1,721,106 research outputs found
Identification of the antimycin A sensitive site for Photosystem I driven cyclic elctron flow in the cyanobacterium Synechocystis PCC 6803.
No full textGlobal gene expression analysis under salt stress using a newly designed long oligonucleotide microarray (Synechocystis PCC6803
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A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment
No full textA newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment Eneas Aguirre-von-Wobeser 1, Jef Huisman1, Bas Ibelings2 and Hans C.P. Matthijs1 1 Universiteit van Amsterdam, Amsterdam, The Netherlands 2 Netherlands Institute of Ecology, Limnological Institute, The Netherlands. The availability of complete genome sequences makes design of microarrays possible. Different microarray platforms exist, all of them presenting advantages and disadvantages. Designs may be based on sequenced PCR fragments or alternatively on in vitro synthesised oligonucleotides. Here we show our oligonucleotide based microarray design for Synechocystis PCC6803. We designed and implemented a 45 to 60-mer oligonucleotide microarray design for the Agilent microarray synthesis system. In this work we discuss the design strategy used, which consisted in optimizing several sequence characteristics of the probes. First, oligonucleotides that had the fewest shared sequences with other parts of the genome were favored. The unique probes were chosen to be close to 60 bases long, with similar theoretical hybridization strength with their complementary targets, and avoiding hairpin and dimer structures that could impair hybridization. A trade of between melting temperature and a favourable low CG content of the probes was a major part of the puzzle to be solved [1]. Three probes per gene have been chosen. The microarray platform performance was tested with 8 h salt-stressed and control RNA. The observed hybridization intensity was modestly affected by probe length, uniqueness of sequence, hybridization strength and hairpin-dimer structures. These effects were accounted for in the calculus design and could be neutralised by normalization. Our results proved internally consistent, since different parts of genes and genes from probable operons were regulated similarly. The expression changes observed due to the salt-stress treatment relate largely to those observed in earlier published salt-stress experiments from other laboratories [2-5]. Some open reading frames showed changes different from those previous observations. The array design, the calculus methods and the results will be discussed. [1] Kucho KI, Yoneda H, Harada M, Ishiura M (2004) Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides. Genes Gen. Syst, 79: 189-197 [2] Paithoonrangsarid K, Shoumskaya MA, Kanesaki Y, Satoh S, Tabata S, Los DA, Zinchenko VV, Hayashi H, Tanticharoen M, Suzuki I, Murata N (2004) Five histidine kinases perceive osmotic stress and regulate distinct sets of genes in Synechocystis. J. Biol. Chem 279: 53078-53086 [3] Marin K, Kanesaki Y, Los DA, Murata N, Suzuki I and Hagemann M (2004) Gene expression profiling reflects physiological processes in salt acclimation of Synechocystis sp strain PCC 6803. Plant Physiol. 136: 3290-3300 [4] Marin K, Suzuki I, Yamaguchi K, Ribbeck K,Yamamoto H, Kanesaki Y, Hagemann M, Murata N (2003) Identification of histidine kinases that act as sensors in the perception of salt stress in Synechocystis sp PCC 6803. Proc. Natl. Acad. Sc. USA 100: 9061-9066 [5] Kanesaki Y, Suzuki I, Allakhverdiev SI, Mikami K, Murata N (2002) Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp PCC 6803 Biochem. Biophys. Res. Commun. 290: 339-34
Physiological and gene expression changes of Synechocytis PCC6803 under nitrogen-limited growth in continuous culture
No full textTranscriptome versus proteomics: the response of Synechocystis sp. PCC6803 to nitrogen starvation
No full textPhotoprotective function of IsiA in Synechocystis PCC 6803
No full textDue to the low solubility of iron, cyanobacteria need to have adaptation mechanisms of their photosynthetic apparatus. IsiA (iron-stress-inducible protein A) has been found as a ring of 18 subunits surrounding PSI trimers under limited stress conditions (Boekema et al., Nature 2001, Bibby et al., Nature 2001). Under prolonged iron deficiency, aggregates of many IsiA subunits are synthesized, some of them not associated with PSI (Yeremenko et al. Biochemistry 2004). We purified IsiA aggregates in the absence of PSI, and found that they contain chlorophyll a, ß-carotene and zeaxanthin. The IsiA aggregates show an extraordinary temperature dependence of the fluorescence emission yield at 687 nm, which was also observed in the membranes from which the aggregates were extracted. At room temperature, the fluorescence quantum yield of IsiA aggregates is much smaller than that of monomeric chlorophyll a in acetone. Time-resolved fluorescence experiments revealed a main lifetime for IsiA aggregates in the hundreds of pico-seconds time range. These results suggest that IsiA aggregates are directly involved in non-photochemical quenching and confirm the photoprotection ability of IsiA under stress conditions
Nutrient limitation of freshwater cyanobacteria : tools to monitor phosphorus limitation at the individual level
No full textChanges in species composition that are often observed in phytoplankton
communities result from a complex interplay between physical and chemical
properties of the aquatic environment on the one hand and the responsiveness of the
individual species on the other hand. The potential role of nutrient limitation in
accommodating these changes in species composition has since long been
recognized. However, the interpretation of results, to the benefit of understanding
nutrient competition between species in phytoplankton communities, is very much
hampered by the limited knowledge that is gained by chemical assay methods for
measurements of actual nutrient concentrations in surface waters
Functional flexibility of light harvesting in cyanobacteria
No full textFunctional flexibility of light harvesting in cyanobacteria Nataliya Yeremenko 1, Roman Kouril 2, Janne A. Ihalainen 3, Sandrine D¿Haene 3, Martin Hagemann 4, Egbert J. Boekema 2, Hans C.P. Matthijs 1 and Jan P. Dekker 3 1 Universiteit van Amsterdam, Amsterdam, The Netherlands; 2 University of Groningen, Groningen, The Netherlands; 3 Vrije Universiteit, Amsterdam, The Netherlands; 4 Universität Rostock, Rostock, Germany Regulation of light harvesting is a matter of high importance in photosynthetic organisms. High plants and algae involve mechanism of state transitions which is regulated by the redox state of the plastoquinone pool and leads to the reversible redistribution of excitation energy between the two photosystems through a reorganization of the antennae and to an overall increase in photosynthetic quantum yield by decreasing the delivery of excess excitation energy to PSII while increasing delivery of excitation energy to PSI (or vice-versa) [1]. Cyanobacteria balance energy input and consumption differently. Under iron-deficient conditions, the content of PSI decreases substantially more than that of PSII [2]. Cyanobacteria respond to this condition by accumulation of IsiA protein which may occurs in two different types of complexes (associated and not associated with PSI) and correspondingly serve different functions [3]. The PSI-IsiA supercomplexes show increasingly larger amounts of bound IsiA proteins with increasing iron starvation. The largest particles consist of double IsiA ring around monomeric PSI and contain about 560 chlorophylls, which together with 96 chlorophylls of the PSI core complex would give a total number of 656 chlorophylls. PSI particles with such large antenna sizes have not been observed before. Fluorescence excitation spectra indicate an efficient light-harvesting function for all PSI-bound chlorophylls. With continious iron starvation the further decline of PSI makes PSII increasingly vulnerable to photooxidation and the surplus synthesis of IsiA not associated with PSI shields PSII from excess light
Supercomplexes of photosystem I and antenna proteins in cyanobacteria and green plants
No full textPhotosystem I (PSI) and Photosystem II (PSII) can form supercomplexes with various types of antenna proteins. One such protein is Light-harvesting complex II (LHCII). In plants it is bound in its trimeric form to dimeric PSII. In spinach and Arabidopsis thaliana most dimers bind 2-4 LHCII trimers. We have characterized the PSI-LHCII complex from Arabidopsis membranes in state two by single particle electron microscopy at about 16 Å. PSI binds one trimer at the site of the PsaL and PsaK subunits. Cyanobacteria express large quantities of the Iron Stress Inducible protein IsiA under iron deficiency. IsiA can assemble into numerous types of single or double rings surrounding PS I. These supercomplexes are functional in light-harvesting, but empty IsiA rings are effective energy dissipators. Electron microscopy studies on over 130 000 particle projections of these supercomplexes show that photosystem I trimers find 18 IsiA copies in a single ring; whereas monomers may bind up to 35 copies in two rings. The double rings are formed by inner rings of 12, 13 or 14 copies and the outer ones of 19, 20 and 21 copies, respectively. This shows that IsiA can form a remarkable large variety of ring-like structures. Work on particles purified from mutants indicates that the PsaF and PsaL subunits facilitate the formation of closed rings around PSI monomers. But these subunits are not obligatory components in the formation of PSI-IsiA supercomplexes
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