Biology subjects

van Dissel, D.

Publications and source records attributed to van Dissel, D..

6 recordsLinked to original sources

bioRxiv2019

Genome-scale Model Constrained by Proteomics Reveals Metabolic Rearrangements in the Heterologous Host Streptomyces coelicolor

Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.

systems biology↗

bioRxiv2019

Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium

The bacterial cell wall is a dynamic, multicomponent structure that provides structural support for cell shape and physical protection from the environment. In monoderm species, the thick cell wall is made up predominantly of peptidoglycan, teichoic acids and a variety of capsular glycans. Filamentous monoderm Actinobacteria, such as Streptomyces coelicolor, incorporate new cell wall material at the apex of their hyphal cells during growth. In this study we use cryo-electron tomography to reveal the structural architecture of the cell wall of this bacterium. Our data shows a density difference between the apex and subapical regions of chemically isolated sacculi. Removal of the teichoic acids with hydrofluoric acid reveals a rough and patchy cell wall and distinct lamellae in a number of sacculi. Absence of the extracellular glycans poly-{beta}-1,6-[N]-acetylglucosamine and a cellulose-like polymer, produced by the MatAB and CslA proteins respectively, results in a thinner sacculus and absence of lamellae and patches. Extracellular glycans might thus form or lead to the formation of the outer cell wall lamella. Based on these findings we propose a revisited model for the complex cell wall architecture of an apically growing bacterium, in which the network of peptidoglycan together with extracellular polymers is structurally supported by teichoic acids.

microbiology↗

bioRxiv2017

Micro-encapsulation extends mycelial viability of Streptomyces lividans 66 and increases enzyme production

BackgroundFilamentous bacteria of the genus Streptomyces produce a large arsenal of industrially relevant antibiotics and enzymes. The industrial production of these molecules occurs in large fermenters, where many streptomycetes form dense mycelial networks called pellets. Pellets are characterized by slow growth and inefficient nutrient transfer and therefore regarded as undesirable from the perspective of productivity. Although non-pelleting strains have increased growth rates, their morphology also leads to a dramatic increase in the viscosity of the culture broth, which negatively impacts the process dynamics.\n\nResultsHere, we applied immobilization of Streptomyces lividans 66 using alginate as semi-solid matrix. This alginate-mediated micro-encapsulation increased the production of the extracellular enzyme tyrosinase more than three-fold. The increased production was accompanied by extended viability of the mycelium and a dramatic reduction in the release of intracellular proteins into the culture broth.\n\nConclusionsOur data demonstrate the utility of microencapsulation as a powerful technique to achieve higher yields and lower downstream-processing costs of streptomycetes.

microbiology↗

bioRxiv2017

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures

Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favoring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.

microbiology↗

bioRxiv2017

Morphology-driven downscaling of Streptomyces lividans to micro-cultivation

Actinobacteria are prolific producers of secondary metabolites and industrially relevant enzymes. Growth of these mycelial microorganisms in small culture volumes is challenging due to their complex morphology. Since morphology and production are typically linked, scaling down culture volumes requires better control over morphogenesis. In larger scale platforms, ranging from shake flasks to bioreactors, the hydrodynamics play an important role in shaping the morphology and determining product formation. Here, we report on the effects of agitation on the mycelial morphology of Streptomyces lividans grown in microtitre plates (MTP). Our work shows that at the proper agitation rates cultures can be scaled down to volumes as small as 100 l while maintaining the same morphology as seen in larger scale platforms. Using image analysis we compared the morphologies of the cultures; when agitated at 1400 rpm the mycelial morphology in microcultures approached that obtained in shake flasks, while product formation was also maintained. Our study shows that the morphology of actinobacteria in microcultures can be controlled in a similar manner as in larger scale cultures by carefully controlling the mixing rate. This could facilitate high-throughput screening and upscaling.

bioengineering↗

bioRxiv2016

Hyphal aggregation and surface attachment of Streptomyces is governed by extracellular poly-β-1,6-N-acetylglucosamine

Streptomycetes are multicellular filamentous microorganisms, which are major producers of antibiotics, anticancer drugs and industrial enzymes. When grown in submerged cultures, the preferred enzyme producer, Streptomyces lividans, forms dense mycelial aggregates or pellets, which requires the activity of the proteins encoded by the matAB and cslA-glxA. Here we show that matAB encodes the biosynthetic genes for the extracellular polymeric substance (EPS) poly-{beta}-1,6-N-acetylglucosamine or PNAG. Heterologous expression of matAB in actinomycetes that naturally lack these genes was sufficient for PNAG production and induction of mycelial aggregation. Also, overexpression of matAB in a non-pelleting cslA mutant restored pellet formation, which could effectively be antagonized by the PNAG-specific hydrolase, dispersin B. Extracellular accumulation of PNAG allowed Streptomyces to attach to hydrophilic surfaces, unlike attachment to hydrophobic surfaces, which involves a cellulase-degradable EPS produced by CslA. Altogether, our data support a model in which pellet formation depends on hydrophilic interactions mediated by PNAG and hydrophobic interactions involving the EPS produced by CslA. These new insights may be harnessed to improve growth and industrial exploitation of these highly versatile natural product and enzyme producers.

microbiology↗