter.

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Selected References

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  1. Allison L. A., Simon L. D., Maliga P. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J. 1996 Jun 3;15(11):2802–2809. [PMC free article] [PubMed] [Google Scholar]
  2. Baumgartner B. J., Rapp J. C., Mullet J. E. 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. 1993 Mar;101(3):781–791. doi: 10.1104/pp.101.3.781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bottomley W., Spencer D., Wheeler A. M., Whitfeld P. R. The effect of a range of RNA polymerase inhibitors on RNA synthesis in higher plant chloroplasts and nuclei. Arch Biochem Biophys. 1971 Mar;143(1):269–275. doi: 10.1016/0003-9861(71)90209-8. [DOI] [PubMed] [Google Scholar]
  4. Ems S. C., Morden C. W., Dixon C. K., Wolfe K. H., dePamphilis C. W., Palmer J. D. Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Mol Biol. 1995 Nov;29(4):721–733. doi: 10.1007/BF00041163. [DOI] [PubMed] [Google Scholar]
  5. Fan H., Sugiura M. A plant basal in vitro system supporting accurate transcription of both RNA polymerase II- and III-dependent genes: supplement of green leaf component(s) drives accurate transcription of a light-responsive rbcS gene. EMBO J. 1995 Mar 1;14(5):1024–1031. doi: 10.1002/j.1460-2075.1995.tb07083.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hajdukiewicz P. T., Allison L. A., Maliga P. The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J. 1997 Jul 1;16(13):4041–4048. doi: 10.1093/emboj/16.13.4041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hedtke B., Börner T., Weihe A. Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science. 1997 Aug 8;277(5327):809–811. doi: 10.1126/science.277.5327.809. [DOI] [PubMed] [Google Scholar]
  8. Hess W. R., Börner T. Organellar RNA polymerases of higher plants. Int Rev Cytol. 1999;190:1–59. doi: 10.1016/s0074-7696(08)62145-2. [DOI] [PubMed] [Google Scholar]
  9. Hess W. R., Prombona A., Fieder B., Subramanian A. R., Börner T. 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. 1993 Feb;12(2):563–571. doi: 10.1002/j.1460-2075.1993.tb05688.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hübschmann T., Börner T. Characterisation of transcript initiation sites in ribosome-deficient barley plastids. Plant Mol Biol. 1998 Feb;36(3):493–496. doi: 10.1023/a:1005924502336. [DOI] [PubMed] [Google Scholar]
  11. Kapoor S., Suzuki J. Y., Sugiura M. Identification and functional significance of a new class of non-consensus-type plastid promoters. Plant J. 1997 Feb;11(2):327–337. doi: 10.1046/j.1365-313x.1997.11020327.x. [DOI] [PubMed] [Google Scholar]
  12. Kapoor S., Wakasugi T., Deno H., Sugiura M. An atpE-specific promoter within the coding region of the atpB gene in tobacco chloroplast DNA. Curr Genet. 1994 Sep;26(3):263–268. doi: 10.1007/BF00309558. [DOI] [PubMed] [Google Scholar]
  13. Kestermann M., Neukirchen S., Kloppstech K., Link G. Sequence and expression characteristics of a nuclear-encoded chloroplast sigma factor from mustard (Sinapis alba). Nucleic Acids Res. 1998 Jun 1;26(11):2747–2753. doi: 10.1093/nar/26.11.2747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lerbs-Mache S. 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. 1993 Jun 15;90(12):5509–5513. doi: 10.1073/pnas.90.12.5509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lerbs S., Bräutigam E., Parthier B. Polypeptides of DNA-dependent RNA polymerase of spinach chloroplasts: characterization by antibody-linked polymerase assay and determination of sites of synthesis. EMBO J. 1985 Jul;4(7):1661–1666. doi: 10.1002/j.1460-2075.1985.tb03834.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Liere K., Maliga P. In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. EMBO J. 1999 Jan 4;18(1):249–257. doi: 10.1093/emboj/18.1.249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Link G. Plastid differentiation: organelle promoters and transcription factors. Results Probl Cell Differ. 1994;20:65–85. doi: 10.1007/978-3-540-48037-2_3. [DOI] [PubMed] [Google Scholar]
  18. Miyagi T., Kapoor S., Sugita M., Sugiura M. 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 atpI coding sequence. Mol Gen Genet. 1998 Feb;257(3):299–307. doi: 10.1007/s004380050651. [DOI] [PubMed] [Google Scholar]
  19. Morden C. W., Wolfe K. H., dePamphilis C. W., Palmer J. D. Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. EMBO J. 1991 Nov;10(11):3281–3288. doi: 10.1002/j.1460-2075.1991.tb04892.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Orii Y., Okunuki K. Studies on cytochrome a. XV. Cytochrome oxidase activity of the Okunuki preparation and its activation by heat, alkali and detergent treatments. J Biochem. 1965 Dec;58(6):561–568. doi: 10.1093/oxfordjournals.jbchem.a128243. [DOI] [PubMed] [Google Scholar]
  21. Orozco E. M., Jr, Chen L. J., Eilers R. J. The divergently transcribed rbcL and atpB genes of tobacco plastid DNA are separated by nineteen base pairs. Curr Genet. 1990 Jan;17(1):65–71. doi: 10.1007/BF00313250. [DOI] [PubMed] [Google Scholar]
  22. Orozco E. M., Jr, Mullet J. E., Hanley-Bowdoin L., Chua N. H. In vitro transcription of chloroplast protein genes. Methods Enzymol. 1986;118:232–253. doi: 10.1016/0076-6879(86)18076-1. [DOI] [PubMed] [Google Scholar]
  23. Serino G., Maliga P. RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol. 1998 Aug;117(4):1165–1170. doi: 10.1104/pp.117.4.1165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Silhavy D., Maliga P. Mapping of promoters for the nucleus-encoded plastid RNA polymerase (NEP) in the iojap maize mutant. Curr Genet. 1998 May;33(5):340–344. doi: 10.1007/s002940050345. [DOI] [PubMed] [Google Scholar]
  25. Sriraman P., Silhavy D., Maliga P. The phage-type PclpP-53 plastid promoter comprises sequences downstream of the transcription initiation site. Nucleic Acids Res. 1998 Nov 1;26(21):4874–4879. doi: 10.1093/nar/26.21.4874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sun E., Wu B. W., Tewari K. K. In vitro analysis of the pea chloroplast 16S rRNA gene promoter. Mol Cell Biol. 1989 Dec;9(12):5650–5659. doi: 10.1128/mcb.9.12.5650. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tanaka K., Tozawa Y., Mochizuki N., Shinozaki K., Nagatani A., Wakasa K., Takahashi H. 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. 1997 Aug 18;413(2):309–313. doi: 10.1016/s0014-5793(97)00906-x. [DOI] [PubMed] [Google Scholar]
  28. Tiller K., Eisermann A., Link G. The chloroplast transcription apparatus from mustard (Sinapis alba L.). Evidence for three different transcription factors which resemble bacterial sigma factors. Eur J Biochem. 1991 May 23;198(1):93–99. doi: 10.1111/j.1432-1033.1991.tb15990.x. [DOI] [PubMed] [Google Scholar]
  29. Tiller K., Link G. Phosphorylation and dephosphorylation affect functional characteristics of chloroplast and etioplast transcription systems from mustard (Sinapis alba L.). EMBO J. 1993 May;12(5):1745–1753. doi: 10.1002/j.1460-2075.1993.tb05822.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tiller K., Link G. Sigma-like plastid transcription factors. Methods Mol Biol. 1995;37:337–348. doi: 10.1385/0-89603-288-4:337. [DOI] [PubMed] [Google Scholar]
  31. Tozawa Y., Tanaka K., Takahashi H., Wakasa K. Nuclear encoding of a plastid sigma factor in rice and its tissue- and light-dependent expression. Nucleic Acids Res. 1998 Jan 15;26(2):415–419. doi: 10.1093/nar/26.2.415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Troxler R. F., Zhang F., Hu J., Bogorad L. Evidence that sigma factors are components of chloroplast RNA polymerase. Plant Physiol. 1994 Feb;104(2):753–759. doi: 10.1104/pp.104.2.753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Vera A., Hirose T., Sugiura M. A ribosomal protein gene (rpl32) from tobacco chloroplast DNA is transcribed from alternative promoters: similarities in promoter region organization in plastid housekeeping genes. Mol Gen Genet. 1996 Jul 19;251(5):518–525. doi: 10.1007/BF02173640. [DOI] [PubMed] [Google Scholar]
  34. Vera A., Sugiura M. Chloroplast rRNA transcription from structurally different tandem promoters: an additional novel-type promoter. Curr Genet. 1995 Feb;27(3):280–284. doi: 10.1007/BF00326161. [DOI] [PubMed] [Google Scholar]
  35. dePamphilis C. W., Palmer J. D. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature. 1990 Nov 22;348(6299):337–339. doi: 10.1038/348337a0. [DOI] [PubMed] [Google Scholar]

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