The antimicrobial compound xantholysin defines a new group of Pseudomonas cyclic lipopeptides

The rhizosphere isolate Pseudomonas putida BW11M1 produces a mixture of cyclic lipopeptide congeners, designated xantholysins. Properties of the major compound xantholysin A, shared with several other Pseudomonas lipopeptides, include antifungal activity and toxicity to Gram-positive bacteria, a supportive role in biofilm formation, and facilitation of surface colonization through swarming. Atypical is the lipopeptide’s capacity to inhibit some Gram-negative bacteria, including several xanthomonads. The lipotetradecadepsipeptides are assembled by XtlA, XtlB and XtlC, three co-linearly operating non-ribosomal peptide synthetases (NRPSs) displaying similarity in modular architecture with the entolysin-producing enzymes of the entomopathogenic Pseudomonas entomophila L48. A shifted serine-incorporating unit in the eight-module enzyme XtlB elongating the central peptide moiety not only generates an amino acid sequence differing at several equivalent positions from entolysin, but also directs xantholysin’s macrocyclization into an octacyclic structure, distinct from the pentacyclic closure in entolysin. Relaxed fatty acid specificity during lipoinitiation by XtlA (acylation with 3-hydroxydodec-5-enoate instead of 3-hydroxydecanoate) and for incorporation of the ultimate amino acid by XtlC (valine instead of isoleucine) account for the production of the minor structural variants xantholysin C and B, respectively. Remarkably, the genetic backbones of the xantholysin and entolysin NRPS systems also bear pronounced phylogenetic similarity to those of the P. putida strains PCL1445 and RW10S2, albeit generating the seemingly structurally unrelated cyclic lipopeptides putisolvin (undecapeptide containing a cyclotetrapeptide) and WLIP (nonapeptide containing a cycloheptapeptide), respectively. This similarity includes the linked genes encoding the cognate LuxR-family regulator and tripartite export system components in addition to individual modules of the NRPS enzymes, and probably reflects a common evolutionary origin. Phylogenetic scrutiny of the modules used for selective amino acid activation by these synthetases indicates that bacteria such as pseudomonads recruit and reshuffle individual biosynthetic units and blocks thereof to engineer reorganized or novel NRPS assembly lines for diversified synthesis of lipopeptides

The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation.

While aggregation-prone proteins are known to accelerate aging and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A, and SERF2 have recently been identified as cellular modifiers of such proteotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with protein segments enriched in negatively charged and hydrophobic, aromatic amino acids. The absence of such segments, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In protein aggregation models in the nematode worm Caenorhabditis elegans, protein aggregation and toxicity were suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that MOAG-4 and SERF2 drive protein aggregation and toxicity by interactions with negatively charged segments in aggregation-prone proteins. Such charge interactions might accelerate primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our study points at charge interactions between cellular modifiers and amyloidogenic proteins as potential targets for interventions to reduce age-related protein toxicity

The Cyclostratigraphy Intercomparison Project (CIP): consistency, merits and pitfalls

Cyclostratigraphy is an important tool for understanding astronomical climate forcing and reading geological time in sedimentary sequences, provided that an imprint of insolation variations caused by Earth’s orbital eccentricity, obliquity and/or precession is preserved (Milankovitch forcing). Numerous stratigraphic and paleoclimate studies have applied cyclostratigraphy, but the robustness of the methodology and its dependence on the investigator have not been systematically evaluated. We developed the Cyclostratigraphy Intercomparison Project (CIP) to assess the robustness of cyclostratigraphic methods using an experimental design of three artificial cyclostratigraphic case studies with known input parameters. Each case study is designed to address specific challenges that are relevant to cyclostratigraphy. Case 1 represents an offshore research vessel environment, as only a drill-core photo and the approximate position of a late Miocene stage boundary are available for analysis. In Case 2, the Pleistocene proxy record displays clear nonlinear cyclical patterns and the interpretation is complicated by the presence of a hiatus. Case 3 represents a Late Devonian proxy record with a low signal-to-noise ratio with no specific theoretical astronomical solution available for this age. Each case was analyzed by a test group of 17-20 participants, with varying experience levels, methodological preferences and dedicated analysis time. During the CIP 2018 meeting in Brussels, Belgium, the ensuing analyses and discussion demonstrated that most participants did not arrive at a perfect solution, which may be partly explained by the limited amount of time spent on the exercises (∼4.5 hours per case). However, in all three cases, the median solution of all submitted analyses accurately approached the correct result and several participants obtained the exact correct answers. Interestingly, systematically better performances were obtained for cases that represented the data type and stratigraphic age that were closest to the individual participants’ experience. This experiment demonstrates that cyclostratigraphy is a powerful tool for deciphering time in sedimentary successions and, importantly, that it is a trainable skill. Finally, we emphasize the importance of an integrated stratigraphic approach and provide flexible guidelines on what good practices in cyclostratigraphy should include. Our case studies provide valuable insight into current common practices in cyclostratigraphy, their potential merits and pitfalls. Our work does not provide a quantitative measure of reliability and uncertainty of cyclostratigraphy, but rather constitutes a starting point for further discussions on how to move the maturing field of cyclostratigraphy forward

First total synthesis of WLIP: on the importance of correct protecting group choice

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CycloNet: European Cyclostratigraphy Network

International audience<p>The study of astronomical climate forcing and the application of cyclostratigraphy experienced a spectacular growth over the last decades. In 2018, the first Cyclostratigraphy Intercomparison Project (CIP)<em> </em>workshop constituted the first attempt to compare different methodological approaches and unite the global community around standard, uniform and reliable procedures. Two major conclusions were: [1] There is a need for further organization of the cyclostratigraphic community (e.g. to streamline different methodologies); [2] Cyclostratigraphy is a trainable skill, but currently many universities lack specific resources for training and education. Today, a regular newsletter, a dedicated free open-access journal “Cyclostratigraphy and Rhythmic Climate Change (CRCC)”, a scientific podcast titled CycloPod, and an educational website “www.cyclostratigraphy.org” connect the cyclostratigraphy community. The newly created CycloNet (Research Foundation Flanders FWO Funding) expands this effort into a real and sustainable scientific research network with partners from all around Europe, and open to the global community. At the same time, CycloNet creates a platform for streamlining and integrating new multi-disciplinary approaches. The main scientific targets for CycloNet in the next five years are: [1] Set up a diverse and sustainable community structure, relying on exchange, interaction and training, [2] Boost research by novel methodological approaches applying advanced signal processing techniques, [3] Organize a second Cyclostratigraphic Intercomparison Project. With this poster, we reach out to the broader community to exchange ideas on concepts and activities that CycloNet can help to develop further towards the future.</p&gt

Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities

The amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions. Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax (https://cordax.switchlab.org), that explores amyloid sequence beyond its current boundaries. Clustering by t-Distributed Stochastic Neighbour Embedding (t-SNE) shows how our approach resulted in an expansion away from hydrophobic amyloid sequences towards clusters of lower aliphatic content and higher charge, or regions of helical and disordered propensities. These clusters uncouple amyloid propensity from solubility representing sequence flavours compatible with surface-exposed patches in globular proteins, functional amyloids or sequences associated to liquid-liquid phase transitions.status: publishe

Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities

An increasing number of amyloid structures are determined. Here, the authors present the structure-based amyloid core sequence prediction method Cordax that is based on machine learning and allows the detection of aggregation-prone regions with higher solubility, disorder and surface exposure, and furthermore predicts the structural topology, orientation and overall architecture of the resulting putative fibril core