Publications by authors named "Jens Georg"

Article Synopsis
  • * Analysis of protein interactions revealed that Ssr1238 binds mainly to RNase P RNA and its associated protein RnpA, as well as other transcripts linked to cell division and RNA maturation.
  • * The findings suggest that Ssr1238 plays a crucial role in coordinating RNA processes and nitrogen metabolism, potentially expanding the known functions of similar proteins in cyanobacteria.
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All organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) are an important aspect of the regulation network underlying the adaptation to such changes. sRNAs base-pair with their target mRNAs, allowing rapid modulation of the proteome.

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The hydrogen peroxide-induced small RNA OxyS has been proposed to originate from the 3' UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions indicate that most OxyS targets belong to the category of "cell cycle," including cell division and cell elongation. Previously, we reported that OxyS inhibits cell division by repressing expression of the essential transcription termination factor , thereby leading to the expression of the KilR protein, which interferes with the function of the major cell division protein, FtsZ.

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We used stochastic simulations and experimental data from E. coli, K. aerogenes, Synechococcus PCC 7002 and Synechocystis PCC 6803 to provide evidence that transcriptional interference via the collision mechanism is likely a prevalent mechanism for bacterial gene regulation.

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Synthetic small RNAs (sRNAs) are gaining increasing attention in the field of synthetic biology and bioengineering for efficient post-transcriptional regulation of gene expression. However, the optimal design of synthetic sRNAs is challenging because alterations may impair functions or off-target effects can arise. Here, we introduce DIGGER-Bac, a toolbox for Design and Identification of seed regions for Golden Gate assembly and Expression of synthetic sRNAs in Bacteria.

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Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as , feedback-regulate RNase E expression via the 5'-untranslated region (5' UTR) in .

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Article Synopsis
  • * Key to this field is the regulation of protein production at various levels, where researchers prefer to manipulate mRNA because it's easier for translation control.
  • * The development of a "plug and play" plasmid toolset allows for the quick creation and testing of synthetic small regulatory RNAs (sRNAs), which can enhance understanding of sRNA functions and their potential applications in bacteria.
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FF ATP synthases produce ATP, the universal biological energy source. ATP synthase complexes on cyanobacterial thylakoid membranes use proton gradients generated either by photosynthesis or respiration. AtpΘ is an ATP synthase regulator in cyanobacteria which is encoded by the gene .

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Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data.

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DnaA is the initiator protein of chromosome replication, but the regulation of its homoeostasis in enterobacteria is not well understood. The DnaA level remains stable at different growth rates, suggesting a link between metabolism and expression. In a bioinformatic prediction, which we made to unravel targets of the sRNA rnTrpL in , the mRNA was the most conserved target candidate.

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NsiR3 (nitrogen stress-inducible RNA 3) is a small noncoding RNA strongly conserved in heterocyst-forming cyanobacteria. In Nostoc sp. PCC 7120, transcription of NsiR3 is induced by nitrogen starvation and depends on the global nitrogen regulator NtcA.

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Motivation: The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is frequently challenging due to the short length and distinct heterogeneity of such homologs. GLobal Automatic Small RNA Search go (GLASSgo) is an efficient tool for the prediction of sRNA homologs from a single input query. To make the algorithm available to a broader community, we offer a Docker container along with a free-access web service.

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Trans-acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post-transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity.

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The membrane-embedded FtsH proteases found in bacteria, chloroplasts, and mitochondria are involved in diverse cellular processes including protein quality control and regulation. The genome of the model cyanobacterium sp PCC 6803 encodes four FtsH homologs designated FtsH1 to FtsH4. The FtsH3 homolog is present in two hetero-oligomeric complexes: FtsH2/3, which is responsible for photosystem II quality control, and the essential FtsH1/3 complex, which helps maintain Fe homeostasis by regulating the level of the transcription factor Fur.

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DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift.

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Article Synopsis
  • Oxygenic photosynthesis in cyanobacteria involves the transcription factor RpaB, which is conserved across a billion years of evolution and plays a key role in coordinating responses to environmental stimuli.
  • Research focusing on the cyanobacterium Synechocystis identified over 150 target promoters regulated by RpaB in response to varying light conditions, revealing distinct mechanisms for repression and activation.
  • RpaB is linked to genes that facilitate photoprotection, cyclic electron flow, and other essential functions, indicating its critical role as a versatile regulator in photosynthesis.
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Nitrogen is frequently limiting microbial growth in the environment. As a response, many filamentous cyanobacteria differentiate heterocysts, cells devoted to N fixation. Heterocyst differentiation is under the control of the master regulator HetR.

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Background: Cyanobacteria have shown promising potential for the production of various biofuels and chemical feedstocks. UTEX 2973 is a fast-growing strain with pronounced tolerance to high temperatures and illumination. Hence, this strain appears to be ideal for the development of photosynthetic biotechnology.

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Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be -acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units.

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The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods.

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Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of gene expression. The functional and evolutionary characterization of sRNAs requires the identification of homologs, which is frequently challenging due to their heterogeneity, short length and partly, little sequence conservation. We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to identify sRNA homologs in complex genomic databases starting from a single sequence.

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Computational methods can often facilitate the functional characterization of individual sRNAs and furthermore allow high-throughput analysis on large numbers of sRNA candidates. This chapter outlines a potential workflow for computational sRNA analyses and describes in detail methods for homolog detection, target prediction, and functional characterization based on enrichment analysis. The cyanobacterial sRNA IsaR1 is used as a specific example.

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To maintain genome integrity, organisms employ DNA damage response, the underlying principles of which are conserved from bacteria to humans. The bacterial small RNA OxyS of is induced upon oxidative stress and has been implicated in protecting cells from DNA damage; however, the mechanism by which OxyS confers genome stability remained unknown. Here, we revealed an OxyS-induced molecular checkpoint relay, leading to temporary cell cycle arrest to allow damage repair.

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Background: The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles.

Results: Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation.

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Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria.

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