Jochen Schmid

Jochen Schmid
University of Münster | WWU · Institute for Molecular Microbiology and Biotechnology (IMMB)

Professor

About

94
Publications
19,122
Reads
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1,202
Citations
Introduction
Additional affiliations
August 2020 - present
University of Münster
Position
  • Professor (Full)
April 2019 - July 2020
Norwegian University of Science and Technology
Position
  • Professor (Associate)
May 2018 - March 2019
Technische Universität München
Position
  • Head of Department
Education
May 2005 - December 2008
Technische Universität Berlin
Field of study
  • Microbiology and Genetics
October 1998 - May 2005
Technische Universität Berlin
Field of study
  • Biotechnology

Publications

Publications (94)
Article
Full-text available
Application of state-of-the-art genome editing tools like CRISPR-Cas9 drastically increase the number of undomesticated micro-organisms amenable to highly efficient and rapid genetic engineering. Adaptation of these tools to new bacterial families can open up entirely new possibilities for these organisms to accelerate as biotechnologically relevan...
Article
Xanthan is an extensively studied viscosifying agent discovered in 1961. Acetylation and pyruvylation have a major influence on its rheological properties and the effect of these groups on the conformation and rheological properties of xanthan have been studied for decades. However, these studies rely mainly on chemical modifications and therefore...
Article
Functional carbohydrate polymers are of immense industrial interest for high value applications. Distinct biosynthetic pathways allow for metabolic engineering approaches for production in microbial cell factories. The most common strategies in recent years included the attenuation of central carbon metabolism, improved substrate utilization or enh...
Preprint
Full-text available
Transcriptional perturbation using inactivated CRISPR-nucleases (dCas) is a common method in eukaryotic organisms. While rare examples of dCas9 based tools for prokaryotes have been described, multiplexing approaches are limited due to the used effector nuclease. For the first time, a dCas12a derived broad host range tool for the targeted activatio...
Article
Full-text available
Paenibacillus polymyxa is a Gram-positive, non-pathogenic soil bacterium that has been extensively investigated for the production of R-R-2,3-butanediol in exceptionally high enantiomeric purity. Rational metabolic engineering efforts to increase productivity and product titers were restricted due to limited genetic accessibility of the organism up...
Article
To date, only limited knowledge is available on how complex cellular behaviors are regulated in P. polymyxa . In this study, we investigate several regulatory proteins which play a role in governing different physiological traits.
Preprint
Despite being unicellular organisms, bacteria undergo complex regulation mechanisms which coordinate different physiological traits. Among others, DegU, DegS, and Spo0A are the pleiotropic proteins which govern various cellular responses and behaviors. However, the functions and regulatory networks between these three proteins are rarely described...
Article
The use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering. These molecular biological tools have been applied for different genetic engineering purposes in multiple organisms, including the quite rarely explored Paenibacillus polymyxa. However,...
Article
Paenibacillus polymyxa is an avid producer of exopolysaccharides of industrial interest. However, due to the complexity of the polymer composition, structural elucidation of the polysaccharide remained unfeasible for a long time. By using a CRISPR-Cas9 mediated knock-out strategy, all single glycosyltransferases as well as the Wzy polymerases were...
Article
The usage of polysaccharides as biodegradable polymers is of growing interest in the context of a sustainable and ecofriendly economy. For this, the production of exopolysaccharides (EPS) by Gluconacetobacter sp. was investigated. Glycerol as carbon source revealed to be beneficial compared to glucose. In addition, pure glycerol could be substitute...
Article
Developing cost-efficient biotechnological processes is a major challenge in replacing fossil-based industrial production processes. The remarkable progress in genetic engineering ensures efficient and fast tailoring of microbial metabolism for a wide range of bioconversions. However, improving intrinsic properties such as tolerance, handling, grow...
Article
Full-text available
Clustered regularly interspaced short palindromic repeats (CRISPR) system has rapidly advanced genetic engineering research. The system has been applied for different genetic engineering purposes in multiple organisms including the quite rarely explored Paenibacillus polymyxa. Only limited studies on CRISPR-based system have been described for this...
Article
Full-text available
Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome engineering and related technologies have revolutionized biotechnology over the last decade by enhancing the efficiency of sophisticated biological systems. Cas12a (Cpf1) is an RNA-guided endonuclease associated to the CRISPR adaptive immune system found in many prok...
Article
Porphyridium exopolysaccharides (EPSs), which contain sulfate and methyl groups, have a similar potential for use in multiple industrial applications as macroalgae counterparts but lack detailed characterization. For this reason, we produced 0.21 g L⁻¹ of P. sordidum EPS and 0.17 g L⁻¹ P. purpureum EPS, followed by a thorough rheological characteri...
Article
Transcriptional perturbation using inactivated CRISPR-nucleases (dCas) is a common method in eukaryotic organisms. While rare examples of dCas9-based tools for prokaryotes have been described, multiplexing approaches are limited due to the used effector nuclease. For the first time, a dCas12a derived tool for the targeted activation and repression...
Article
Microalgae as photosynthetic microorganisms are the source of valuable compounds such as proteins, carotenoids, lipids and carbohydrate polymers. Among the different phyla, Porphyridium as part of the red microalgae (Rhodophyta) are of high importance as producers of sulfated polysaccharides. As the name suggests these microalgae are typically red;...
Article
A model-based rheological characterization of four sphingans in combination with four prominent surfactants of cosmetic formulations of cationic, anionic, zwitterionic and neutral headgroup characteristics was performed. The impact of the surfactants on the rheological properties, based on changes in the mechanical models was evaluated in respect t...
Article
Due to the relatively low yield of exopolysaccharides from microalgae compared to other microorganisms, their production is more challenging and needs to be optimized. Porphyridium sordidum and Porphyridium purpureum growth and exopolysaccharide production were optimized by testing influence of light at different wavelengths and varying nutrients a...
Chapter
This chapter describes the production processes for various microbial polysaccharides, starting from substrates to fermentation and downstream processing, with a special focus on bioreactor design and process variants. The main scope is on the differences between fungal and bacterial polysaccharide production based on hyphal growth and cell divisio...
Chapter
Microbial polysaccharides belong to the class of biopolymers, which consist as carbohydrate macromolecules synthesized by microbes. Polysaccharides make up one of the three major classes of biopolymers, next to polypeptides (proteins) and polynucleotides (deoxyribonucleic acids), and among these are industrially the most important based on the tonn...
Article
Full-text available
Scleroglucan is a β-glucan exopolysaccharide (EPS) efficiently produced by Sclerotium rolfsii ATCC 201126, with attractive properties for a wide range of industries. Its production was herein comparatively assessed with nine alternative C- and twelve N-sources. When comparing conventional sucrose-based Production Medium PM20 (8.41 g C/L + NaNO3 as...
Article
Full-text available
Um eine Professur zu übernehmen, bedarf es einer Fülle an formalen Voraussetzungen und die Wege dorthin sind vielfältig und häufig verworren. Welcher dieser Wege ans Ziel führt, ist neben dem Alter und der Publikationsleistung auch stark von der Kultur der Wissenschaftsbereiche abhängig. Während in den Naturwissenschaften eine Habilitation oft noch...
Chapter
The bacterial glycome comprises all carbohydrates, carbohydrate derivatives as well as glycoconjugates. These compounds are incorporated in many different functions within the cell and can be found in nearly all parts of the cellular system, from cytoplasm to outer decoration of the cell wall and the cell wall itself. The glycome also comprises sug...
Article
Bacterial extracellular polysaccharides serve important cell protective, structural, and signaling roles. They have particularly attracted attention as adhesives and matrix components promoting biofilm formation, which significantly contributes to resistance against antibiotics. In the root nodule symbiosis between rhizobia and leguminous plants, e...
Chapter
This chapter will deal with the structural diversity of bacterial (exo)polysaccharides based on the biosynthesis pathways and the highly specific glycosyltransferase proteins. Especially the so called Wzx/Wzy biosynthesis pathway will be explained in detail and the challenges and prospects of tailoring the chemical structures and thus polysaccharid...
Article
Scientists have combined functional and computational analysis to predict the substrate specificity of a family of glycosyltransferases from Arabidopsis thaliana, creating a tool that enables researchers to classify the donor and acceptor specificity of glycosyltransferase enzymes.
Article
Full-text available
Motivated by multiple national and international agreements aiming to in-crease the share of clean, affordable renewable energy and limit CO2emis-sions, Fraunhofer IGB BioCat focuses its work on the development of new combined chemical-biotechnological technolo-gies for the conversion of CO2and energy into fuels and chemicals. In general, the techn...
Article
Die Zahl akademischer Nachwuchsführungskräfte ist in den vergangenen zehn Jahren stark gestiegen. Nicht immer geht mit einer Zunahme an Pflichten auch ein Mehr an Rechten einher. Nachwuchsführungskräfte des Zukunftsforums Biotechnologie der DECHEMA unterbreiten Verbesserungsvorschläge. Link zum Artikel. https://www.wissenschaftsmanagement-online.d...
Article
The distinct biosynthesis pathways for microbial exopolysaccharide production provide different engineering strategies to tailor the chemical structures of the final polymers. This review focuses on the latest insights in the various pathways and identifies bottlenecks as well as promising targets for tailoring microbial polysaccharide production....
Chapter
Bacterial exopolysaccharides (EPS) often confer a survival advantage by protecting the cell against abiotic and biotic stresses, including host defensive factors. They are also main components of the extracellular matrix involved in cell-cell recognition, surface adhesion and biofilm formation. Biosynthesis of a growing number of EPS has been repor...
Article
Rheology-controlling agents are of importance for numerous products in a variety of industries. Replacement of synthetic chemicals with natural additives is desired in light of current environmental awareness and limited fossil resources. This study investigates the rheological features of Paenan, an exopolysaccharide produced by Paenibacillus poly...
Article
Full-text available
Abstract The unsaturated long-chain ,-dicarboxylic acid 1,18-cis-octadec-9-enedioic acid (cis-ODA) is a versatile precursor of various valuable compounds, such as polymers, and can be obtained from renewable resources. This makes cis-ODA highly attractive for the chemical industry where there is a growing interest in sustainable processes. Howeve...
Article
Dodecanedioic acid (DDA) is highly useful to the chemical industry as a versatile precursor for producing the polyamide nylon-6,12, which is used for many technical applications, such as heat and chemical-resistant sheaths. However, DDA synthesis has several drawbacks, such as high energy input and cost-intensive removal of by-products. Therefore,...
Article
An aniline blue fluorescence assay was constructed to quantify two fungal β-(1,3)–glucans with β-(1,6)–sidechains: scleroglucan and schizophyllan. Calibration curves were linear in the range from 30 mg/l to 6 g/l with R² > 99.8%. The assay was robust against d-glucose (50 g/l), oxalic acid (22.5 g/l), protein (0.667 g/l), and KCl (13.3 g/l). Sclero...
Article
Full-text available
Lysinibacillus xylanilyticus belongs to the family Bacillaceae and was first described in 2010 with the type strain L. xylanilyticus XDB9. It is able to both degrade xylan and use it as the sole carbon source. Here, we describe the 4.8-Mb genome of the strain L. xylanilyticus SR-86, which was isolated from organic waste.
Article
As a graduate student, PhD student, or even a PostDoc, one is standing at the shores of the ocean of science. This is certainly a very overwhelming time. Its beauty and hidden treasures gave rise to the desire to set the sails of curiosity and investigation. Yet at that time, its riffs and reefs we could not foresee nor its wakes and unpredictabili...
Article
Full-text available
Background Hexuronic acids such as D-galacturonic acid and D-glucuronic acid can be utilized via different pathways within the metabolism of microorganisms. One representative, the oxidative pathway, generates α-keto-glutarate as the direct link entering towards the citric acid cycle. The penultimate enzyme, keto-deoxy glucarate dehydratase/decarbo...
Article
Full-text available
Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly no genetic information is available, despite its good xanthan-producing properties. We performed an Illumina-based sequencing approach of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding sequences and a G+C content of 65%.
Article
No abstract is available for this article.
Article
Full-text available
Many microorganisms are capable of producing and secreting exopolysaccharides (EPS), which have important implications in medical fields, food applications or in the replacement of petro-based chemicals. We describe an analytical platform to be automated on a liquid handling system that allows the fast and reliable analysis of the type and the amou...
Article
Full-text available
The Research topic “Microbial exopolysaccharides from genes to applications” covers 12 articles dealing with the highly diverse class of microbial exopolysaccharides (EPSs). Many bacteria, archaea, yeast, and filamentous fungi are able to produce EPSs under different conditions. These biopolymers significantly differ in monomer composition, substit...
Article
Full-text available
The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition G...
Article
Full-text available
In diesem Werkstattbericht beschreiben wir die Hintergründe und die Erfahrungen mit einem inter- disziplinären Forschungsseminar an der Technischen Universität München (TUM). In diesem überfachlichen Seminar haben wir eine interdisziplinäre Lern- und Forschungsumgebung für Studierende unterschiedlicher Fakultäten geschaffen, innerhalb der sie gegeb...
Article
Full-text available
Industrial biotechnology relies on the availability of highly efficient enzymes and production strains for the development of economically viable processes. Recent advances in the field of genome editing will greatly speed up the implementation of desired metabolic pathways and their optimization, thereby facilitating fast and cost-effective produc...
Article
Full-text available
Bacteria produce a wide range of exopolysaccharides which are synthesized via different biosynthesis pathways. The genes responsible for synthesis are often clustered within the genome of the respective production organism. A better understanding of the fundamental processes involved in exopolysaccharide biosynthesis and the regulation of these pro...
Article
Full-text available
Microbial exopolysaccharides (EPS) are a structurally very diverse class of molecules. A number of them have found their application in rather diverging fields that extend from medicine, food, and cosmetics on the one side to construction, drilling, and chemical industry on the other side. The analysis of microbial strains for their competence in p...
Article
Full-text available
EINE VERANTWORTUNGSVOLL GENUTZTE GRÜNE GENTECHNIK IST KEINE RISIKOTECHNOLOGIE! DER SCHULTERSCHLUSS VON FORSCHERN UND ANWENDERN DER GENTECHNIK WIRD WICHTIG, UM EINE DISKREDITIERUNG EINZELNER BEREICHE DER BIOTECHNOLOGIE ZU VERHINDERN.
Article
Full-text available
Uronate dehydrogenases catalyse the oxidation of uronic acids to aldaric acids, which represent 'top value-added chemicals' that have the potential to substitute petroleum-derived chemicals. The identification and annotation of three uronate dehydrogenases derived from Fulvimarina pelagi HTCC2506, Streptomyces viridochromogenes DSM 40736 and Oceani...
Article
Microbial exo-polysaccharides can serve as valuable biopolymers in medicine, food and the feed industry as well as in various technical applications as substitutes of petro-based polymers or with unusual performance. Due to their different natural functions, they have vastly diverse structures, which lead to a very different properties. This struct...
Article
Four alginates possessing different guluronic/mannuronic acid ratios and one acetylated alginate were investigated with respect to their behavior during intercalation into layered double hydroxides. Two alginates were commercial products while the others were synthesized via bacterial fermentation and in one sample followed by enzymatic treatment....
Article
Full-text available
Microbial exopolysaccharides (EPS) are multifunctional biogenic polymers, which exist in highly diverse chemical structures. To facilitate a fast determination of the carbohydrate composition of novel isolated strains or modified EPS variants a fast screening and analytical method is required. The platform as realized and described in this article...
Conference Paper
Microbial exopolysaccharides (EPS) represent a valuable class of multifunctional biogenic polymers, which reveal their high number of functionalities based on individual structures – i.e. types, interconnection and substitution of saccharide monomers. By those variable characteristics, they obtain important technical advantages in combination with...
Article
Microbial polysaccharides have a wide range of functional properties and show high relevance in industrial applications. The possibility to create tailor-made polysaccharides by genetic engineering will further enhance the product portfolio and may open new fields of application. Here, we have examined in detail the recently sequenced genome of the...
Article
Biocatalysis is a promising tool for the sustainable production of chemicals. When cofactor depending enzymatic reactions are involved the applicability of the right cofactor is a central issue. One important example in this regard is the production of alcohols by nicotinamide cofactor (NAD(P)(+)) depending alcohol dehydrogenases. AdhZ3 from E. col...
Book
Full-text available
This discussion paper is the joint effort of the Dechema Zukunftsforum Biotechnologie. Fourty years after the first study dealing with the potential of biotechnology the Zukunftsforum, as a group of young scientists takes a look at the role of biotechnology to realize the bioeconomy.
Article
A fast carbohydrate screening platform processible in 96-well format is described. The method is suitable for the determination of various carbohydrates out of complex mixtures as obtained by acidic hydrolysis of carbohydrates polymers. The chromatographic conditions for an efficient separation (12 min) and the derivatization process with 1-phenyl-...
Article
Full-text available
Kozakia baliensis belongs to the family Acetobacteraceae and was described for the first time in 2002. These acetic acid bacteria are able to produce acetic acid from various carbon sources and 2- and 5-keto-d-gluconate from glucose. The novel K. baliensis strain SR-745 was isolated from a pineapple fruit bought in a German supermarket. The strain...
Article
Microbial exopolysaccharides (EPS) are biogenic and biodegradable polymers. The range of their application is extending steadily and in some areas they are already competing with conventional petrochemical products such as polyacrylates. Despite growing interest in microbial EPS, biosynthesis and production on a molecular scale are still not fully...
Conference Paper
Weiße Gentechnologie – Von Vitaminen & Aromen zu Industriechemikalien Die moderne Biotechnologie wird je nach Anwendungsfeld in verschiedene Bereiche unterteilt, die gern mit einer Farbe belegt werden, die das Anwendungsfeld besonders gut illustriert. So spricht man im medizinischen Bereich (z.B. Herstellung von Biopharmazeutika, Diagnostik) von d...
Chapter
Full-text available
Exopolysaccharides (EPS) produced by filamentous fungi often interfere with common methods for the extraction of nucleic acids or proteins. Similar precipitation behavior (e.g., by formation of hetero-triple helixes between the EPS and nucleic acid strands) severely minimizes yields of DNA or RNA extraction. In fungal strains that produce very high...
Conference Paper
The talk will deal with novel biorefinery concepts to realize a biobased economy. Conversion of biomass into chemical monomers and polymers is in the focus. A crucial difference between plant biomass and mineral oil lies in the quantity and locality of its availability. While mineral oil and its primary products can be transported through pipeline...
Article
Full-text available
In analyzing the reductive power of Escherichia coli K-12 for metabolic engineering approaches, we identified YahK and YjgB, two medium-chain dehydrogenases/reductases subgrouped to the cinnamyl alcohol dehydrogenase family, as being important. Identification was achieved using a stepwise purification protocol starting with crude extract. For exact...
Article
Since its first description in the early 1960s, scleroglucan attracted much attention from both academia and industry. Scleroglucan is an exopolysaccharide secreted by the basidiomycete Sclerotium rolfsii and appreciated as a multipurpose compound applicable in many industrial fields, including oil industry, food industry and pharmacy. In this revi...
Article
Scleroglukan, ein Exopolysaccharid, bestehend aus β-1,3 verknüpfter Glukose mit einer β-1,6-glycosidischen Verzweigung an jeder dritten Einheit, wird von dem Basidiomyzeten Sclerotium rolfsii sekretiert. Sowohl die Biosynthese von Scleroglucan als auch der Syntheseweg des Hauptnebenprodukts Oxalat wurden auf Sequenzebene analysiert, um durch Metabo...
Data
60 mers. Summary for all 60-mer probes designed for microarray hybridization.
Data
selected 60 mers. 60-mer probes used for comparative microarray hybridization.
Data
454 summary. Summary of 454 sequencing and assembly.
Data
KOG categories. Unigenes grouped into the KOG categories 'Carbohydrate transport and metabolism (G)' and 'Energy production and conversion (C)'.
Data
251706710005_4. Raw data for experiment EPSmax13_37 h, Sample B.
Data
SAMS results. Summary of annotation results using SAMS.
Data
SSH results. Unigenes identified via SSH and Reverse Northern hybridization.