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Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities [article]

Elena Butaite, Jos Kramer, Stefan Wyder, Rolf Kuemmerli
2018 bioRxiv   pre-print
Many bacteria rely on the secretion of siderophores to scavenge iron from the environment. Laboratory studies revealed that abiotic and biotic factors together determine how much siderophores bacteria make, and whether siderophores can be exploited by non-producing cheaters or be deployed by producers to inhibit competitors. Here, we explore whether these insights apply to natural communities, by comparing the production of the siderophore pyoverdine among 930 Pseudomonas strains from 48 soil
more » ... d pond communities. We found that pH, iron content, carbon concentration, and community diversity determine pyoverdine production levels, and the extent to which strains are either stimulated or inhibited by heterologous (non-self) pyoverdines. While pyoverdine non-producers occurred in both habitats, their prevalence was higher in soils. Environmental and genetic analysis suggest that non-producers can evolve as cheaters, exploiting heterologous pyoverdine, but also due to pyoverdine disuse in environments with increased iron availability. Overall, we found that environmental factors explained between-strain variation in pyoverdine production much better in soils than in ponds, presumably because high strain mixing in ponds prevents local adaption. Our study sheds light on the complexity of natural bacterial communities, and provides first insights into the multivariate nature of siderophore-based iron acquisition and competition among environmental pseudomonads.
doi:10.1101/263004 fatcat:fs75vi43fnbaxa3vi5hkr7ejte

Quantification of ortholog losses in insects and vertebrates

Stefan Wyder, Evgenia V Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M Zdobnov
2007 Genome Biology  
Click here for file Genome Biology 2007, Volume 8, Issue 11, Article R242 Wyder et al. R242.4 Genome Biology 2007, Volume 8, Issue 11, Article R242 Wyder et al.  ...  R242.6 Genome Biology 2007, Volume 8, Issue 11, Article R242 Wyder et al. R242.10  ... 
doi:10.1186/gb-2007-8-11-r242 pmid:18021399 pmcid:PMC2258195 fatcat:5ayh3l26i5givb7ilnnhnlpx24

Probing the evolutionary robustness of two repurposed drugs targeting iron uptake in Pseudomonas aeruginosa [article]

Chiara Rezzoagli, David Wilson, Michael Weigert, Stefan Wyder, Rolf Kuemmerli
2017 bioRxiv   pre-print
Treatments that inhibit the expression or functioning of bacterial virulence factors hold great promise to be both effective and exert weaker selection for resistance than conventional antibiotics. However, the evolutionary robustness argument, based on the idea that anti-virulence treatments disarm rather than kill pathogens, is controversial. Here we probe the evolutionary robustness of two repurposed drugs, gallium and flucytosine, targeting the iron-scavenging pyoverdine of the
more » ... human pathogen Pseudomonas aeruginosa. We subjected replicated cultures of bacteria to two concentrations of each drug for 20 consecutive days in human serum as an ex-vivo infection model. We screened evolved populations and clones for resistance phenotypes, including the restoration of growth and pyoverdine production, and the evolution of iron uptake by-passing mechanisms. We whole-genome sequenced evolved clones to identify the genetic basis of resistance. We found that mutants resistant against anti-virulence treatments readily arose, but their selective spreading varied between treatments. Flucytosine resistance quickly spread in all populations due to disruptive mutations in upp, a gene encoding an enzyme required for flucytosine activation. Conversely, resistance against gallium arose only sporadically, and was based on mutations in transcriptional regulators, upregulating pyocyanin production, a redox-active molecule promoting siderophore-independent iron acquisition. The spread of gallium resistance could be hampered because pyocyanin-mediated iron delivery benefits resistant and susceptible cells alike. Our work highlights that anti-virulence treatments are not evolutionarily robust per se. Instead, evolutionary robustness is a relative measure, with specific treatments occupying different positions on a continuous scale.
doi:10.1101/195974 fatcat:v7ta5cegkffdnktibmlwxagh6e

The FgfrL1 receptor is required for development of slow muscle fibers

Ruth Amann, Stefan Wyder, Anne M. Slavotinek, Beat Trueb
2014 Developmental Biology  
FgfrL1, which interacts with Fgf ligands and heparin, is a member of the fibroblast growth factor receptor (Fgfr) family. FgfrL1-deficient mice show two significant alterations when compared to wildtype mice: They die at birth due to a malformed diaphragm and they lack metanephric kidneys. Utilizing gene arrays, qPCR and in situ hybridization we show here that the diaphragm of FgfrL1 knockout animals lacks any slow muscle fibers at E18.5 as indicated by the absence of slow fiber markers Myh7,
more » ... l2 and Myl3. Similar lesions are also found in other skeletal muscles that contain a high proportion of slow fibers at birth, such as the extraocular muscles. In contrast to the slow fibers, fast fibers do not appear to be affected as shown by expression of fast fiber markers Myh3, Myh8, Myl1 and MylPF. At early developmental stages (E10.5, E15.5), FgfrL1-deficient animals express slow fiber genes at normal levels. The loss of slow fibers cannot be attributed to the lack of kidneys, since Wnt4 knockout mice, which also lack metanephric kidneys, show normal expression of Myh7, Myl2 and Myl3. Thus, FgfrL1 is specifically required for embryonic development of slow muscle fibers.
doi:10.1016/j.ydbio.2014.08.016 pmid:25172430 fatcat:fvenri6m7zgltd53mopeccr32q

Propionibacterium spp. and Acidipropionibacterium spp [chapter]

Meral Turgay, Hans-Peter Bachmann, Stefan Irmler, Ueli von Ah, Marie-Therese Fröhlich-Wyder, Hélène Falentin, Stéphanie-Marie Deutsch, Gwénaël Jan, Anne Thierry
2020 Reference Module in Food Science  
doi:10.1016/b978-0-08-100596-5.23016-3 fatcat:o2jje4lax5agniwbv3uftuvi6u

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets [article]

Stefan Wyder, Michael T Raissig, Ueli Grossniklaus
2017 bioRxiv   pre-print
Genomic imprinting leads to different expression levels of maternally and paternally derived alleles. Over the last years, major progress has been made in identifying novel imprinted candidate genes in plants, owing to affordable next-generation sequencing technologies. However, reports on sequencing the transcriptome of hybrid F1 seed tissues strongly disagree about how many and which genes are imprinted. This raises questions about the relative impact of biological, environmental, technical,
more » ... nd analytic differences or biases. Here, we adopt a statistical approach, frequently used in RNA-seq data analysis, which properly models count overdispersion and considers replicate information of reciprocal crosses. We show that our statistical pipeline outperforms other methods in identifying imprinted genes in simulated and real data. Accordingly, reanalysis of genome-wide imprinting studies in Arabidopsis and maize shows that, at least for the Arabidopsis dataset, an increased agreement across datasets can be observed. For maize, however, consistent reanalysis did not yield in a larger overlap between the datasets. This suggests that the discrepancy across publications might be partially due to different analysis pipelines but that technical, biological, and environmental factors underlie much of the discrepancy between datasets. Finally, we show that the set of genes that can be characterized regarding allelic bias by all studies with minimal confidence is small (~8,000/27,416 genes for Arabidopsis and ~12,000/39,469 for maize). In conclusion, we propose to use biologically replicated reciprocal crosses, high sequence coverage, and a generalized linear model approach to identify differentially expressed alleles in developing seeds.
doi:10.1101/180745 fatcat:e22iszt6rnhippued6fg6z33ee

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates

Toshiaki Matsui, Toshiyuki Yamamoto, Stefan Wyder, Evgeny M Zdobnov, Tatsuhiko Kadowaki
2009 BMC Genomics  
Large-scale comparison of metazoan genomes has revealed that a significant fraction of genes of the last common ancestor of Bilateria (Urbilateria) is lost in each animal lineage. This event could be one of the underlying mechanisms involved in generating metazoan diversity. However, the present functions of these ancient genes have not been addressed extensively. To understand the functions and evolutionary mechanisms of such ancient Urbilaterian genes, we carried out comprehensive expression
more » ... rofile analysis of genes shared between vertebrates and honey bees but not with the other sequenced ecdysozoan genomes (honey bee-vertebrate specific, HVS genes) as a model. We identified 30 honey bee and 55 mouse HVS genes. Many HVS genes exhibited tissue-selective expression patterns; intriguingly, the expression of 60% of honey bee HVS genes was found to be brain enriched, and 24% of mouse HVS genes were highly expressed in either or both the brain and testis. Moreover, a minimum of 38% of mouse HVS genes demonstrated neuron-enriched expression patterns, and 62% of them exhibited expression in selective brain areas, particularly the forebrain and cerebellum. Furthermore, gene ontology (GO) analysis of HVS genes predicted that 35% of genes are associated with DNA transcription and RNA processing. These results suggest that HVS genes include genes that are biased towards expression in the brain and gonads. They also demonstrate that at least some of Urbilaterian genes retained in the specific animal lineage may be selectively maintained to support the species-specific phenotypes.
doi:10.1186/1471-2164-10-17 pmid:19138430 pmcid:PMC2656531 fatcat:4dbylogbyrbd7m23zepf54226e

Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities

Elena Butaitė, Michael Baumgartner, Stefan Wyder, Rolf Kümmerli
2017 Nature Communications  
All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and
more » ... d communities of Pseudomonas bacteria. We find that pyoverdine non-and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from nonproducers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities.
doi:10.1038/s41467-017-00509-4 pmid:28871205 pmcid:PMC5583256 fatcat:dswd3wye2nctxo4rt6wiwkg74i

RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression

Violeta Spaniol, Stefan Wyder, Christoph Aebi, Yung-Fu Chang
2013 PLoS ONE  
Moraxella catarrhalis, a major nasopharyngeal pathogen of the human respiratory tract, is exposed to rapid downshifts of environmental temperature when humans breathe cold air. The prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis is greatest in winter. We investigated how M. catarrhalis uses the physiologic exposure to cold air to regulate pivotal survival systems that may contribute to M. catarrhalis virulence. Results: In this study we used the
more » ... A-seq techniques to quantitatively catalogue the transcriptome of M. catarrhalis exposed to a 26uC cold shock or to continuous growth at 37uC. Validation of RNA-seq data using quantitative RT-PCR analysis demonstrated the RNA-seq results to be highly reliable. We observed that a 26uC cold shock induces the expression of genes that in other bacteria have been related to virulence a strong induction was observed for genes involved in high affinity phosphate transport and iron acquisition, indicating that M. catarrhalis makes a better use of both phosphate and iron resources after exposure to cold shock. We detected the induction of genes involved in nitrogen metabolism, as well as several outer membrane proteins, including ompA, m35-like porin and multidrug efflux pump (acrAB) indicating that M. catarrhalis remodels its membrane components in response to downshift of temperature. Furthermore, we demonstrate that a 26uC cold shock enhances the induction of genes encoding the type IV pili that are essential for natural transformation, and increases the genetic competence of M. catarrhalis, which may facilitate the rapid spread and acquisition of novel virulence-associated genes. Conclusion: Cold shock at a physiologically relevant temperature of 26uC induces in M. catarrhalis a complex of adaptive mechanisms that could convey novel pathogenic functions and may contribute to enhanced colonization and virulence.
doi:10.1371/journal.pone.0068298 pmid:23844181 pmcid:PMC3699543 fatcat:iodisly4b5arhc34bi2uvscyom

Fate of polydnavirus DNA of the egg–larval parasitoid Chelonus inanitus in the host Spodoptera littoralis

Stefan Wyder, Fabian Blank, Beatrice Lanzrein
2003 Journal of insect physiology  
CiV12 and CiV16.8 probes were from non-coding regions (Wyder et al., 2002) .  ...  In addition, viral probes were situated outside the coding regions (Wyder et al., 2002) .  ... 
doi:10.1016/s0022-1910(03)00056-8 pmid:12770628 fatcat:x3xyyc7ycrccjmhvuaolvz4rvm

Clostridium perfringens Beta-Toxin Induces Necrostatin-Inhibitable, Calpain-Dependent Necrosis in Primary Porcine Endothelial Cells

Delphine Autheman, Marianne Wyder, Michel Popoff, Katharina D'Herde, Stephan Christen, Horst Posthaus, Stefan Bereswill
2013 PLoS ONE  
Clostridium perfringens b-toxin (CPB) is a b-barrel pore-forming toxin and an essential virulence factor of C. perfringens type C strains, which cause fatal hemorrhagic enteritis in animals and humans. We have previously shown that CPB is bound to endothelial cells within the intestine of affected pigs and humans, and that CPB is highly toxic to primary porcine endothelial cells (pEC) in vitro. The objective of the present study was to investigate the type of cell death induced by CPB in these
more » ... ells, and to study potential host cell mechanisms involved in this process. CPB rapidly induced lactate dehydrogenase (LDH) release, propidium iodide uptake, ATP depletion, potassium efflux, a marked rise in intracellular calcium [Ca 2+ ] i , release of high-mobility group protein B1 (HMGB1), and caused ultrastructural changes characteristic of necrotic cell death. Despite a certain level of caspase-3 activation, no appreciable DNA fragmentation was detected. CPB-induced LDH release and propidium iodide uptake were inhibited by necrostatin-1 and the two dissimilar calpain inhibitors PD150606 and calpeptin. Likewise, inhibition of potassium efflux, chelation of intracellular calcium and treatment of pEC with cyclosporin A also significantly inhibited CPB-induced LDH release. Our results demonstrate that rCPB primarily induces necrotic cell death in pEC, and that necrotic cell death is not merely a passive event caused by toxin-induced membrane disruption, but is propagated by host cell-dependent biochemical pathways activated by the rise in intracellular calcium and inhibitable by necrostatin-1, consistent with the emerging concept of programmed necrosis ("necroptosis").
doi:10.1371/journal.pone.0064644 pmid:23734212 pmcid:PMC3667183 fatcat:pkxt7dpnabegdivqgfcwhfr544

Probing the evolutionary robustness of two repurposed drugs targeting iron uptake in Pseudomonas aeruginosa

Chiara Rezzoagli, David Wilson, Michael Weigert, Stefan Wyder, Rolf Kümmerli
2018 Evolution, Medicine and Public Health  
We probed the evolutionary robustness of two antivirulence drugs, gallium and flucytosine, targeting the iron-scavenging pyoverdine in the opportunistic pathogen Pseudomonas aeruginosa. Using an experimental evolution approach in human serum, we showed that antivirulence treatments are not evolutionarily robust per se, but vary in their propensity to select for resistance. Treatments that inhibit the expression or functioning of bacterial virulence factors hold great promise to be both
more » ... and exert weaker selection for resistance than conventional antibiotics. However, the evolutionary robustness argument, based on the idea that antivirulence treatments disarm rather than kill pathogens, is controversial. Here, we probe the evolutionary robustness of two repurposed drugs, gallium and flucytosine, targeting the iron-scavenging pyoverdine of the opportunistic human pathogen Pseudomonas aeruginosa. We subjected replicated cultures of bacteria to two concentrations of each drug for 20 consecutive days in human serum as an ex vivo infection model. We screened evolved populations and clones for resistance phenotypes, including the restoration of growth and pyoverdine production, and the evolution of iron uptake by-passing mechanisms. We whole-genome sequenced evolved clones to identify the genetic basis of resistance. We found that mutants resistant against antivirulence treatments readily arose, but their selective spreading varied between treatments. Flucytosine resistance quickly spread in all populations due to disruptive mutations in upp, a gene encoding an enzyme required for flucytosine activation. Conversely, resistance against gallium arose only sporadically, and was based on mutations in transcriptional regulators, upregulating pyocyanin production, a redox-active molecule promoting siderophore-independent iron acquisition. The spread of gallium resistance was presumably hampered because pyocyanin-mediated iron delivery benefits resistant and susceptible cells alike. Our work highlights that antivirulence treatments are not evolutionarily robust per se. Instead, evolutionary robustness is a relative measure, with specific treatments occupying different positions on a continuous scale.
doi:10.1093/emph/eoy026 pmid:30455950 pmcid:PMC6234326 fatcat:afoa5lbiffhsnmifo3xn26oyzq

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

Fabrizio Menardo, Coraline R Praz, Stefan Wyder, Roi Ben-David, Salim Bourras, Hiromi Matsumae, Kaitlin E McNally, Francis Parlange, Andrea Riba, Stefan Roffler, Luisa K Schaefer, Kentaro K Shimizu (+4 others)
2016 Nature Genetics  
Throughout the history of agriculture, many new crop species (polyploids or artificial hybrids) have been introduced to diversify products or to increase yield. However, little is known about how these new crops influence the evolution of new pathogens and diseases. Triticale is an artificial hybrid of wheat and rye, and it was resistant to the fungal pathogen powdery mildew (Blumeria graminis) until 2001 (refs. 1,2,3). We sequenced and compared the genomes of 46 powdery mildew isolates
more » ... several formae speciales. We found that B. graminis f. sp. triticale, which grows on triticale and wheat, is a hybrid between wheat powdery mildew (B. graminis f. sp. tritici) and mildew specialized on rye (B. graminis f. sp. secalis). Our data show that the hybrid of the two mildews specialized on two different hosts can infect the hybrid plant species originating from those two hosts. We conclude that hybridization between mildews specialized on different species is a mechanism of adaptation to new crops introduced by agriculture.
doi:10.1038/ng.3485 pmid:26752267 fatcat:khc4nwvonzg2llnqyke5bteifi

Characterization of Chelonus inanitus polydnavirus segments: sequences and analysis, excision site and demonstration of clustering

Stefan Wyder, Sonja Zumbach, Verena Saladin, Andreas Gruber, Beatrice Lanzrein, Anita Hochuli, Adrian Tschannen
2002 Journal of General Virology  
Polydnaviruses (genera Ichnovirus and Bracovirus) have a segmented genome of circular doublestranded DNA molecules, replicate in the ovary of parasitic wasps and are essential for successful parasitism of the host. Here we show the first detailed analysis of various segments of a bracovirus, the Chelonus inanitus virus (CiV). Four segments were sequenced and two of them, CiV12 and CiV14, were found to be closely related while CiV14.5 and CiV16.8 were unrelated. CiV12, CiV14.5 and CiV16.8 are
more » ... que while CiV14 occurs also nested in another larger segment. All four segments are predicted to contain genes and predictions could be substantiated in most cases. Comparison with databases revealed no significant similarities at either the nucleotide or amino acid level. Inverted repeats with identities between 77 % and 92 % and lengths between 26 bp and 100 bp were found on all segments outside of predicted genes. Hybridization experiments indicate that CiV12 and CiV14 are both flanked by other virus segments, suggesting that proviral CiV segments are clustered in the genome of the wasp. The integration/excision site of CiV14 was analysed and compared to that of CiV12. On both termini of proviral CiV12 and CiV14 as well as in the excised circular molecule and the rejoined DNA a very similar repeat of 14 bp was found. A model to illustrate where the terminal repeats might recombine to yield the circular molecule is presented. Excision of CiV12 and CiV14 is restricted to the female and sets in at a very specific time-point in pupal-adult development. 0001-7987 # 2002 SGM CEH
doi:10.1099/0022-1317-83-1-247 pmid:11752722 fatcat:vxba3jgx7bekjih47yn5je2koy

Development of new methods for the quantitative detection and typing of Lactobacillus parabuchneri in dairy products

Hélène Berthoud, Daniel Wüthrich, Rémy Bruggmann, Daniel Wechsler, Marie-Therese Fröhlich-Wyder, Stefan Irmler
2017 International Dairy Journal  
Determination of histamine The presence of histamine in culture supernatants was assayed as described by Fr€ ohlich-Wyder et al. (2013) .  ...  Although the species L. buchneri and L. parabuchneri are closely related phylogenetically, the latter is not able to metabolize xylose (Fr€ ohlich-Wyder et al., 2013) .  ... 
doi:10.1016/j.idairyj.2016.10.005 fatcat:kyo63sbccjajtj6ejyuwb4ct3y
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