Experimental and bioinformatic approaches for analyzing and visualizing cyanobacterial nitrogen and hydrogen metabolism

Electronic Journal of Biotechnology

Volumn 10, Issue 4, 2007, Pages 549-562

  Wünschiers, Röbbe ^a,d   Axelsson, Rikard ^b   Vellguth, Martin ^a,b   Lindblad, Peter ^c  

^a UNIVERSITY OF COLOGNE   (Germany)

^b Uppsala University ^*  (Germany)

^c UPPSALA UNIVERSITY   (Sweden)

^d SunGene GmbH and Co KGaA   (Germany)

Author keywords

Bioinformatics; Cyanobacteria; DNA microarrays; Gene expression; Metabolic pathways; Nitrogen availability; Nitrogen fixation

Indexed keywords

CATALYSIS; GENE EXPRESSION; HYDROGEN; METABOLISM; NITROGEN FIXATION; PROTEINS;

CYANOBACTERIA; DNA-MICROARRAYS; METABOLIC PATHWAYS; NITROGEN AVAILABILITY;

BIOINFORMATICS;

HYDROGEN; NITROGEN; OLIGONUCLEOTIDE;

ARTICLE; BIOINFORMATICS; CHEMICAL ANALYSIS; CONTROLLED STUDY; CYANOBACTERIUM; DNA MICROARRAY; GENE EXPRESSION; HYBRIDIZATION; INFORMATION PROCESSING; NITROGEN FIXATION; NITROGEN METABOLISM; NONHUMAN; PHOTOSYNTHESIS; PROTEIN SECONDARY STRUCTURE; RNA ISOLATION;

CYANOBACTERIA; NOSTOC SP.; NOSTOC SP. PCC 7120;

EID: 37849028368     PISSN: None     EISSN: 07173458     Source Type: Journal    
DOI: 10.2225/vol10-issue4-fulltext-2     Document Type: Article

References (47)

1. ADAMS, David G. Heterocyst formation in cyanobacteria. Current Opinion in Microbiology, December 2000, vol. 3, no. 6, p. 618-624.
2. BAUM, Michael; BIELAU, Simone; RITTNER, Nicole; SCHMID, Kathrin; EGGELBUSCH, Kathrin; DAHMS, Michael; SCHLAUERSBACH, Andrea; TAHEDL, Harald; BEIER, Markus; GÜIMIL, Ramon; SCHEFFLER, Matthias; HERMANN, Carsten; FUNK, Jörg-Michael; WIXMERTEN, Anke; REBSCHER, Hans; HÖNIG, Matthias; ANDREAE, Claas; BÜCHNER, Daniel; MOSCHEL, Erich; GLATHE, Andreas; JÄGER, Evelyn; THOM, Marc; GREIL, Andreas; BESTVATER, Felix; OBERMEIER, Frank; BURGMAIER, Josef; THOME, Klaus; WEICHERT, Sigrid; HEIN, Silke; BINNEWIES, Tim; FOITZIK, Volker; MÜLLER, Manfred; STÄHLER, Cord Friedrich and STÄHLER, Peer Friedrich. Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Research, December 2003, vol. 31, no. 23, p. e151.
3. BEIER, Markus and HOHEISEL, Jörg D. Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays. Nucleic Acids Research, February 2000, vol. 28, no. 4, p. e11.
4. BÖHME, Herbert. Regulation of nitrogen fixation in heterocyst-forming cyanobacteria. Trends in Plant Science, September 1998, vol. 3, no. 9, p. 346-351.
5. DIXON, Ray and KAHN, Daniel. Genetic regulation of biological nitrogen fixation. Nature Reviews Microbiology, August 2004, vol. 2, no. 8, p. 621-631.
6. DUTTA, Debajyoti; DE, Debojyoti; CHAUDHURI, Surabhi and BHATTACHARYA, Sanjoy K. Hydrogen production by Cyanobacteria. Microbial Cell Factories, December 2005, vol. 4, no. 1, p. 36.
7. EBERWINE, James; YEH, Hermes; MIYASHIRO, Kevin; CAO, Yanxiang; NAIR, Suresh; FINNELL, Richard; ZETTEL, Martha and COLEMAN, Paul. Analysis of gene expression in single live neurons. Proceedings of the National Academy of Sciences of the United States of America, April 1992, vol. 89, no. 7, p. 3010-3014.
8. EHIRA, Shigeki; OHMORI, Masayuki and SATO, Naoki. Identification of Low-temperature-regulated ORFs in the cyanobacterium Anabaena sp. strain PCC 7120: distinguishing the effects of low temperature from the effects of photosystem II excitation pressure. Plant and Cell Physiology, August 2005, vol. 46, no. 8, p. 1237-1245.
9. EHIRA, Shigeki and OHMORI, Masayuki. NrrA, a nitrogen-responsive response regulator facilitates heterocyst development in the cyanobacterium Anabaena sp. strain PCC 7120. Molecular Microbiology, March 2006, vol. 59, no. 6, p. 1692-1703.
10. FAY, Peter. Oxygen relations of nitrogen fixation in cyanobacteria. Microbiological Reviews, June 1992, vol. 56, no. 2, p. 340-373.
11. GOLDEN, James W. and YOON, Ho-Sung. Heterocyst formation in Anabaena. Current Opinions in Microbiology, December 1998, vol. 1, no. 6, p. 623-629.
12. GÜIMIL, Ramon; BEIER, Markus; SCHEFFLER, Matthias; REBSCHER, Hans; FUNK, Jörg-Michael; WIXMERTEN, Anke; BAUM, Michael; HERMANN, Carsten; TAHEDL, Harald; MOSCHEL, Erich; OBERMEIER, Frank; SOMMER, I.; BÜCHNER, Daniel; VIEHWEGER, R.; BURGMAIER, Josef; STÄHLER, Cord Friedrich; MÜLLER, Manfred and STÄHLER, Peer Friedrich. Geniom® technology - the benchtop array facility. Nucleosides, Nucleotides and Nucleic Acids, October 2003, vol. 22, no. 5-8, p. 1721-1723.
13. HAPPE, Thomas; SCHÜTZ, Kathrin and BÖHME, Herbert. Transcriptional and mutational analysis of the uptake hydrogenase of the filamentous cyanobacterium Anabaena variabilis ATCC 29413. Journal of Bacteriology, March 2000, vol. 182, no. 6, p. 1624-1631.
14. HASAN, Ahmad; STENGELE, Klaus-Peter; GIEGRICH, Heiner; CORNWELL, Paul; ISHAM, Kenneth R.; SACHLEBEN, Richard A.; PFLEIDERER, Wolfgang and FOOTE, Robert S. Photolabile protecting groups for nucleotides: synthesis and photodeprotection rates. Tetrahedron, March 1997, vol. 53, no. 12, p. 4247-4264.
15. HASELKORN, Robert and BUIKEMA, William J. Nitrogen fixation in cyanobacteria. In: STACEY, Gary; BURRIS, Robert H. and EVANS, Harold J. eds. Biological Nitrogen Fixation. Chapman & Hall, Inc. NY, USA, 1992, p. 166-190.
16. HEDDAD, Mounia and ADAMSKA, Iwona. The evolution of light stress proteins in photosynthetic organisms. Comparative and Functional Genomics, December 2002, vol. 3, no. 6, p. 504-510.
17. HERRERO, Antonia; MURO-PASTOR, Alicia M. and FLORES, Enrique. Nitrogen control in cyanobacteria. Journal of Bacteriology, January 2001, vol. 183, no. 2, p. 411-425.
18. HERRERO, Antonia; MURO-PASTOR, Alicia M.; VALLADARES, Ana and FLORES, Enrique. Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria. FEMS Microbiology Reviews, October 2004, vol. 28, no. 4, p. 469-487.
19. HIGO, Akiyoshi; KATOH, Hiroshi; OHMORI, Kazuko; IKEUCHI, Masahiko and OHMORI, Masayuki. The role of a gene cluster for trehalose metabolism in dehydration tolerance of the filamentous cyanobacterium Anabaena sp. PCC 7120. Microbiology, April 2006, vol. 152, no. 4, p. 979-987.
20. HOFACKER, Ivo L.; FONTANA, Walter; STADLER, Peter F.; BONHOEFFER, L. Sebastian; TACKER, Manfred and SCHUSTER, Peter. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie, February 1994, vol. 125, no. 2, p. 167-188.
21. IMASHIMIZU, Masahiko; YOSHIMURA, Hidehisa; KATOH, Hiroshi; EHIRA, Shigeki and OHMORI, Masayuki. NaCl enhances cellular cAMP and upregulates genes related to heterocyst development in the cyanobacterium, Anabaena sp. strain PCC 7120. FEMS Microbiology Letters, November 2005, vol. 252, no. 1, p. 97-103.
22. JONES, Kathryn M. and HASELKORN, Robert. Newly identified cytochrome c oxidase operon in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 specifically induced in heterocysts. Journal of Bacteriology, May 2002, vol. 184, no. 9, p. 2491-2499.
23. KANEKO, Takakazu; NAKAMURA, Yasukazu; WOLK, C. Peter; KURITZ, Tanya; SASAMOTO, Shigemi; WATANABE, Akiko; IRIGUCHI, Mayumi; ISHIKAWA, Atsuko; KAWASHIMA, Kumiko; KIMURA, Takaharu; KISHIDA, Yoshie; KOHARA, Mitsuyo; MATSUMOTO, Midori; MATSUNO, Ai; MURAKI, Akiko; NAKAZAKI, Naomi; SHIMPO, Sayaka; SUGIMOTO, Masako; TAKAZAWA, Masaki; YAMADA, Manabu; YASUDA, Miho and TABATA, Satoshi. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Research, October 2001, vol. 8, no. 5, p. 205-213.
24. KAWASHIMA, Shuichi; KATAYAMA, Toshiaki; SATO, Yoko and KANEHISA, Minoru. KEGG API: A web service using SOAP/WSDL to access the KEGG system. Genome Informatics, 2003, vol. 14, p. 673-674.
25. KUO, Winston Patrick; JENSSEN, Tor-Kristian; BUTTE, Atul J.; OHNO-MACHADO, Lucila and KOHANE, Isaac S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics, March 2002, vol. 18, no. 3, p. 405-412.
26. LECHNO-YOSSEF, Sigal; FAN, Qing; EHIRA, Shigeki; SATO, Naoki and WOLK, C. Peter. Mutations in four regulatory genes have interrelated effects on heterocyst maturation in Anabaena sp. strain PCC 7120. Journal of Bacteriology, November 2006, vol. 188, no. 21, p. 7387-7395.
27. LOCKHART, David J.; DONG, Helin; BYRNE, Michael C.; FOLLETTIE, Maximillian T.; GALLO, Michael V.; CHEE, Mark S.; MITTMANN, Michael; WANG, Chunwei; KOBAYASHI, Michiko; NORTON, Heidi and BROWN, Eugene L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology, December 1996, vol. 14, no. 13, p. 1675-1680.
28. MANIATIS, Tom; FRITCH, Edward F. and SAMBROOK, Joseph. Synthesis and cloning of cDNA. In: SAMBROOK, Joseph and RUSSELL, David W. Molecular cloning. Cold Spring Harbor Laboratory Press, 1982, p. 212-246.
29. MARTÍN-FIGUEROA, Eugenio; NAVARRO, Francisco and FLORENCIO, Francisco J. The GS-GOGAT pathway is not operative in the heterocysts. Cloning and expression of glsF gene from the cyanobacterium Anabaena sp. PCC 7120. FEBS Letters, July 2000, vol. 476, no. 3, p. 282-286.
30. MASUKAWA, H.; MOCHIMARU, M. and SAKURAI, H. Disruption of the uptake hydrogenase gene, but not of the bidirectional hydrogenase gene, leads to enhanced photobiological hydrogen production by the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120. Applied Microbiology and Biotechnology, April 2002, vol. 58, no. 5, p. 618-624.
31. MEEKS, John C. and ELHAI, Jeff. Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states. Microbiology and Molecular Biology Reviews, March 2002, vol. 66, no. 1, p. 94-121.
32. MONTANÉ, Marie-Hélène and KLOPPSTECH, Klaus. The family of light-harvesting-related proteins (LHCs, ELIPs, HLIPs): was the harvesting of light their primary function? Gene, November 2000, vol. 258, no. 1-2, p. 1-8.
33. MURO-PASTOR, Alicia M.; VALLADARES, Ana; FLORES, Enrique and HERRERO, Antonia. The hetC gene is a direct target of the NtcA transcriptional regulator in cyanobacterial heterocyst development. Journal of Bacteriology, November 1999, vol. 181, no. 21, p. 6664-6669.
34. MURRY, Marcia A. and WOLK, C. Peter. Evidence that the barrier to the penetration of oxygen into heterocysts depends upon two layers of the cell envelope. Archives of Microbiology, May 1989, vol. 151, no. 6, p. 469-474.
35. ORR, J. and HASELKORN, R. Regulation of glutamine synthetase activity and synthesis in free-living and symbiotic Anabaena spp. Journal of Bacteriology, November 1982, vol. 152, no. 2, p. 626-635.
36. POZHITKOV, Alex; NOBLE, Peter A.; DOMAZETLOSO, Tomislav; NOLTE, Arne W.; SONNENBERG, Rainer; STAEHLER, Peer; BEIER, Markus and TAUTZ, Diethard. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research, May 2006, vol. 34, no. 9, p. e66.
37. PRINCE, Roger C. and KHESHGI, Haroon S. The photobiological production of hydrogen: potential efficiency and effectiveness as a renewable fuel. Critical Reviews in Microbiology, February 2005, vol. 31, no. 1, p. 19-31.
38. SCHMETTERER, Georg. Cyanobacterial respiration. In: BRYANT, D.A. ed. The Molecular Biology of Cyanobacteria. Kluwer Academic Publisher, NL, 1994, p. 409-435.
39. SINGH, S.; KATE, B.N. and BANERJEE, U.C. Bioactive compounds from cyanobacteria and microalgae: an overview. Critical Reviews in Biotechnology, July 2005, vol. 25, no. 3, p. 73-95.
40. SINGH-GASSON, Sangeet; GREEN, Roland D.; YUE, Yongjian; NELSON, Clark; BLATTNER, Fred; SUSSMAN, Michael R. and CERRINA, Franco. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology, October 1999, vol. 17, no. 10, p. 974-978.
41. STANIER, R.Y.; KUNISAWA, R.; MANDEL, M. and COHEN-BAZIRE, G. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriological Reviews, June 1971, vol. 35, no. 2, p. 171-205.
42. VALLADARES, Ana; HERRERO, Antonia; PILS, Dietmar; SCHMETTERER, Georg and FLORES, Enrique. Cytochrome c oxidase genes required for nitrogenase activity and diazotrophic growth in Anabaena sp. PCC 7120. Molecular Microbiology, March 2003, vol. 47, no. 5, p. 1239-1249.
43. VÁZQUEZ-BERMÚDEZ, María Félix; HERRERO, Antonia and FLORES, Enrique. 2-Oxoglutarate increases the binding affinity of the NtcA (nitrogen control) transcription factor for the Synechococcus glnA promoter. FEBS Letters, February 2002, vol. 512, no. 1-3, p. 71-74.
44. VÁZQUEZ-BERMÚDEZ, María Félix; HERRERO, Antonia and FLORES, Enrique. Carbon supply and 2-oxoglutarate effects on expression of nitrate reductase and nitrogen-regulated genes in Synechococcus sp. strain PCC 7942. FEMS Microbiology Letters, April 2003, vol. 221, no. 2, p. 155-159.
45. WOLK, C. Peter. Heterocyst formation in Anabaena. In: BRUN, Yves and SHIMKETS, Lawrence J. eds. Prokaryotic Development. American Society for Microbiology, USA, 2000, p. 83-104.
46. WÜNSCHIERS, Röbbe and LINDBLAD, Peter. Light-dependent hydrogen metabolism and generation by Cyanobacteria. In: NALVA, Hari Singh ed. Handbook of Photochemistry and Photobiology. American Scientific Publishers, North Lewis Way, CA, USA, 2003, vol. 4, p. 295-328.
47. ZHOU, Yingyao and ABAGYAN, Ruben. Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics, January 2002, vol. 3, p. 3.