Comparative analysis of the primary transcriptome of synechocystis sp. PCC 6803

DNA Research

Volumn 21, Issue 5, 2014, Pages 527-539

  Matthias, Kopf ^a   Klähn, Stephan ^a   Ingeborg, Scholz ^a   Jasper, K F Matthiessen ^a   Wolfgang, R Hess ^a   Björn, Voß ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Comparative transcriptome analysis; Cyanobacteria; Regulation of gene expression; SRNA; Transcriptional unit

Indexed keywords

NITROGEN; TRANSCRIPTOME; TRANSFER RNA; UNTRANSLATED RNA; 3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACTERIAL RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; COLD STRESS; CONTROLLED STUDY; DARKNESS; IRON DEPLETION; LIGHT INTENSITY; NONHUMAN; OPERON; PROMOTER REGION; READING FRAME; REGULON; RNA ISOLATION; SIGNAL PROCESSING; START CODON; STEADY STATE; STRESS; SYNECHOCYSTIS; TRANSCRIPTION INITIATION SITE; BACTERIAL GENOME; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHOTOSYNTHESIS;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; OPERON; PHOTOSYNTHESIS; RNA, BACTERIAL; SYNECHOCYSTIS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTOME;

EID: 84908187157     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsu018     Document Type: Article

References (49)

1. Georgianna, D.R. and Mayfield, S.P. 2012, Exploiting diversity and synthetic biology for the production of algal biofuels, Nature, 488, 329-35.
2. Peralta-Yahya, P.P, Zhang, F., del Cardayre, S.B. and Keasling J.D. 2012, Microbial engineering for the production of advanced biofuels, Nature, 488, 320-8.
3. McKinlay, J.B. and Harwood, CS. 2010, Photobiological production of hydrogen gas as a biofuel, Curr. Opin. Biotechnol., 21, 244-51.
4. Deng, M.-D. and Coleman, J.R. 1999, Ethanol synthesis by genetic engineering in cyanobacteria, Appl. Environ. Microbiol., 65, 523-8.
5. Atsumi, S., Higashide, W. and Liao, J.C. 2009, Direct photosynthetic recycling of carbondioxide to isobutyraldehyde, Nat. Biotechnol., 27, 1177-80.
6. Takahama, K., Matsuoka, M., Nagahama, K. and 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, 302-5.
7. Lindberg, P., Park, S. and Melis, A. 2010, Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the Model Organism, Metab. Eng., 12, 70-9.
8. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. 2010, Microbial biosynthesis of alkanes, Science, 329, 559-62.
9. Haselkorn, R. 1991, Genetic systems in cyanobacteria. In: Jeffrey, H.M. (Ed.), Methods in Enzymology. Academic Press, Waltham, USA, pp. 418-30.
10. Porter, R.D. 1988, DNA transformation. In: Lester Packer, A.N.G. (Ed.), Methods in Enzymology. Academic Press, Waltham, USA, pp. 703-12.
11. Williams, J.G.K. 1988, Construction of specific mutations in photosystem II photosynthetic reaction center by genetic engineering methods in Synechocystis 6803. In: Lester Packer, A.N.G. (Ed.), Methods in Enzymology. Academic Press, Waltham, USA, pp. 766-78.
12. Grigorieva, G. and Shestakov, S. 1982, Transformation in the cyanobacterium Synechocystis sp. 6803, FEMS Microbiol. Lett., 13, 367-70.
13. Kaniya, Y., Kizawa, A., Miyagi, A., et al. 2013, Deletion of the transcriptional regulator cyAbrB2 deregulates primary carbon metabolism in Synechocystis sp. PCC 6803, Plant Physiol., 162, 1153-63.
14. Knoop, H., Zilliges, Y., Lockau, W. and Steuer, R. 2010, The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth, Plant Physiol., 154, 410-22.
15. Knoop, H., Gründel, M., Zilliges, Y., et al. 2013, Fluxbalance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803, PLoS Comput Biol., 9, e1003081.
16. Fulda, S., Mikkat, S., Huang, F., et al. 2006, Proteome analysis of salt stress response in the cyanobacterium Synechocystis sp. strain PCC 6803, Proteomics, 6, 2733-45.
17. 2 limitation revealed by quantitative proteo-mics, J. Proteome Res., 9, 5896-912.
18. Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A. and Ikeuchi, M. 2001, DNA microarray analysis of cyanobacterial gene expression during acclimation to high light, Plant Cell Online, 13, 793-806.
19. Georg, J., Voß, B., Scholz, I., Mitschke, J., Wilde, A. and Hess, W.R. 2009, Evidence for a major role of antisense RNAs in cyanobacterial gene regulation, Mol. Syst. Biol., 5, 305.
20. Hernández-Prieto, M.A., Schön, V., Georg, J., et al. 2012, Iron deprivation in Synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling, G3 (Bethesda), 2, 1475-95.
21. Mitschke, J., Georg, J., Scholz, I., et al. 2011, Anexperimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803, Proc. Natl. Acad. Sci. USA, 108, 2124-9.
22. Sharma, C.M., Hoffmann, S., Darfeuille, F., et al. 2010, The primary transcriptome of the major human pathogen Helicobacter pylori, Nature, 464, 250-5.
23. Mitschke, J., Vioque, A., Haas, F., Hess, W.R. and MuroPastor, A.M. 2011, Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120, Proc. Natl. Acad. Sci. USA, 108, 20130-5.
24. Trautmann, D., Voß, B., Wilde, A., Al-Babili, S. and Hess, W.R. 2012, Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803, DNA Res., 19, 435-48.
25. Rippka, R., Deruelles, J., Waterbury, J.B., Herdman, M. and Stanier, R.Y. 1979, Generic assignments, strain histories and properties of pure cultures of cyanobacteria, Microbiology, 111, 1-61.
26. Pinto, F., Thapper, A., Sontheim, W. and Lindblad, P. 2009, Analysis of current and alternative phenol based RNA ex-tractionmethodologies forcyanobacteria, BMCMol. Biol., 10, 79.
27. Hein, S., Scholz, I., Voß, B. and Hess, W.R. 2013, Adaptation and modification of three CRISPR loci in two closely related cyanobacteria, RNA Biol., 10, 852-64.
28. Hoffmann, S., Otto, C., Kurtz, S., et al. 2009, Fast mapping of short sequences with mismatches, insertionsand deletions using index structures, PLoS Comput. Biol., 5, e1000502.
29. Bischler, T., Kopf, M. and Voß, B. 2014, Transcriptmapping based on dRNA-seq data, BMC Bioinformatics, 15, 122.
30. Sesto, N., Wurtzel, O., Archambaud, C., Sorek, R. and Cossart, P. 2013, The excludon: anewconceptinbacterial antisense RNA-mediated gene regulation, Nat. Rev. Microbiol., 11, 75-82.
31. Steglich, C., Futschik, M.E., Lindell, D., Voß, B., Chisholm, S.W. and Hess, W.R. 2008, The challenge of regulation in a minimal photoautotroph: non-coding RNAs in Prochlorococcus, PLoS Genet., 4, e1000173.
32. Eisenhut, M., Georg, J., Klähn, S., et al. 2012, Theantisense RNA As1-flv4 in the cyanobacterium Synechocystis sp. PCC 6803 prevents premature expression of the flv4-2 operon upon shift in inorganic carbon supply, J. Biol. Chem., 287, 33153-62.
33. Bersanini, L., Battchikova, N., Jokel, M., et al. 2014, Flavodiiron protein Flv2/Flv4-related photoprotective mechanism dissipates excitation pressure of PSII in cooperation with phycobilisomes in cyanobacteria, Plant Physiol., 164, 805-18.
34. Zhang, P., Allahverdiyeva, Y., Eisenhut, M. and Aro, E.-M. 2009, Flavodiiron proteins in oxygenic photosynthetic organisms: photoprotection of photosystem II by Flv2 and Flv4 in Synechocystissp. PCC6803, PLoS ONE, 4, e5331.
35. Voß, B., Georg, J., Schon, V., Ude, S. and Hess, W. 2009, Biocomputational prediction of non-coding RNAs in model cyanobacteria, BMC Genomics, 10, 123.
36. Suzuki, S., Ferjani, A., Suzuki, I. and Murata, N. 2004, The SphS-SphR two component system is the exclusive sensor for the induction of gene expression in response to phosphate limitation in Synechocystis, J. Biol. Chem., 279, 13234-40.
37. Hess, W.R., Berghoff, B.A., Steglich, C., Wilde, A. and Klug, G. 2014, Riboregulators and the role of Hfq in photosynthetic prokaryotes, RNA Biol., 11, 1-14.
38. Montesinos, M.L., Muro-Pastor, A.M., Herrero, A. and Flores, E. 1998, Ammonium/methylammonium permeases of a cyanobacterium: identification and analysis of three nitrogen-regulated amt genes in Synechocystis sp. PCC 6803, J. Biol. Chem., 273, 31463-70.
39. Wang, H.-L., Postier, B.L. and Burnap, R.L. 2004, Alterations in global patterns of gene expression in Synechocystis sp. PCC 6803 in response to inorganic carbon limitation and the inactivation of ndhR, a LysR family regulator, J. Biol. Chem., 279, 5739-51.
40. Krasikov, V., Aguirre von Wobeser, E., Dekker, H.L., Huisman, J. and Matthijs, H.C.P. 2012, Time-series resolution of gradual nitrogen starvation and its impact on photosynthesis in the cyanobacterium Synechocystis PCC 6803, Physiol. Plant., 145, 426-39.
41. Song, J.-Y., Cho, H.S., Cho, J.-I., Jeon, J.-S., Lagarias, J.C. and Park, Y.-I. 2011, Near-UVcyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803, Proc. Natl. Acad. Sci. U.S.A., 108, 10780-5.
42. Kopf, M., Klähn, S., Pade, N., et al. 2014, Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803, DNA Res., 21, 255-66.
43. Kim, D., Hong, J.S.-J., Qiu, Y., et al. 2012, Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling, PLoS Genet., 8, e1002867.
44. Vesper, O., Amitai, S., Belitsky, M., et al. 2011, Selective translationofleaderless mRNAsbyspecializedribosomes generated by MazF in Escherichia coli, Cell, 147, 147-57.
45. Dugar, G., Herbig, A., Forstner, K.U., et al. 2013, High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates, PLoS Genet., 9, e1003495.
46. Buikema, W.J. and Haselkorn, R. 2001, Expression of the Anabaena hetR gene from a copper-regulated promoter leads to heterocyst differentiation under repressing conditions, Proc. Natl. Acad. Sci. USA, 98, 2729-34.
47. Ehira, S. and Ohmori, M. 2006, NrrA directly regulates expression of hetR during heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120, J. Bacteriol., 188, 8520-5.
48. Rajagopalan, R. and Callahan, S.M. 2010, Temporal and spatial regulation of the four transcription start sites of hetR from Anabaena sp. strain PCC 7120, J. Bacteriol., 192, 1088-96.
49. Muro-Pastor, A.M, Valladares, A., Flores, E. and Herrero, A. 2002, Mutual dependence of the expression of the cell differentiationregulatoryprotein HetR and the global nitrogen regulator NtcA during heterocyst development, Mol. Microbiol., 44, 1377-85.