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Item type:Publication, Access status: with files , A novel acidic laminarinase derived from Jermuk hot spring metagenome(Springer, 2025-07-26); ; ; ; Abstract: Laminarinase, an enzyme with a specific affinity for laminarin—a complex polysaccharide found in the cell walls of brown algae and select marine organisms—was investigated in this study. We cloned and characterized a gene encoding a putative glycoside hydrolase family 16 (GH16) laminarinase derived from the Jermuk hot spring metagenome. The resulting product, named Jermuk-LamM, represents a novel 1,3-β-d-glucanase with 48.1% amino acid sequence similarity to previously characterized GH16 family members catalogued in the NCBI database. To date, this stands as the sole described endo-1,3-β-d-glucanase from the Fidelibacterota phylum, which was recently reclassified from Marinimicrobia. Jermuk-LamM, identified as an acidic laminarinase, exhibits optimal enzymatic activity at pH 5.0 and a temperature of 55 °C, maintaining its function for a duration of at least 7 h. Jermuk-LamM is an enzyme that efficiently hydrolyzes both soluble and insoluble (1,3)-β-d-glucans, as well as (1,3;1,4)-β-d-glucans, with a marked preference for laminarin. This enzymatic activity facilitates the valorization of macroalgal biomass by predominantly producing monosaccharides and disaccharides. These hydrolysis products can subsequently be converted into energy carriers such as alcohol, methane, and hydrogen. The enzyme’s specific activities, coupled with its resistance to various additives, render Jermuk-LamM a promising candidate for various industrial applications, encompassing the realms of biofuel and pharmaceutical production. Key points: • Jermuk hot springs have significant potential as a source of novel enzymes. • Jermuk-LamM has less than 50% amino acid similarity to known enzymes. • It is the first enzyme characterized from the Fidelibacterota phylum.Publicationtype: Journal Article14 5 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Valorization of whey-based side streams for microbial biomass, molecular hydrogen, and hydrogenase production(2023-07-01); ; ; Abstract: Side streams of the dairy industry are a suitable nutrient source for cultivating microorganisms, producing enzymes, and high-value chemical compounds. The heterotrophic Escherichia coli and chemolithoautotroph Ralstonia eutropha are of major biotechnological interest. R. eutropha is a model organism for producing O2-tolerant [NiFe]-hydrogenases (Hyds) (biocatalysts), and E. coli has found widespread use as an expression platform for producing recombinant proteins, molecular hydrogen (H2), and other valuable products. Aiming at developing suitable cultivation media from side streams of the dairy industry, the pre-treatment (filtration, dilution, and pH adjustment) of cheese (sweet) whey (SW) and curd (acid) whey (AW), with and without the use of ß-glucosidase, has been performed. Growth parameters (oxidation–reduction potential (ORP), pH changes, specific growth rate, biomass formation) of E. coli BW25113 and R. eutropha H16 type strains were monitored during cultivation on filtered and non-filtered SW and AW at 37 °C, pH 7.5 and 30 °C, pH 7.0, respectively. Along with microbial growth, measurements of pH and ORP indicated good fermentative growth. Compared to growth on fructose-nitrogen minimal salt medium (control), a maximum cell yield (OD600 4.0) and H2-oxidizing Hyd activity were achieved in the stationary growth phase for R. eutropha. Hyd-3-dependent H2 production by E. coli utilizing whey as a growth substrate was demonstrated. Moreover, good biomass production and prolonged H2 yields of ~ 5 mmol/L and cumulative H2 ~ 94 mL g/L dry whey (DW) (ß-glucosidase-treated) were observed during the cultivation of the engineered E. coli strain. These results open new avenues for effective whey treatment using thermostable β-glucosidase and confirm whey as an economically viable commodity for biomass and biocatalyst production. Key points: • Archaeal thermostable β-glucosidase isolated from the metagenome of a hydrothermal spring was used for lactose hydrolysis in whey. • Hydrogenase enzyme activity was induced during the growth of Ralstonia eutropha H16 on whey. • Enhanced biomass and H2 production was shown in a genetically modified strain of Escherichia coli. Graphical abstract: [Figure not available: see fulltext.].Publicationtype: Journal Article13 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , A host-vector toolbox for improved secretory protein overproduction in bacillus subtilis(Springer, 2022-07-08); ; ; ; Abstract: Target proteins in biotechnological applications are highly diverse. Therefore, versatile flexible expression systems for their functional overproduction are required. In order to find the right heterologous gene expression strategy, suitable host-vector systems, which combine different genetic circuits, are useful. In this study, we designed a novel Bacillus subtilis expression toolbox, which allows the overproduction and secretion of potentially toxic enzymes. This toolbox comprises a set of 60 expression vectors, which combine two promoter variants, four strong secretion signals, a translation-enhancing downstream box, and three plasmid backbones. This B. subtilis toolbox is based on a tailor-made, clean deletion mutant strain, which is protease and sporulation deficient and exhibits reduced autolysis and secondary metabolism. The appropriateness of this alternative expression platform was tested for the overproduction of two difficult-to-produce eukaryotic model proteins. These included the sulfhydryl oxidase Sox from Saccharomyces cerevisiae, which forms reactive hydrogen peroxide and undesired cross-linking of functional proteins, and the human interleukin-1β, a pro-inflammatory cytokine. For the best performing Sox and interleukin, overproducing and secreting variants of these new B. subtilis toolbox fermentation strategies were developed and tested. This study demonstrates the suitability of the prokaryotic B. subtilis host-vector system for the extracellular production of two eukaryotic proteins with biotechnological relevance. Key points: • Construction of a versatile Bacillus subtilis gene expression toolbox. • Verification of the toolbox by the secretory overproduction of two difficult-to-express proteins. • Fermentation strategy for an acetoin-controlled overproduction of heterologous proteins.Publicationtype: Journal ArticleScopus© Citations 6 71 86 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence(Springer, 2022-04-09); ; ; ; Abstract: The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB—up to 2.5 times, P450—up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. Key Points: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome. Graphical abstract: [Figure not available: see fulltext.]Publicationtype: Journal ArticleScopus© Citations 4 25 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Enrichment of phosphate-accumulating organisms (PAOs) in a microfluidic model biofilm system by mimicking a typical aerobic granular sludge feast/famine regime(Springer, 2022-01-15); ; ; ; Wastewater treatment using aerobic granular sludge has gained increasing interest due to its advantages compared to conventional activated sludge. The technology allows simultaneous removal of organic carbon, nitrogen, and phosphorus in a single reactor system and is independent of space-intensive settling tanks. However, due to the microscale, an analysis of processes and microbial population along the radius of granules is challenging. Here, we introduce a model system for aerobic granular sludge on a small scale by using a machine-assisted microfluidic cultivation platform. With an implemented logic module that controls solenoid valves, we realized alternating oxic hunger and anoxic feeding phases for the biofilms growing within. Sampling during ongoing anoxic cultivation directly from the cultivation channel was achieved with a robotic sampling device. Analysis of the biofilms was conducted using optical coherence tomography, fluorescence in situ hybridization, and amplicon sequencing. Using this setup, it was possible to significantly enrich the percentage of polyphosphate-accumulating organisms (PAO) belonging to the family Rhodocyclaceae in the community compared to the starting inoculum. With the aid of this miniature model system, it is now possible to investigate the influence of a multitude of process parameters in a highly parallel way to understand and efficiently optimize aerobic granular sludge-based wastewater treatment systems. Key points • Development of a microfluidic model to study EBPR. • Feast-famine regime enriches polyphosphate-accumulating organisms (PAOs). • Microfluidics replace sequencing batch reactors for aerobic granular sludge research.Publicationtype: Journal ArticleScopus© Citations 5 52 173 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , An overview of drive systems and sealing types in stirred bioreactors used in biotechnological processesNo matter the scale, stirred tank bioreactors are the most commonly used systems in biotechnological production processes. Single-use and reusable systems are supplied by several manufacturers. The type, size, and number of impellers used in these systems have a significant influence on the characteristics and designs of bioreactors. Depending on the desired application, classic shaft-driven systems, bearing-mounted drives, or stirring elements that levitate freely in the vessel may be employed. In systems with drive shafts, process hygiene requirements also affect the type of seal used. For sensitive processes with high hygienic requirements, magnetic-driven stirring systems, which have been the focus of much research in recent years, are recommended. This review provides the reader with an overview of the most common agitation and seal types implemented in stirred bioreactor systems, highlights their advantages and disadvantages, and explains their possible fields of application. Special attention is paid to the development of magnetically driven agitators, which are widely used in reusable systems and are also becoming more and more important in their single-use counterparts. Key Points • Basic design of the most frequently used bioreactor type: the stirred tank bioreactor • Differences in most common seal types in stirred systems and fields of application • Comprehensive overview of commercially available bioreactor seal types • Increased use of magnetically driven agitation systems in single-use bioreactorsPublicationtype: Journal ArticleScopus© Citations 13 140 210 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Characterization of an extremely thermo-active archaeal β-glucosidase and its activity towards glucan and mannan in concert with an endoglucanaseA metagenome from an enrichment culture of a hydrothermal vent sample taken at Vulcano Island (Italy) was sequenced and an endoglucanase-encoding gene (vulcel5A) was identified in a previous work. VulCel5A with maximal activity at 115 °C was characterized as the most heat-active endoglucanase to date. Based on metagenome sequences, genomes were binned and bin4 included vulcel5A as well as a putative GH1 β-glycosidase-encoding gene (vulbgl1A) with highest identities to sequences from the archaeal genus Thermococcus. The recombinant β-glucosidase VulBgl1A produced in E. coli BL21 pQE-80L exhibited highest activity at 105 °C and pH 7.0 (76.12 ± 5.4 U/mg, 100%) using 4NP β-D-glucopyranoside as substrate and 61% relative activity at 120 °C. Accordingly, VulBgl1A represents one of the most heat-active β-glucosidases to date. The enzyme has a broad substrate specificity with 155% activity towards 4NP β-D-mannopyranoside in comparison with 4NP β-D-glucopyranoside. Moreover, nearly complete hydrolysis of cellobiose was demonstrated. The enzyme exhibited a high glucose tolerance with 26% residual activity in presence of 2 M glucose and was furthermore activated at glucose concentrations of up to 0.5 M. When the endoglucanase VulCel5A and the β-glucosidase VulBgl1A were applied simultaneously at 99 °C, 158% activity towards barley β-glucan and 215% towards mannan were achieved compared with the activity of VulCel5A alone (100%). Consequently, a significant increase in glucose formation was observed when both enzymes were incubated with β-glucan and mannan suggesting a synergistic effect. Hence, the two archaeal extremozymes are ideal candidates for complete glucan and mannan saccharification at temperatures above the boiling point of water.Publicationtype: Journal Article128 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Biofilm systems as tools in biotechnological production(2019-07-04); ; The literature provides more and more examples of research projects that develop novel production processes based on microorganisms organized in the form of biofilms. Biofilms are aggregates of microorganisms that are attached to interfaces. These viscoelastic aggregates of cells are held together and are embedded in a matrix consisting of multiple carbohydrate polymers as well as proteins. Biofilms are characterized by a very high cell density and by a natural retentostat behavior. Both factors can contribute to high productivities and a facilitated separation of the desired end-product from the catalytic biomass. Within the biofilm matrix, stable gradients of substrates and products form, which can lead to a differentiation and adaptation of the microorganisms’ physiology to the specific process conditions. Moreover, growth in a biofilm state is often accompanied by a higher resistance and resilience towards toxic or growth inhibiting substances and factors. In this short review, we summarize how biofilms can be studied and what most promising niches for their application can be. Moreover, we highlight future research directions that will accelerate the advent of productive biofilms in biology-based production processes.Publicationtype: Review ArticleScopus© Citations 22 50 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Extremely thermoactive archaeal endoglucanase from a shallow marine hydrothermal vent from Vulcano IslandAlready-characterized microbial cellulases have proven to be highly useful for industrial processes, since they can withstand harsh industrial conditions with characteristics such as high thermo- and acid stability. These properties provide promising features for the process of plant biomass degradation and biofuel generation. Nevertheless, the number of known extremely thermoactive archaeal cellulases is low. Hence, the discovery of archaeal cellulases with different characteristics is crucial for the development of efficient and sustainable biorefinery. In this work, the metagenome of a high-temperature enrichment culture from marine environment of Vulcano Island was screened for the presence of novel endoglucanase-encoding genes of archaeal origin. The ORF vul_cel5A was detected, and the deduced protein was characterized as the most thermoactive endoglucanase described to date. Vul_Cel5A was identified as a thermoactive glycoside hydrolase family 5 endoglucanase, with the highest sequence identity (72-75%) to putative endoglucanases from archaeal genera. Vul_Cel5A showed the highest activity at notable 115 °C towards barley β-glucan (210.7 U/mg), and lichenan (209.9 U/mg), and further towards carboxymethyl cellulose (38.6 U/mg) and locust bean gum (83.0 U/mg). The endoglucanase exhibited a half-life time of 46 min at 100 °C and did not show any loss of activity after incubation for 48 h at 75 °C. Furthermore, Vul_Cel5A showed high affinity to barley β-glucan with a Km of 0.52 mg/mL and showed tolerance against various chemical reagents. Due to the outstanding high thermoactivity and thermostability and tolerance to acidic conditions, Vul_Cel5A represents a promising novel archaeal endo-β-glucanase for application in biorefineries for an efficient biomass pre-treatment.Publicationtype: Journal Article306 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Rational design and metabolic analysis of escherichia coli for effective production of L-tryptophan at high concentrationL-tryptophan (L-trp) is a biosynthetic precursor of various bioactive components with pharmaceutical interest. The development of an efficient L-trp production strain using targeted molecular engineering approaches is challenging due to the requirement of several precursors and the complex regulations of the pathways involved. In this study, we present a rationally engineered and genetically stable L-trp overproducing Escherichia coli strain. The streamlined strain E. coli S028 is able to efficiently produce 34–40 g/L of L-trp with a yield of 0.15 g L-trp/g glucose and a productivity of 0.60 g/L/h in fed-batch fermentations. The titer and productivity of L-trp achieved are over twice as much as those reported so far for rationally developed L-trp producers. In addition, for the first time, both intracellular and extracellular concentrations of L-trp and the key metabolites in a L-trp hyperproducer strain were measured with an automated fast-sampling unit which is connected to a well-controlled bioreactor. The time series metabolic analysis gives valuable information about the regulation of L-trp synthesis in a highly productive strain and reveals targets for further improvement. Among others, it was found that L-trp and the byproduct glutamate (L-glu) accumulated to an extremely high level in the cell initially whereas the intracellular concentrations of glutamine (L-gln) stayed at a relatively low level throughout the fermentation. The metabolic analysis suggests that (a) the engineered serine biosynthesis pathway was able to effectively synthesize the substrate serine (intracellular concentration > 8 mM) for L-trp production, while (b) the substrate L-gln with an intracellular concentration of 0.8–1.2 mM seems to limit the biosynthesis of L-trp, even though L-glu was overproduced intra- and extracellularly. Thus, an increased availability of glutamine synthetase which catalyzes L-glu conversion to L-gln and an overexpression of the L-trp exporter gene could be important targets for further strain improvement.Publicationtype: Journal Article90