An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 5, 2011, Pages 2124-2129

  Mitschke, Jan ^a   Georg, Jens ^a   Scholz, Ingeborg ^a   Sharma, Cynthia M ^b   Dienst, Dennis ^c   Bantscheff, Jens ^a   Voß, Björn ^a   Steglich, Claudia ^a   Wilde, Annegret ^d   Vogel, Jörg ^b   Hess, Wolfgang R ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c HUMBOLDT UNIVERSITY   (Germany)

^d JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Gene expression regulation; Promoter prediction; RNA polymerase

Indexed keywords

BACTERIAL RNA; NOCODING RNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; GENE CONTROL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SYNECHOCYSTIS; TRANSCRIPTIONAL START SITE;

BASE SEQUENCE; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; PHOTOSYNTHESIS; RNA, UNTRANSLATED; SEQUENCE HOMOLOGY, NUCLEIC ACID; SYNECHOCYSTIS; TRANSCRIPTION, GENETIC;

CYANOBACTERIA; SYNECHOCYSTIS SP.;

EID: 79952174199     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1015154108     Document Type: Article

References (40)

1. McKinlay JB, Harwood CS (2010) Photobiological production of hydrogen gas as a biofuel. Curr Opin Biotechnol 21:244-251.
2. Deng MD, Coleman JR (1999) Ethanol synthesis by genetic engineering in cyanobacteria. Appl Environ Microbiol 65:523-528.
3. Atsumi S, Higashide W, Liao JC (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 27:1177-1180.
4. Takahama K, Matsuoka M, Nagahama K, Ogawa T (2003) Construction and analysis of a recombinant cyanobacterium expressing a chromosomally inserted gene for an ethylene-forming enzyme at the psbAI locus. J Biosci Bioeng 95:302-305. (Pubitemid 36438890)
5. Lindberg P, Park S, Melis A (2010) Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metab Eng 12:70-79.
6. Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB (2010) Microbial biosynthesis of alkanes. Science 329:559-562.
7. Kaneko T, et al. (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. (Pubitemid 126682796)
8. Sharma CM, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250-255.
9. Herrero A, Muro-Pastor AM, Flores E (2001) Nitrogen control in cyanobacteria. J Bacteriol 183:411-425. (Pubitemid 32049030)
10. Vogel J, Axmann IM, Herzel H, Hess WR (2003) Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res 31:2890-2899. (Pubitemid 37442133)
11. Gierga G, Voss B, Hess WR (2009) The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. RNA Biol 6:222-227.
12. Aichi M, Takatani N, Omata T (2001) Role of NtcB in activation of nitrate assimilation genes in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 183:5840-5847. (Pubitemid 32917401)
13. Georg J, et al. (2009) Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol 5:305.1-305.17.
14. Voss B, Georg J, Schön V, Ude S, Hess WR (2009) Biocomputational prediction of noncoding RNAs in model cyanobacteria. BMC Genomics 10:123.1-123.15.
15. Vioque A (1992) Analysis of the gene encoding the RNA subunit of ribonuclease P from cyanobacteria. Nucleic Acids Res 20:6331-6337.
16. Tous C, Vega-Palas MA, Vioque A (2001) Conditional expression of RNase P in the cyanobacterium Synechocystis sp. PCC6803 allows detection of precursor RNAs. Insight in the in vivo maturation pathway of transfer and other stable RNAs. J Biol Chem 276:29059-29066.
17. Wassarman KM, Saecker RM (2006) Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 314:1601-1603. (Pubitemid 44907154)
18. He Q, Dolganov N, Bjorkman O, Grossman AR (2001) The high light-inducible polypeptides in Synechocystis PCC6803. Expression and function in high light. J Biol Chem 276:306-314. (Pubitemid 32050857)
19. Gutekunst K, et al. (2005) LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator. Mol Microbiol 58:810-823. (Pubitemid 41532477)
20. Oliveira P, Lindblad P (2005) LexA, a transcription regulator binding in the promoter region of the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803. FEMS Microbiol Lett 251:59-66. (Pubitemid 41309064)
21. Oliveira P, Lindblad P (2008) An AbrB-Like protein regulates the expression of the bidirectional hydrogenase in Synechocystis sp. strain PCC 6803. J Bacteriol 190:1011-1019. (Pubitemid 351170944)
22. Dühring U, Axmann IM, Hess WR, Wilde A (2006) An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc Natl Acad Sci USA 103:7054-7058.
23. Georg J, Honsel A, Voss B, Rennenberg H, Hess WR (2010) A long antisense RNA in plant chloroplasts. New Phytol 186:615-622.
24. Horie Y, et al. (2007) Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria. Mol Genet Genomics 278:331-346. (Pubitemid 47247273)
25. Takahashi T, Nakai N, Muramatsu M, Hihara Y (2010) Role of multiple HLR1 sequences in the regulation of the dual promoters of the psaAB genes in Synechocystis sp. PCC 6803. J Bacteriol 192:4031-4036.
26. Muramatsu M, Sonoike K, Hihara Y (2009) Mechanism of downregulation of photosystem I content under high-light conditions in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology 155:989-996.
27. Opdyke JA, Kang JG, Storz G (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186:6698-6705. (Pubitemid 39332106)
28. Hernández JA, et al. (2006) Identification of a furA cis antisense RNA in the cyanobacterium Anabaena sp. PCC 7120. J Mol Biol 355:325-334. (Pubitemid 41785741)
29. Hernández JA, et al. (2010) Mutants of Anabaena sp. PCC 7120 lacking alr1690 and alpha-furA antisense RNA show a pleiotropic phenotype and altered photosynthetic machinery. J Plant Physiol 167:430-437.
30. Wurtzel O, et al. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res 20:133-141.
31. Cho BK, et al. (2009) The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27:1043-1049.
32. Backofen R, Hess WR (2010) Computational prediction of sRNAs and their targets in bacteria. RNA Biol 7:33-42.
33. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35:e128.1-e128.7.
34. Thomason MK, Storz G (2010) Bacterial antisense RNAs: How many are there, and what are they doing? Annu Rev Genet 44:167-188.
35. Thomas JC, Ughy B, Lagoutte B, Ajlani G (2006) A second isoform of the ferredoxin: NADP oxidoreductase generated by an in-frame initiation of translation. Proc Natl Acad Sci USA 103:18368-18373. (Pubitemid 44871663)
36. McNamara BP, Wolfe AJ (1997) Coexpression of the long and short forms of CheA, the chemotaxis histidine kinase, by members of the family Enterobacteriaceae. J Bacteriol 179:1813-1818. (Pubitemid 27100475)
37. Franco-Zorrilla JM, et al. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033-1037. (Pubitemid 47185180)
38. Knoop H, Zilliges Y, Lockau W, Steuer R (2010) The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth. Plant Physiol 154:410-422.
39. Sittka A, et al. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4:e1000163.
40. Navarro F, Martín-Figueroa E, Florencio FJ (2000) Electron transport controls transcription of the thioredoxin gene (trxA) in the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol Biol 43:23-32. (Pubitemid 30600107)