@phdthesis{Makower2016,
  author    = {Makower, Katharina},
  title     = {The roles of secondary metabolites in microcystis inter-strain interactions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93916},
  school      = {Universit{\"a}t Potsdam},
  pages     = {X, 131},
  year      = {2016},
  abstract  = {Among the bloom-forming and potentially harmful cyanobacteria, the genus Microcystis represents a most diverse taxon, on the genomic as well as on morphological and secondary metabolite levels. Microcystis communities are composed of a variety of diversified strains. The focus of this study lies on potential interactions between Microcystis representatives and the roles of secondary metabolites in these interaction processes. The role of secondary metabolites functioning as signaling molecules in the investigated interactions is demonstrated exemplary for the prevalent hepatotoxin microcystin. The extracellular and intracellular roles of microcystin are tested in microarray-based transcriptomic approaches. While an extracellular effect of microcystin on Microcystis transcription is confirmed and connected to a specific gene cluster of another secondary metabolite in this study, the intracellularly occurring microcystin is related with several pathways of the primary metabolism. A clear correlation of a microcystin knockout and the SigE-mediated regulation of carbon metabolism is found. According to the acquired transcriptional data, a model is proposed that postulates the regulating effect of microcystin on transcriptional regulators such as the alternative sigma factor SigE, which in return captures an essential role in sugar catabolism and redox-state regulation. For the purpose of simulating community conditions as found in the field, Microcystis colonies are isolated from the eutrophic lakes near Potsdam, Germany and established as stably growing under laboratory conditions. In co-habitation simulations, the recently isolated field strain FS2 is shown to specifically induce nearly immediate aggregation reactions in the axenic lab strain Microcystis aeruginosa PCC 7806. In transcriptional studies via microarrays, the induced expression program in PCC 7806 after aggregation induction is shown to involve the reorganization of cell envelope structures, a highly altered nutrient uptake balance and the reorientation of the aggregating cells to a heterotrophic carbon utilization, e.g. via glycolysis. These transcriptional changes are discussed as mechanisms of niche adaptation and acclimation in order to prevent competition for resources.},
  language  = {en}
}
@article{CalderanRodriguesLuzarowskiMonteBelloetal.2021,
  author    = {Calderan-Rodrigues, Maria Juliana and Luzarowski, Marcin and Monte-Bello, Carolina Cassano and Minen, Romina Ines and Z{\"u}hlke, Boris M. and Nikoloski, Zoran and Skirycz, Aleksandra and Caldana, Camila},
  title     = {Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana},
  series = {Frontiers in plant science : FPLS},
  volume    = {12},
  journal   = {Frontiers in plant science : FPLS},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2021.758933},
  pages     = {15},
  year      = {2021},
  abstract  = {As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.},
  language  = {en}
}
@article{DunsingPetrichChiantia2021,
  author    = {Dunsing, Valentin and Petrich, Annett and Chiantia, Salvatore},
  title     = {Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection},
  series = {eLife},
  volume    = {10},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.69687},
  pages     = {33},
  year      = {2021},
  abstract  = {Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.},
  language  = {en}
}
@article{GarciaBuckHamiltonetal.2018,
  author    = {Garcia, Sarahi L. and Buck, Moritz and Hamilton, Joshua J. and Wurzbacher, Christian and Grossart, Hans-Peter and McMahon, Katherine D. and Eiler, Alexander},
  title     = {Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria},
  series = {mSphere},
  volume    = {3},
  journal   = {mSphere},
  number    = {3},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {2379-5042},
  doi       = {10.1128/mSphere.00202-18},
  pages     = {8},
  year      = {2018},
  abstract  = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.},
  language  = {en}
}
@article{GarciaBuckMcMahonetal.2015,
  author    = {Garcia, Sarahi L. and Buck, Moritz and McMahon, Katherine D. and Grossart, Hans-Peter and Eiler, Alexander and Warnecke, Falk},
  title     = {Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community},
  series = {Molecular ecology},
  volume    = {24},
  journal   = {Molecular ecology},
  number    = {17},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.13319},
  pages     = {4449 -- 4459},
  year      = {2015},
  abstract  = {Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.},
  language  = {en}
}
@article{BapolisiKielbBekiretal.2022,
  author    = {Bapolisi, Alain Murhimalika and Kielb, Patrycja and Bekir, Marek and Lehnen, Anne-Catherine and Radon, Christin and Laroque, Sophie and Wendler, Petra and M{\"u}ller-Werkmeister, Henrike and Hartlieb, Matthias},
  title     = {Antimicrobial polymers of linear and bottlebrush architecture},
  series = {Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation},
  volume    = {43},
  journal   = {Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation},
  number    = {19},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1521-3927},
  doi       = {10.1002/marc.202200288},
  pages     = {14},
  year      = {2022},
  abstract  = {Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.},
  language  = {en}
}