Bridging the gap between genomics and metabolomics based perspectives of myxobacterial secondary metabolite production capability

Bacterial secondary metabolites often exhibit potent biological activities with precise target specificity, making them a valuable asset for the identification of drug leads. However, a striking discrepancy is regularly seen between the genome-inscribed capacity for the production of secondary metabolites and the number of known compound classes detected from many microorganisms under laboratory cultivation conditions. Methods using improved analytical approaches to connect the bacterial secondary metabolome to biosynthetic gene clusters, aiming to uncover new candidate compounds from high resolution mass spectrometric ‘big data’ by statistical data treatment, as well as automated secondary metabolite biosynthetic gene cluster annotation coupled to various genome mining techniques are therefore about to transform natural product discovery. This work describes contributions to mass spectrometry- and genomics-guided compound identification, structure elucidation, investigation of biosynthesis routes and biological activity evaluation covering five different myxobacterial secondary metabolite scaffolds. Special focus lies on improving workflows for secondary metabolite identification using mass spectrometry data. By successfully combining several approaches to find novel bacterial secondary metabolites, this study underlines current prospects for closing the gap between genomics- and metabolomics-centric approaches to access bacterial secondary metabolite diversity.Bakterielle Sekundärmetabolite haben oft starke biologische Aktivität und hohe „Target“-spezifität, weshalb sie wertvolle Wirkstoffleitstrukturen darstellen. Es besteht jedoch eine große Diskrepanz zwischen der Anzahl der aus Bakterien unter Laborbedingungen nachweisbaren Sekundärmetaboliten und der in ihrem Genom codierten Produktionskapazität für Naturstoffe. Sowohl die Zuordnung bakterieller Sekundärmetabolom-Bestandteile zu Biosynthesegenclustern als auch die Entdeckung neuer Kandidatensubstanzen verlangen daher nach verbesserten analytischen Methoden gekoppelt mit Genomanalysetechniken. Methoden, die auf statistischer Analyse großer Mengen hochauflösender Massenspektrometriedaten sowie automatischer Genclusterannotation beruhen, verändern derzeit die Naturstoffforschung grundlegend. Diese Arbeit beschreibt Beiträge zu Massenspektrometrie- und Genomikgeleiteter Identifizierung, Strukturaufklärung, Beschreibung von Biosyntheserouten sowie Evaluierung der Bioaktivität fünf verschiedener neuartiger Grundstrukturen von Sekundärmetaboliten aus Myxobakterien. Spezielles Augenmerk liegt dabei auf der Verbesserung der Arbeitsabläufe um Sekundärmetaboliten mittels Massenspektrometrie zu identifizieren. Die Studien zeigen, wie durch erfolgreiche Kombination mehrerer Ansätze zur Identifizierung neuer bakterieller Sekundärmetabolite und zur Beschreibung ihrer Diversität die Lücke zwischen Genomik- und Metabolomikbasierten Ansätzen geschlossen werden kann

Myxobacteria-Derived Outer Membrane Vesicles: Potential Applicability Against Intracellular Infections

In 2019, it was estimated that 2.5 million people die from lower tract respiratory infections annually. One of the main causes of these infections is Staphylococcus aureus, a bacterium that can invade and survive within mammalian cells. S. aureus intracellular infections are difficult to treat because several classes of antibiotics are unable to permeate through the cell wall and reach the pathogen. This condition increases the need for new therapeutic avenues, able to deliver antibiotics efficiently. In this work, we obtained outer membrane vesicles (OMVs) derived from the myxobacteria Cystobacter velatus strain Cbv34 and Cystobacter ferrugineus strain Cbfe23, that are naturally antimicrobial, to target intracellular infections, and investigated how they can affect the viability of epithelial and macrophage cell lines. We evaluated by cytometric bead array whether they induce the expression of proinflammatory cytokines in blood immune cells. Using confocal laser scanning microscopy and flow cytometry, we also investigated their interaction and uptake into mammalian cells. Finally, we studied the effect of OMVs on planktonic and intracellular S. aureus. We found that while Cbv34 OMVs were not cytotoxic to cells at any concentration tested, Cbfe23 OMVs affected the viability of macrophages, leading to a 50% decrease at a concentration of 125,000 OMVs/cell. We observed only little to moderate stimulation of release of TNF-alpha, IL-8, IL-6 and IL-1beta by both OMVs. Cbfe23 OMVs have better interaction with the cells than Cbv34 OMVs, being taken up faster by them, but both seem to remain mostly on the cell surface after 24 h of incubation. This, however, did not impair their bacteriostatic activity against intracellular S. aureus. In this study, we provide an important basis for implementing OMVs in the treatment of intracellular infections

Quasar induced galaxy formation: a new paradigm ?

We discuss observational evidence that quasars play a key role in the formation of galaxies starting from the detailed study of the quasar HE0450-2958 and extending the discussion to a series of converging evidence that radio jets may trigger galaxy formation. The direct detection with VISIR at the ESO-VLT of the 7 kpc distant companion galaxy of HE0450-2958 allows us to spatially separate the sites of quasar and star formation activity in this composite system made of two ultra-luminous infrared galaxies (ULIRGs). No host galaxy has yet been detected for this quasar, but the companion galaxy stellar mass would bring HE0450-2958 in the local M(BH)-M(stellar bulge) relation if it were to merge with the QSO. This is bound to happen because of their close distance (7 kpc) and small relative velocity (~60-200 km/s). We conclude that we may be witnessing the building of the M(BH)-M(stellar bulge) relation, or at least of a major event in that process. The star formation rate (~340 Msun/yr), age (40-200 Myr) and stellar mass ([5-6]x10^10 Msun) are consistent with jet-induced formation of the companion galaxy. We suggest that HE0450-2958 may be fueled in fresh material by cold gas accretion from intergalactic filaments. We map the projected galaxy density surrounding the QSO as a potential tracer of intergalactic filaments and discuss a putative detection. Comparison to other systems suggests that inside-out formation of quasar host galaxies and jet-induced galaxy formation may be a common process. Two tests are proposed for this new paradigm: (1) the detection of offset molecular gas or dust emission with respect to the position of distant QSOs, (2) the delayed formation of host galaxies as a result of QSO activity, hence the two step building of the M(BH)/M(stellar bulge) ratio.Comment: 15 pages, 8 figures, accepted for publication in Astronomy and Astrophysics (with minor corrections

Evolution of the Most Massive Galaxies to z=0.6: I. A New Method for Physical Parameter Estimation

We use principal component analysis (PCA) to estimate stellar masses, mean stellar ages, star formation histories (SFHs), dust extinctions and stellar velocity dispersions for ~290,000 galaxies with stellar masses greater than $10^{11}Msun and redshifts in the range 0.4<z<0.7 from the Baryon Oscillation Spectroscopic Survey (BOSS). We find the fraction of galaxies with active star formation first declines with increasing stellar mass, but then flattens above a stellar mass of 10^{11.5}Msun at z~0.6. This is in striking contrast to z~0.1, where the fraction of galaxies with active star formation declines monotonically with stellar mass. At stellar masses of 10^{12}Msun, therefore, the evolution in the fraction of star-forming galaxies from z~0.6 to the present-day reaches a factor of ~10. When we stack the spectra of the most massive, star-forming galaxies at z~0.6, we find that half of their [OIII] emission is produced by AGNs. The black holes in these galaxies are accreting on average at ~0.01 the Eddington rate. To obtain these results, we use the stellar population synthesis models of Bruzual & Charlot (2003) to generate a library of model spectra with a broad range of SFHs, metallicities, dust extinctions and stellar velocity dispersions. The PCA is run on this library to identify its principal components over the rest-frame wavelength range 3700-5500A. We demonstrate that linear combinations of these components can recover information equivalent to traditional spectral indices such as the 4000A break strength and HdA, with greatly improved S/N. This method is able to recover physical parameters such as stellar mass-to-light ratio, mean stellar age, velocity dispersion and dust extinction from the relatively low S/N BOSS spectra. We examine the sensitivity of our stellar mass estimates to the input parameters in our model library and the different stellar population synthesis models.Comment: 20 pages, 18 Figures, submitted to MNRA

The Mice at play in the CALIFA survey: A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (>10^11Msol) gas-rich spirals NGC4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties and stellar population diagnostics, over the full optical extent of both galaxies. The Mice provide a perfect case study highlighting the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars likely induced in both galaxies. The barred spiral NGC4676B exhibits a strong twist in both its stellar and ionised gas disk. On the other hand, the impact of the merger on the stellar populations has been minimal thus far: star formation induced by the recent close passage has not contributed significantly to the global star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks extend to ~6.6kpc above the disk plane. The measured ram pressure and mass outflow rate (~8-20Msol/yr) are similar to superwinds from local ULIRGs, although NGC4676A has only a moderate infrared luminosity of 3x10^10Lsol. Energy beyond that provided by the mechanical energy of the starburst appears to be required to drive the outflow. We compare the observations to mock kinematic and stellar population maps from a merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.Comment: 23 pages, 13 figures, accepted to A&A. A version with a complete set of high resolution figures is available here: http://www-star.st-and.ac.uk/~vw8/resources/mice_v8_astroph.pd

Sussing merger trees: the impact of halo merger trees on galaxy properties in a semi-analytic model

A halo merger tree forms the essential backbone of a semi-analytic model for galaxy formation and evolution. Recent studies have pointed out that extracting merger trees from numerical simulations of structure formation is non-trivial; different tree building algorithms can give differing merger histories. These differences should be carefully understood before merger trees are used as input for models of galaxy formation. We investigate the impact of different halo merger trees on a semi-analytic model. We find that the z = 0 galaxy properties in our model show differences between trees when using a common parameter set. The star formation history of the universe and the properties of satellite galaxies can show marked differences between trees with different construction methods. Independently calibrating the semi-analytic model for each tree can reduce the discrepancies between the z = 0 global galaxy properties, at the cost of increasing the differences in the evolutionary histories of galaxies. Furthermore, the underlying physics implied can vary, resulting in key quantities such as the supernova feedback efficiency differing by factors of 2. Such a change alters the regimes where star formation is primarily suppressed by supernovae. Therefore, halo merger trees extracted from a common halo catalogue using different, but reliable, algorithms can result in a difference in the semi-analytic model. Given the uncertainties in galaxy formation physics, however, these differences may not necessarily be viewed as significant

Downsizing by Shutdown in Red Galaxies

We address the origin of the `downsizing' of elliptical galaxies, according to which the stars in more massive galaxies formed earlier and over a shorter period than those in less massive galaxies. We show that this could be the natural result of a shutdown of star formation in dark matter haloes above a critical mass of 10^12MSun. This is demonstrated using a semianalytic simulation of galaxy formation within the standard hierarchical scenario of structure formation. The assumed threshold mass is motivated by the prediction of stable shock heating above this mass and the finding that such a shutdown reproduces the observed distribution of galaxies in luminosity and colour.The shutdown at a critical halo mass introduces a characteristic stellar mass for the transition of galaxies into the `red sequence' of the galaxy colour-magnitude diagram. Central galaxies of haloes that are more massive today have reached this mass earlier and can therefore grow further along the red sequence by dry mergers, ending up more massive and containing older stars. Small galaxies formed in haloes below the critical mass can shutdown late, when they fall into haloes above the critical mass and become satellites. While our semianalytic simulation that incorporates an explicit shutdown reproduces downsizing as inferred from the stellar ages of ellipticals, we explain why it is much harder to detect downsizing using the mass functions of different galaxy types.Comment: 21 pages, 13 figures, submitted to MNRA

A Semi-Analytic Model for the Co-evolution of Galaxies, Black Holes, and Active Galactic Nuclei

We present a new semi-analytic model that self-consistently traces the growth of supermassive black holes (BH) and their host galaxies within the context of the LCDM cosmological framework. In our model, the energy emitted by accreting black holes regulates the growth of the black holes themselves, drives galactic scale winds that can remove cold gas from galaxies, and produces powerful jets that heat the hot gas atmospheres surrounding groups and clusters. We present a comprehensive comparison of our model predictions with observational measurements of key physical properties of low-redshift galaxies, such as cold gas fractions, stellar metallicities and ages, and specific star formation rates. We find that our new models successfully reproduce the exponential cutoff in the stellar mass function and the stellar and cold gas mass densities at z~0, and predict that star formation should be largely, but not entirely, quenched in massive galaxies at the present day. We also find that our model of self-regulated BH growth naturally reproduces the observed relation between BH mass and bulge mass. We explore the global formation history of galaxies in our models, presenting predictions for the cosmic histories of star formation, stellar mass assembly, cold gas, and metals. We find that models assuming the "concordance" LCDM cosmology overproduce star formation and stellar mass at high redshift (z>2). A model with less small-scale power predicts less star formation at high redshift, and excellent agreement with the observed stellar mass assembly history, but may have difficulty accounting for the cold gas in quasar absorption systems at high redshift (z~3-4).Comment: MNRAS accepte

Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics.

Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research

Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria.

There is astounding discrepancy between the genome-inscribed production capacity and the set of known secondary metabolite classes from many microorganisms as detected under laboratory cultivation conditions. Genome-mining techniques are meant to fill this gap, but in order to favor discovery of structurally novel as well as bioactive compounds it is crucial to amend genomics-based strategies with selective filtering principles. In this study, we followed a self-resistance guided approach aiming at the discovery of inhibitors of topoisomerase, known as valid target in both cancer and antibiotic therapy. A common host self-defense mechanism against such inhibitors in bacteria is mediated by so-called pentapeptide repeat proteins (PRP). Genes encoding the biosynthetic machinery for production of an alleged topoisomerase inhibitor were found on the basis of their collocation adjacent to a predicted PRP in the genome of the myxobacteriu