Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

Schriek, Sarah; Rückert, Christian; Staiger, Dorothee; Pistorius, Elfriede K.; Michel, Klaus-Peter

doi:10.1186/1471-2164-8-437

Cited by 40 publications

(43 citation statements)

References 62 publications

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“…strain PCC 6803, and Alr2310 is most similar to Sll0228 (Schriek et al. ) whose inactivation also leads to lack of any agmatinase activity in Synechocystis cell‐free extracts (Quintero et al. ).…”

Section: Discussionmentioning

confidence: 99%

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst‐forming cyanobacterium Anabaena

Burnat

Flores

2014

MicrobiologyOpen

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Arginine decarboxylase produces agmatine, and arginase and agmatinase are ureohydrolases that catalyze the production of ornithine and putrescine from arginine and agmatine, respectively, releasing urea. In the genome of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, ORF alr2310 putatively encodes an ureohydrolase. Cells of Anabaena supplemented with [14C]arginine took up and catabolized this amino acid generating a set of labeled amino acids that included ornithine, proline, and glutamate. In an alr2310 deletion mutant, an agmatine spot appeared and labeled glutamate increased with respect to the wild type, suggesting that Alr2310 is an agmatinase rather than an arginase. As determined in cell-free extracts, agmatinase activity could be detected in the wild type but not in the mutant. Thus, alr2310 is the Anabaena speB gene encoding agmatinase. The Δalr2310 mutant accumulated large amounts of cyanophycin granule polypeptide, lacked nitrogenase activity, and did not grow diazotrophically. Growth tests in solid media showed that agmatine is inhibitory for Anabaena, especially under diazotrophic conditions, suggesting that growth of the mutant is inhibited by non-metabolized agmatine. Measurements of incorporation of radioactivity from [14C]leucine into macromolecules showed, however, a limited inhibition of protein synthesis in the Δalr2310 mutant. Analysis of an Anabaena strain producing an Alr2310-GFP (green fluorescent protein) fusion showed expression in vegetative cells but much less in heterocysts, implying compartmentalization of the arginine decarboxylation pathway in the diazotrophic filaments of this heterocyst-forming cyanobacterium.

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Section: Discussionmentioning

confidence: 99%

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst‐forming cyanobacterium Anabaena

Burnat

Flores

2014

MicrobiologyOpen

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“…The model we present here is an extension of the iJN678 model described in Nogales et al (2012). Pathways that were amended include the tricarboxylic acid cycle (Zhang and Bryant, 2011), Arg metabolism (Schriek et al, 2007(Schriek et al, , 2008(Schriek et al, , 2009, and Pro metabolism (Knoop et al, 2010). A full list of the modifications we made can be found in Supplemental Data S1.…”

Section: Adaptation Of the Synechocystis Model And Creation Of The Comentioning

confidence: 99%

A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

et al. 2014

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Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the user with little insight in addition to statistical information. In this article, we present a visualization tool for the metabolic network of Synechocystis sp. PCC 6803, an important model cyanobacterium for sustainable biofuel production. We illustrate how this metabolic map can be used to integrate experimental and computational data for Synechocystis sp. PCC 6803 systems biology and metabolic engineering studies. Additionally, we discuss how this map, and the software infrastructure that we supply with it, can be used in the development of other organism-specific metabolic network visualizations. In addition to the Python console package VoNDA (http://vonda.sf.net), we provide a working demonstration of the interactive metabolic map and the associated Synechocystis sp. PCC 6803 genome-scale stoichiometric model, as well as various ready-to-visualize microarray data sets, at http://f-a-m-e.org/synechocystis.

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“…Why would high-nitrate conditions give rise to the apparent repression of a storage polymer for nitrogen? However, it has been reported before that the regulation of cyanophycin synthesis depends on a complex interrelation between cyanophycin synthesis, L-Arg catabolism, and photosynthesis (Ziegler et al, 1998;Stephan et al, 2000;Maheswaran et al, 2006;Schriek et al, 2007). It might be that cyanophycin synthetase acts as a cyanophycin lyase as well.…”

Section: Linking Physiology With Gene Expressionmentioning

confidence: 99%

Concerted Changes in Gene Expression and Cell Physiology of the CyanobacteriumSynechocystissp. Strain PCC 6803 during Transitions between Nitrogen and Light-Limited Growth

et al. 2011

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Physiological adaptation and genome-wide expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to gradual transitions between nitrogen-limited and light-limited growth conditions were measured in continuous cultures. Transitions induced changes in pigment composition, light absorption coefficient, photosynthetic electron transport, and specific growth rate. Physiological changes were accompanied by reproducible changes in the expression of several hundred open reading frames, genes with functions in photosynthesis and respiration, carbon and nitrogen assimilation, protein synthesis, phosphorus metabolism, and overall regulation of cell function and proliferation. Cluster analysis of the nearly 1,600 regulated open reading frames identified eight clusters, each showing a different temporal response during the transitions. Two large clusters mirrored each other. One cluster included genes involved in photosynthesis, which were upregulated during light-limited growth but down-regulated during nitrogen-limited growth. Conversely, genes in the other cluster were down-regulated during light-limited growth but up-regulated during nitrogen-limited growth; this cluster included several genes involved in nitrogen uptake and assimilation. These results demonstrate complementary regulation of gene expression for two major metabolic activities of cyanobacteria. Comparison with batch-culture experiments revealed interesting differences in gene expression between batch and continuous culture and illustrates that continuous-culture experiments can pick up subtle changes in cell physiology and gene expression.

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Bioinformatic evaluation of L-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of L-arginine catabolism in the cyanobacterium Synechocystis sp. PCC 6803

Cited by 40 publications

References 62 publications

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst‐forming cyanobacterium Anabaena

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst‐forming cyanobacterium Anabaena

A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

Concerted Changes in Gene Expression and Cell Physiology of the CyanobacteriumSynechocystissp. Strain PCC 6803 during Transitions between Nitrogen and Light-Limited Growth

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