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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 01 February 2011, Vol.108(5), pp.2124-9
    Description: There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5' annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.
    Keywords: Transcription, Genetic ; Synechocystis -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2011, Vol.108(5), pp.2124-2129
    Description: There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ~64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5' annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research. ; Includes references ; p. 2124-2129.
    Keywords: Transcription (Genetics) -- Physiological Aspects ; Cyanobacteria -- Genetic Aspects ; Genetic Regulation -- Research ; Rna Polymerases -- Properties;
    ISSN: 0027-8424
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  • 3
    In: Molecular Microbiology, May 2014, Vol.92(4), pp.840-852
    Description: The bacterial ‐binding protein functions in post‐transcriptional regulation of gene expression. There is evidence in a range of bacteria for specific subcellular localization of ; however, the mechanism and role of localization remain unclear. Cyanobacteria harbour a subfamily of that is structurally conserved but exhibits divergent binding sites. Mutational analysis in the cyanobacterium sp. 6803 revealed that several conserved amino acids on the proximal side of the hexamer are crucial not only for ‐dependent accumulation but also for phototaxis, the latter of which depends on type pili. Co‐immunoprecipitation and yeast two‐hybrid analysis show that the secretion 1 (a component of the type pilus base) is an interaction partner of . Fluorescence microscopy revealed that is localized to the cytoplasmic membrane in a 1‐dependent manner. Concomitantly, ‐dependent accumulation is abrogated in a Δ mutant, indicating that localization to the pilus base via interaction with PilB1 is essential for function in cyanobacteria.
    Keywords: Protein Binding – Analysis ; RNA – Analysis;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 4
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    Description: Presentation I gave at the ESF conference 'Biology of Plastids - Towards a Blueprint for Synthetic Organelles' in 2014 in Pultusk, Poland. It was right after the kick-off of my participation in the EU-funded Ribonets project at the Institute for Synthetic Microbiology (@synmibi) in Düsseldorf....
    Keywords: Synthetic Biology
    Source: DataCite
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  • 5
    Video
    Video
    Figshare
    Description: Presentation I gave at the ESF conference 'Biology of Plastids - Towards a Blueprint for Synthetic Organelles' in 2014 in Pultusk, Poland. It was right after the kick-off of my participation in the EU-funded Ribonets project at the Institute for Synthetic Microbiology (@synmibi) in Düsseldorf....
    Keywords: Synthetic Biology
    Source: DataCite
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  • 6
    Description: A presentation I gave during my visit at the Terauchi lab at Ritsumeikan University, Japan, in June 2017....
    Keywords: Microbiology ; Molecular Biology
    Source: DataCite
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  • 7
    Description: A presentation I gave during my visit at the Terauchi lab at Ritsumeikan University, Japan, in June 2017....
    Keywords: Microbiology ; Molecular Biology
    Source: DataCite
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  • 8
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(12), p.e0189816
    Description: Cyclic triterpenes constitute one of the most diverse groups of plant natural products. Besides the intriguing biochemistry of their biosynthetic pathways, plant triterpenes exhibit versatile bioactivities, including antimicrobial effects against plant and human pathogens. While prokaryotes have been extensively used for the heterologous production of other classes of terpenes, the synthesis of cyclic triterpenes, which inherently includes the two-step catalytic formation of the universal linear precursor 2,3-oxidosqualene, is still a major challenge. We thus explored the suitability of the metabolically versatile photosynthetic α-proteobacterium Rhodobacter capsulatus SB1003 and cyanobacterium Synechocystis sp. PCC 6803 as alternative hosts for biosynthesis of cyclic plant triterpenes. Therefore, 2,3-oxidosqualene production was implemented and subsequently combined with different cyclization reactions catalyzed by the representative oxidosqualene cyclases CAS1 (cycloartenol synthase), LUP1 (lupeol synthase), THAS1 (thalianol synthase) and MRN1 (marneral synthase) derived from model plant Arabidopsis thaliana. While successful accumulation of 2,3-oxidosqualene could be detected by LC-MS analysis in both hosts, cyclase expression resulted in differential production profiles. CAS1 catalyzed conversion to only cycloartenol, but expression of LUP1 yielded lupeol and a triterpenoid matching an oxidation product of lupeol, in both hosts. In contrast, THAS1 expression did not lead to cyclic product formation in either host, whereas MRN1-dependent production of marnerol and hydroxymarnerol was observed in Synechocystis but not in R. capsulatus. Our findings thus indicate that 2,3-oxidosqualene cyclization in heterologous phototrophic bacteria is basically feasible but efficient conversion depends on both the respective cyclase enzyme and individual host properties. Therefore, photosynthetic α-proteo- and cyanobacteria are promising alternative candidates for providing new bacterial access to the broad class of triterpenes for biotechnological applications.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: BMC Microbiology, 2017, Vol. 17
    Description: 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 (Delta ssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in Delta ssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping s factor SigA, concurrently supporting dissociation of group 2 s factors during recovery from nitrogen starvation.Conclusions: The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 s factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria.
    Keywords: Transcriptional Regulation ; Small Rna ; S Factor ; Rna Polymerase ; Cyanobacteria ; Natural Sciences ; Biological Sciences ; Microbiology ; Naturvetenskap ; Biologiska Vetenskaper ; Mikrobiologi
    ISSN: 1471-2180
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  • 10
    Language: English
    In: Biotechnology for biofuels, 06 February 2014, Vol.7(1), pp.21
    Description: The production of biofuels in photosynthetic microalgae and cyanobacteria is a promising alternative to the generation of fuels from fossil resources. To be economically competitive, producer strains need to be established that synthesize the targeted product at high yield and over a long time. Engineering cyanobacteria into forced fuel producers should considerably interfere with overall cell homeostasis, which in turn might counteract productivity and sustainability of the process. Therefore, in-depth characterization of the cellular response upon long-term production is of high interest for the targeted improvement of a desired strain. The transcriptome-wide response to continuous ethanol production was examined in Synechocystis sp. PCC6803 using high resolution microarrays. In two independent experiments, ethanol production rates of 0.0338% (v/v) ethanol d-1 and 0.0303% (v/v) ethanol d-1 were obtained over 18 consecutive days, measuring two sets of biological triplicates in fully automated photobioreactors. Ethanol production caused a significant (~40%) delay in biomass accumulation, the development of a bleaching phenotype and a down-regulation of light harvesting capacity. However, microarray analyses performed at day 4, 7, 11 and 18 of the experiment revealed only three mRNAs with a strongly modified accumulation level throughout the course of the experiment. In addition to the overexpressed adhA (slr1192) gene, this was an approximately 4 fold reduction in cpcB (sll1577) and 3 to 6 fold increase in rps8 (sll1809) mRNA levels. Much weaker modifications of expression level or modifications restricted to day 18 of the experiment were observed for genes involved in carbon assimilation (Ribulose bisphosphate carboxylase and Glutamate decarboxylase). Molecular analysis of the reduced cpcB levels revealed a post-transcriptional processing of the cpcBA operon mRNA leaving a truncated mRNA cpcA* likely not competent for translation. Moreover, western blots and zinc-enhanced bilin fluorescence blots confirmed a severe reduction in the amounts of both phycocyanin subunits, explaining the cause of the bleaching phenotype. Changes in gene expression upon induction of long-term ethanol production in Synechocystis sp. PCC6803 are highly specific. In particular, we did not observe a comprehensive stress response as might have been expected.
    Keywords: Chromosomes ; Ethanol Fuels ; Gene Expression;
    ISSN: 1754-6834
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