BibSonomyburst/user/microbioBibSonomy RSS feed for /user/microbio2012-02-15T11:55:31+01:00http://www.bibsonomy.org/bibtex/2360d6f6b7b103a12630fc529c0d5f681/microbiomicrobio2008-10-28T11:38:56+01:00imported <span class="authorEditorList"><a href="/author/Dienst">Dennis Dienst</a>, <a href="/author/Duehring">Ulf Duehring</a>, <a href="/author/Mollenkopf">Hans-Joachim Mollenkopf</a>, <a href="/author/Vogel">Joerg Vogel</a>, <a href="/author/Golecki">Jochen Golecki</a>, <a href="/author/Hess">R. Wolfgang Hess</a>, and <a href="/author/Wilde">Annegret Wilde</a> </span><em>Microbiology</em> <em>154(Pt 10):3134-3143</em> (<em>2008</em>)Tue Oct 28 11:38:56 CET 2008MicrobiologyPt 103134-3143The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 68031542008imported The ssr3341 locus was previously suggested to encode an orthologue of the RNA chaperone Hfq in the cyanobacterium Synechocystis sp. strain PCC 6803. Insertional inactivation of this gene resulted in a mutant that was not naturally transformable and exhibited a non-phototactic phenotype compared with the wild-type. The loss of motility was complemented by reintroduction of the wild-type gene, correlated with the re-establishment of type IV pili on the cell surface. Microarray analyses revealed a small set of genes with drastically reduced transcript levels in the knockout mutant compared with the wild-type cells. Among the most strongly affected genes, slr1667, slr1668, slr2015, slr2016 and slr2018 stood out, as they belong to two operons that had previously been shown to be involved in motility, controlled by the cAMP receptor protein SYCRP1. This suggests a link between cAMP signalling, motility and possibly the involvement of RNA-based regulation. http://www.bibsonomy.org/bibtex/2ec9ffb6cc96212683ac242e000392152/microbiomicrobio2008-08-08T13:57:07+02:00imported <span class="authorEditorList"><a href="/author/Legewie">Stefan Legewie</a>, <a href="/author/Dienst">Dennis Dienst</a>, <a href="/author/Wilde">Annegret Wilde</a>, <a href="/author/Herzel">Hanspeter Herzel</a>, and <a href="/author/Axmann">Ilka Axmann</a> </span><em>Biophysical Journal</em> (<em>July 2008</em>)<em>PMID: 18599624 . </em>Fri Aug 08 13:57:07 CEST 2008Biophysical JournalJulyPMID: 18599624Small RNAs Establish Delays and Temporal Thresholds in Gene Expression2008imported Non-coding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but it remains poorly understood how they affect the dynamics of transcriptional networks. We analyzed the temporal characteristics of the cyanobacterial iron stress response by mathematical modeling and quantitative experimental analyses, and focused on the role of a recently discovered small non-coding RNA, IsrR. We found that IsrR is responsible for a pronounced delay in the accumulation of isiA mRNA encoding the late-phase stress protein, IsiA, and that it ensures a rapid decline in isiA levels once external stress triggers are removed. These kinetic properties allow the system to selectively respond to sustained (as opposed to transient) stimuli, and thus establish a temporal threshold, which prevents energetically costly IsiA accumulation under short-term stress conditions. Biological information is frequently encoded in the quantitative aspects of intracellular signals (e.g., amplitude and duration). Our simulations reveal that competitive inhibition and regulated degradation allow intracellular regulatory networks to efficiently discriminate between transient and sustained inputs.http://www.bibsonomy.org/bibtex/261fcd468696964b95bbfbe6ad871ebac/microbiomicrobio2008-08-08T13:57:07+02:00imported <span class="authorEditorList"><a href="/author/Sobotka">Roman Sobotka</a>, <a href="/author/Dühring">Ulf Dühring</a>, <a href="/author/Komenda">Josef Komenda</a>, <a href="/author/Peter">Enrico Peter</a>, <a href="/author/Gardian">Zdenko Gardian</a>, <a href="/author/Tichy">Martin Tichy</a>, <a href="/author/Grimm">Bernhard Grimm</a>, and <a href="/author/Wilde">Annegret Wilde</a> </span><em>The Journal of Biological Chemistry</em> (<em>July 2008</em>)<em>PMID: 18625715 . </em>Fri Aug 08 13:57:07 CEST 2008The Journal of Biological ChemistryJulyPMID: 18625715Importance of the cyanobacterial Gun4 protein for chlorophyll metabolism and assembly of photosynthetic complexes2008imported Gun4 is a porphyrin binding protein that activates magnesium chelatase, a multimeric enzyme catalyzing the first committed step in chlorophyll biosynthesis. In plants, GUN4 has been implicated in plastid-to-nucleus retrograde signalling processes that coordinate both photosystem II and photosystem I nuclear gene expression with chloroplast function. In this work we present the functional analysis of Gun4 from the cyanobacterium Synechocystis sp. PCC 6803. Affinity co-purification of the FLAG-tagged Gun4 with the ChlH subunit of the magnesium chelatase confirmed the association of Gun4 with the enzyme in cyanobacteria. Inactivation of the gun4 gene abolished photoautotrophic growth of the resulting gun4 mutant strain that exhibited a decreased activity of magnesium chelatase. Consequently, the cellular content of chlorophyll-binding proteins was highly inadequate, especially that of proteins of photosystem II. Immunoblot analyses, blue native polyacrylamide gel electrophoresis and radiolabeling of the membrane protein complexes suggested that the availability of the photosystem II antenna protein CP47 is a limiting factor for the photosystem II assembly in the gun4 mutant.http://www.bibsonomy.org/bibtex/2a7fcf4b35f040ba8951cd0f2fed64713/microbiomicrobio2008-08-08T13:46:10+02:00cyanobacteria expression iron_stress light_harvesting redox_stress regulation_of_gene <span class="authorEditorList"><a href="/author/Duehring">U. Duehring</a>, <a href="/author/Axmann">Im Axmann</a>, <a href="/author/Hess">W. R. Hess</a>, and <a href="/author/Wilde">A. Wilde</a> </span><em>PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA</em> <em>103(18):7054-7058</em> (<em>2006</em>)Fri Aug 08 13:46:10 CEST 2008PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA187054-7058An internal antisense RNA regulates expression of the photosynthesis gene isiA1032006cyanobacteria expression iron_stress light_harvesting redox_stress regulation_of_gene Small regulatory noncoding RNAs exist in both eukaryotic and prokaryotic organisms. Most of these RNA transcripts are transencoded RNAs with short and only partial antisense complementarity to their target RNAs, which regulate gene expression by modifying mRNA stability and translation. In contrast, reports on the function of cis-encoded, perfectly complementary antisense RNAs in eubacteria are rare. Cyanobacteria respond to iron deficiency by expressing IsiA (iron stress-induced protein A), which forms a giant ring structure around photosystem I. Here, we show that this process is controlled by IsrR (iron stress-repressed RNA), a cis-encoded antisense RNA transcribed from the isiA noncoding strand. Artificial overexpression of IsrR under iron stress causes a strongly diminished number of IsiA-photosystem I supercomplexes, whereas IsrR depletion results in premature expression of IsiA. The coupled degradation of IsrR/isiA mRNA duplexes appears to be a reversible switch that can respond to environmental changes. IsrR is the only RNA known so far to regulate a photosynthesis component.http://www.bibsonomy.org/bibtex/24416df445cea52104905722029172e49/microbiomicrobio2008-07-15T11:10:10+02:00IFZ circadian_clock cyanobacteria networks robustness systems_biology <span class="authorEditorList"><a href="/author/Clodong">Sebastien Clodong</a>, <a href="/author/Duehring">Ulf Duehring</a>, <a href="/author/Kronk">Luiza Kronk</a>, <a href="/author/Wilde">Annegret Wilde</a>, <a href="/author/Axmann">Ilka Axmann</a>, <a href="/author/Herzel">Hanspeter Herzel</a>, and <a href="/author/Kollmann">Markus Kollmann</a> </span><em>MOLECULAR SYSTEMS BIOLOGY</em> (<em>2007</em>)Tue Jul 15 11:10:10 CEST 2008MOLECULAR SYSTEMS BIOLOGYFunctioning and robustness of a bacterial circadian clock32007IFZ circadian_clock cyanobacteria networks robustness systems_biology Cyanobacteria are the simplest known cellular systems that regulate their biological activities in daily cycles. For the cyanobacterium Synechococcus elongatus, it has been shown by in vitro and in vivo experiments that the basic circadian timing process is based on rhythmic phosphorylation of KaiC hexamers. Despite the excellent experimental work, a full systems level understanding of the in vitro clock is still lacking. In this work, we provide a mathematical approach to scan different hypothetical mechanisms for the primary circadian oscillator, starting from experimentally established molecular properties of the clock proteins. Although optimised for highest performance, only one of the in silico-generated reaction networks was able to reproduce the experimentally found high amplitude and robustness against perturbations. In this reaction network, a negative feedback synchronises the phosphorylation level of the individual hexamers and has indeed been realised in S. elongatus by KaiA sequestration as confirmed by experiments.http://www.bibsonomy.org/bibtex/23dcea2360c114b92e714eb362e66634e/microbiomicrobio2008-07-15T11:10:10+02:00IFZ imported <span class="authorEditorList"><a href="/author/Duehring">Ulf Duehring</a>, <a href="/author/Ossenbuehl">Friedrich Ossenbuehl</a>, and <a href="/author/Wilde">Annegret Wilde</a> </span><em>JOURNAL OF BIOLOGICAL CHEMISTRY</em> <em>282(15):10915-10921</em> (<em>2007</em>)Tue Jul 15 11:10:10 CEST 2008JOURNAL OF BIOLOGICAL CHEMISTRY1510915-10921Late assembly steps and dynamics of the cyanobacterial photosystem I2822007IFZ imported The dynamics of photosystem I assembly in cyanobacteria have been addressed using in vivo pulse-chase labeling of Synechocystis sp. PCC 6803 proteins in combination with blue native polyacrylamide gel electrophoresis. The analyses indicate the existence of three different monomeric photosystem I complexes and also the high stability of photosystem I trimers. We show that in addition to a complete photosystem I monomer, containing all 11 subunits, we detected a PsaK-less monomer and a short-lived PsaL/PsaK-less complex. The latter two monomers were missing in the ycf37 mutant of Synechocystis sp. PCC 6803 that accumulates also less trimers. Pulse-chase experiments suggest that the three monomeric complexes have different functions in the biogenesis of the trimer. Based on these findings we propose a model where PsaK is incorporated in the latest step of photosystem I assembly. The PsaK-less photosystem I monomer may represent an intermediate complex that is important for the exchange of the two PsaK variants during high light acclimation. Implications of the presented data with respect to Ycf37 function are discussed.http://www.bibsonomy.org/bibtex/26435a761a1819f0d00a48daf8ae39150/microbiomicrobio2008-07-15T11:10:10+02:00IFZ imported <span class="authorEditorList"><a href="/author/Wilson">Adjele Wilson</a>, <a href="/author/Boulay">Clemence Boulay</a>, <a href="/author/Wilde">Annegret Wilde</a>, <a href="/author/Kerfeld">Cheryl A. Kerfeld</a>, and <a href="/author/Kirilovsky">Diana Kirilovsky</a> </span><em>PLANT CELL</em> <em>19(2):656-672</em> (<em>2007</em>)Tue Jul 15 11:10:10 CEST 2008PLANT CELL2656-672Light-induced energy dissipation in iron-starved cyanobacteria: Roles of OCP and IsiA proteins192007IFZ imported In response to iron deficiency, cyanobacteria synthesize the iron stress-induced chlorophyll binding protein IsiA. This protein protects cyanobacterial cells against iron stress. It has been proposed that the protective role of IsiA is related to a blue light-induced nonphotochemical fluorescence quenching (NPQ) mechanism. In iron-replete cyanobacterial cell cultures, strong blue light is known to induce a mechanism that dissipates excess absorbed energy in the phycobilisome, the extramembranal antenna of cyanobacteria. In this photoprotective mechanism, the soluble Orange Carotenoid Protein (OCP) plays an essential role. Here, we demonstrate that in iron-starved cells, blue light is unable to quench fluorescence in the absence of the phycobilisomes or the OCP. By contrast, the absence of IsiA does not affect the induction of fluorescence quenching or its recovery. We conclude that in cyanobacteria grown under iron starvation conditions, the blue light-induced nonphotochemical quenching involves the phycobilisome OCP-related energy dissipation mechanism and not IsiA. IsiA, however, does seem to protect the cells from the stress generated by iron starvation, initially by increasing the size of the photosystem I antenna. Subsequently, the IsiA converts the excess energy absorbed by the phycobilisomes into heat through a mechanism different from the dynamic and reversible light-induced NPQ processes.