Localization of Insertion Sequences in Plasmids for L-Cysteine Production in E. coli.

Insertion sequence elements (ISE) are often found to be responsible for the collapse of production in synthetically engineered Escherichia coli. By the transposition of ISE into the open reading frame of the synthetic pathway, E. coli cells gain selection advantage over cells expressing the metabolic burdensome production genes. Here, we present the exact entry sites of insertion sequence (IS) families 3 and 5 within plasmids for l-cysteine production in evolved E. coli populations. Furthermore, we identified an uncommon occurrence of an 8-bp direct repeat of IS5 which is atypical for this particular family, potentially indicating a new IS5 target site.

Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review.

Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.

Value-Added Squalene in Single-Cell Oil Produced with Cutaneotrichosporon oleaginosus for Food Applications.

Single-cell oil (SCO) produced by oleaginous microorganisms is potentially a more land-efficient and sustainable alternative to vegetable oil. The cost of SCO production can be reduced by value-added co-products like squalene, a highly relevant compound for the food, cosmetic, and pharmaceutical industry. For the first time, squalene in the oleaginous yeast Cutaneotrichosporon oleaginosus was analyzed, reaching 172.95 ± 61.31 mg/100 g oil in a lab-scale bioreactor. Using the squalene monooxygenase inhibitor terbinafine, cellular squalene was significantly increased to 2169 ± 262 mg/100 g SCO, while the yeast remained highly oleaginous. Further, SCO from a 1000 L scale production was chemically refined. The squalene content in the deodorizer distillate (DD) was found to be higher than that in DD from typical vegetable oils. Overall, this study demonstrates squalene as a value-added compound in SCO from C. oleaginosus for application in food and cosmetics without the use of genetic modifications.

Effects of Probiotic Saccharomyces boulardii Supernatant on Viability, Nano-Mechanical Properties of Cytoplasmic Membrane and Pro-Inflammatory Gene Expression in Human Gastric Cancer AGS Cells.

BACKGROUND: Gastric cancer has been recognized as the second most probable cause of death in humans from cancer diseases around the world. Postbiotics, supernatant, and metabolites from probiotic microorganisms have recently been used widely to prevent and treat cancer diseases in humans, without any undesirable side effects. This study explores the antiproliferative and antitumor activities of the probiotic Saccharomyces cerevisiae var. boulardii supernatant (SBS) against AGS cancer cells, a human gastric adenocarcinoma cell line. METHODS: We evaluated cell growth inhibitory and mechanical properties of the cytoplasmic membrane and the downregulation of survivin and proinflammatory genes in AGS cells treated with SBS after 24 and 48 h. RESULTS: SBS significantly inhibits the AGS cell growth, and the concentrations with IC50 values after 24 and 48 h treatments are measured as 2266 and 1956 µg/mL, respectively. Regarding the AFM images and Young`s modulus analysis, SBS significantly induces morphological changes in the cytoplasmic membrane of the treated AGS cells. Expression of survivin, NFƙB, and IL-8 genes is significantly suppressed in AGS cells treated with SBS. CONCLUSIONS: Considering the antitumor activities of SBS on AGS cell line, it can be regarded as a prospective therapeutic and preventive strategy against human stomach cancer disease.

Metabolic stress constrains microbial L-cysteine production in Escherichia coli by accelerating transposition through mobile genetic elements.

BACKGROUND: L-cysteine is an essential chemical building block in the pharmaceutical-, cosmetic-, food and agricultural sector. Conventionally, L-cysteine production relies on the conversion of keratinous biomass mediated by hydrochloric acid. Today, fermentative production based on recombinant E. coli, where L-cysteine production is streamlined and facilitated by synthetic plasmid constructs, is an alternative process at industrial scale. However, metabolic stress and the resulting production escape mechanisms in evolving populations are severely limiting factors during industrial biomanufacturing. We emulate high generation numbers typically reached in industrial fermentation processes with Escherichia coli harbouring L-cysteine production plasmid constructs. So far no genotypic and phenotypic alterations in early and late L-cysteine producing E. coli populations have been studied. RESULTS: In a comparative experimental design, the E. coli K12 production strain W3110 and the reduced genome strain MDS42, almost free of insertion sequences, were used as hosts. Data indicates that W3110 populations acquire growth fitness at the expense of L-cysteine productivity within 60 generations, while production in MDS42 populations remains stable. For the first time, the negative impact of predominantly insertion sequence family 3 and 5 transposases on L-cysteine production is reported, by combining differential transcriptome analysis with NGS based deep plasmid sequencing. Furthermore, metabolic clustering of differentially expressed genes supports the hypothesis, that metabolic stress induces rapid propagation of plasmid rearrangements, leading to reduced L-cysteine yields in evolving populations over industrial fermentation time scales. CONCLUSION: The results of this study implicate how selective deletion of insertion sequence families could be a new route for improving industrial L-cysteine or even general amino acid production using recombinant E. coli hosts. Instead of using minimal genome strains, a selective deletion of certain IS families could offer the benefits of adaptive laboratory evolution (ALE) while maintaining enhanced L-cysteine production stability.

Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of δ-cadinol.

BACKGROUND: Terpene synthases are versatile catalysts in all domains of life, catalyzing the formation of an enormous variety of different terpenoid secondary metabolites. Due to their diverse bioactive properties, terpenoids are of great interest as innovative ingredients in pharmaceutical and cosmetic applications. Recent advances in genome sequencing have led to the discovery of numerous terpene synthases, in particular in Basidiomycota like the wood rotting fungus Coniophora puteana, which further enhances the scope for the manufacture of terpenes for industrial purposes. RESULTS: In this study we describe the identification of two novel (+)-δ-cadinol synthases from C. puteana, Copu5 and Copu9. The sesquiterpene (+)-δ-cadinol was previously shown to exhibit cytotoxic activity therefore having an application as possible, new, and sustainably sourced anti-tumor agent. In an Escherichia coli strain, optimized for sesquiterpene production, titers of 225 mg l-1 and 395 mg l-1, respectively, could be achieved. Remarkably, both enzymes share the same product profile thereby representing the first two terpene synthases from Basidiomycota with identical product profiles. We solved the crystal structure of Copu9 in its closed conformation, for the first time providing molecular details of sesquiterpene synthase from Basidiomycota. Based on the Copu9 structure, we conducted structure-based mutagenesis of amino acid residues lining the active site, thereby altering the product profile. Interestingly, the mutagenesis study also revealed that despite the conserved product profiles of Copu5 and Copu9 different conformational changes may accompany the catalytic cycle of the two enzymes. This observation suggests that the involvement of tertiary structure elements in the reaction mechanism(s) employed by terpene synthases may be more complex than commonly expected. CONCLUSION: The presented product selectivity and titers of Copu5 and Copu9 may pave the way towards a sustainable, biotechnological production of the potentially new bioactive (+)-δ-cadinol. Furthermore, Copu5 and Copu9 may serve as model systems for further mechanistic studies of terpenoid catalysis.

Life cycle greenhouse gas emissions of microalgal fuel from thin-layer cascades.

Thin-layer cascades (TLCs) enable algae cultivation at high cell densities, thus increasing biomass yields and facilitating the harvest process. This makes them a promising technology for industrial-scale algal fuel production. Using Life Cycle Assessment (LCA), we calculate the greenhouse gas (GHG) emissions of aviation fuel produced using algal biomass from TLCs. We find that the impact (81 g CO2e per MJ) is lower than that of fuel from algal biomass cultivated in open race way ponds (94 g CO2e). However, neither of the two cultivation systems achieve sufficient GHG savings for compliance with the Renewable Energy Directive II. Seawater desalination in particular dominates the TLC impact, indicating a trade-off between carbon and water footprint. In both cultivation systems, the mixing power and fertilizer consumption present further significant impacts. There is uncertainty in the correlation between mixing power and algal oil yield, which should be investigated by future experimental studies.

Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations.

While chemical steps involved in bioactive cembranoid biosynthesis have been examined, the corresponding enzymatic mechanisms leading to their formation remain elusive. In the tobacco plant, Nicotiana tabacum, a putative cembratriene-ol synthase (CBTS) initiates the catalytic cascade that lead to the biosynthesis of cembratriene-4,6-diols, which displays antibacterial- and anti-proliferative activities. We report here on structural homology models, functional studies, and mechanistic explorations of this enzyme using a combination of biosynthetic and computational methods. This approach guided us to develop an efficient de novo production of five bioactive non- and monohydroxylated cembranoids. Our homology models in combination with quantum and classical simulations suggested putative principles of the CBTS catalytic cycle, and provided a possible rationale for the formation of premature olefinic side products. Moreover, the functional reconstruction of a N. tabacum-derived class II P450 with a cognate CPR, obtained by transcriptome mining provided for production of bioactive cembratriene-4,6-diols. Our combined findings provide mechanistic insights into cembranoid biosynthesis, and a basis for the sustainable industrial production of highly valuable bioactive cembranoids.

Biogas yields and composition from oil-extracted halophilic algae residues in conventional biogas plants operated at high salinities.

CO2-induced climate change drives the development of renewable processes for industrial products. Algae processes can actively fix and convert CO2 into value adding products, such as oils. Algae lipids hence counteract climate change and provide access to renewable commodities. In this context, valorization of algal residues remaining after oil extraction is a challenge for the emerging cyclic bioeconomy. This study focuses on the valorization of oil-extracted algae residues derived from the halophilic strain Scenedesmus obliquus via anaerobic digestion. We examined the effect of prior oil extraction on microbial digestibility and increasing salt content in the substrate with regard to biogas yield and composition. Our cumulative data demonstrate that the supercritical CO2 oil extraction acts as a physical pretreatment that facilitates enhanced hydrolysis of both polymeric call wall carbohydrates and cellular proteins, providing methane yields of 213.2 LN kg-1 VS day-1. Methane yields were 20% higher than literature values obtained with the same algae strain in the absence of prior oil extraction. We obtained these superior results albeit all lipids and nonpolar proteins had been extracted from the biogas substrate. Our data indicate that continuous anaerobic digestion without loss of fermentation efficiency is feasible up to a salt concentration of 2% w/v, if conventional, agricultural biogas plants are gradually adapted to the salt content of the substrate. Monofermentation of the investigated oil-extracted algae residue is technically feasible at loading rates of 1.5 kg VS m-3 day-1, but a supplementation with carbohydrate rich biomass would prove beneficial to alleviate ammonia inhibition.

Matrix-free laser desorption ionization mass spectrometry as a functional tool for the analysis and differentiation of complex phenolic mixtures in propolis: a new approach to quality control.

Matrix-free laser desorption ionization (LDI) is a rapid and versatile technique for the ionization of small, UV-light-absorbing molecules. Indeed, many natural products such as polyphenols exhibit inherent LDI properties, potentially facilitating their detection from highly complex samples such as crude extracts. With this in mind, the present work thoroughly evaluated the potential of LDI as an analytical tool for the chemical profiling and differentiation of propolis samples obtained from different global regions. Propolis is a complex bee product containing, among others, significant amounts of phenolic constituents that may show LDI effects. The present work will demonstrate that LDI not only provides reproducible and highly specific fingerprint spectra for each of the tested samples, it further allows their clear differentiation by principal compound analysis (PCA). Contrary to classical analytical approaches such as LC- or GC-MS, LDI does not require time-consuming sample preparation and method optimization procedures. Thus, the technique represents a most interesting analytical tool and potent supplement to classic LC-MS for quality control of herbal pharmaceuticals and dietary supplements. Present results clearly support this approach and further suggest the use of LDI as a versatile tool for the automated analysis of large sample batches on an industrial scale. Graphical abstract ᅟ.

Studies on the scale-up of biomass production with Scenedesmus spp. in flat-plate gas-lift photobioreactors.

Microalgae are flagged as next-generation biomass feedstock for sustainable chemicals and fuels, because they actively metabolize the climate gas CO2, do not impact food production, and are not associated with land-use change. Scaling microalgae cultivation processes from lab to pilot scale is key to assessing their economic and ecologic viability. In this work, process performances of two different Scenedesmus species were studied using a 300 L flat-plate gas-lift photobioreactor system (14 m2 photosynthetically active area) equipped with a customized, broad-spectrum LED illumination system. Scaling up of batch processes from laboratory scale (1.8 L, 0.09 m2) to the geometrically equivalent pilot scale resulted in reduced volumetric biomass productivities of up to 11% and reduced areal biomass productivities of up to 7.5% at the pilot scale. Since biofilm formation was solely detected at pilot scale, biofilm most likely impaired scalability. Nevertheless, repeated addition of nutrients (BG-11) at pilot scale resulted in a 13.5 gCDW L-1 biomass concentration within a 15 day process time with S. obtusiusculus at constant incident-photon flux densities of 1400 µmol photons m-2 s-1 and more than 19.5 gCDW L1 after 30 days with Scenedesmus ovalternus SAG 52.80 at constant incident-photon flux densities of 750 µmol photons m-2 s-1. This resulted in areal biomass productivities of 14 gCDW m-2 day-1 (S. ovalternus) and 19 gCDW m-2 day-1 (S. obtusiusculus), respectively.

Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems.

UNLABELLED: Microbial fermentation of agro-industrial waste holds great potential for reducing the environmental impact associated with the production of lipids for industrial purposes from plant biomass. However, the chemical complexity of many residues currently prevents efficient conversion into lipids, creating a high demand for strains with the ability to utilize all energy-rich components of agricultural residues. Here, we present results of genome and transcriptome analyses of Trichosporon oleaginosus. This oil-accumulating yeast is able to grow on a wide variety of substrates, including pentoses and N-acetylglucosamine, making it an interesting candidate for biotechnological applications. Transcriptomics shows specific changes in gene expression patterns under lipid-accumulating conditions. Furthermore, gene content and expression analyses indicate that T. oleaginosus is well-adapted for the utilization of chitin-rich biomass. We also focused on the T. oleaginosus mating type, because this species is a member of the Tremellomycetes, a group that has been intensively analyzed as a model for the evolution of sexual development, the best-studied member being Cryptococcus neoformans. The structure of the T. oleaginosus mating-type regions differs significantly from that of other Tremellomycetes and reveals a new evolutionary trajectory paradigm. Comparative analysis shows that recruitment of developmental genes to the ancestral tetrapolar mating-type loci occurred independently in the Trichosporon and Cryptococcus lineages, supporting the hypothesis of a trend toward larger mating-type regions in fungi. IMPORTANCE: Finite fossil fuel resources pose sustainability challenges to society and industry. Microbial oils are a sustainable feedstock for biofuel and chemical production that does not compete with food production. We describe genome and transcriptome analyses of the oleaginous yeast Trichosporon oleaginosus, which can accumulate up to 70% of its dry weight as lipids. In contrast to conventional yeasts, this organism not only shows an absence of diauxic effect while fermenting hexoses and pentoses but also effectively utilizes xylose and N-acetylglucosamine, which are building blocks of lignocellulose and chitin, respectively. Transcriptome analysis revealed metabolic networks that govern conversion of xylose or N-acetylglucosamine as well as lipid accumulation. These data form the basis for a targeted strain optimization strategy. Furthermore, analysis of the mating type of T. oleaginosus supports the hypothesis of a trend toward larger mating-type regions in fungi, similar to the evolution of sex chromosomes in animals and plants.

The first structure of a bacterial diterpene cyclase: CotB2.

Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Šresolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.

The effect of proteolysis on the induction of cell death by monomeric alpha-lactalbumin.

α-Lactalbumin (α-la) is a major whey protein found in milk. Previous data suggested that α-la has antiproliferative effects in human adenocarcinoma cell lines such as Caco-2 and HT-29. However, the cell death inducing α-la was not a naturally occurring monomer but either a multimeric variant or an α-la:oleic acid complex (HAMLET/BAMLET). Proteolysis showed that both human and bovine α-la are susceptible to digestion. ELISA assays assessing cell death with the native undigested α-la fractions showed that undigested protein fractions did have a significant cell death effect on CaCo-2 cells. Bovine α-la was also more effective than human α-la. A reduction in activity corresponded with lower concentrations of the protein and partial digestion and fragmentation of the protein using trypsin and pepsin. This suggests that the tertiary structure is vital for the apoptotic effect.

Oxidative metabolism of the anti-cancer agent mitoxantrone by horseradish, lacto-and lignin peroxidase.

Mitoxantrone (MH(2)X), an anthraquinone-type anti-cancer agent used clinically in the treatment of human malignancies, is oxidatively activated by the peroxidase/H(2)O(2) enzyme system. In contrast to the enzymatic mechanisms of drug oxidation, the chemical transformations of MH(2)X are not well described. In this study, MH(2)X metabolites, produced by the horseradish, lacto- or lignin peroxidase (respectively HRP, LPO and LIP)/H(2)O(2) system, were investigated by steady-state spectrokinetic and HPLC-MS methods. At an equimolar mitoxantrone/H(2)O(2) ratio, the efficacy of the enzyme-catalyzed oxidation of mitoxantrone decreased in the following order: LPO > HRP > LIP, which accorded with the decreasing size of the substrate access channel in the enzyme panel examined. In all cases, the central drug oxidation product was the redox-active cyclic metabolite, hexahydronaphtho-[2,3-f]-quinoxaline-7,12-dione (MH(2)), previously identified in the urine of mitoxantrone-treated patients. As the reaction progressed, data gathered in this study suggests that further oxidation of the MH(2) side-chains occurred, yielding the mono- and dicarboxylic acid derivatives respectively. Based on the available data a further MH(2) derivative is proposed, in which the amino-alkyl side-chain(s) are cyclised. With increasing H(2)O(2) concentrations, these novel MH(2) derivatives were oxidised to additional metabolites, whose spectral properties and MS data indicated a stepwise destruction of the MH(2) chromophore due to an oxidative cleavage of the 9,10-anthracenedione moiety. The novel metabolites extend the known sequence of peroxidase-induced mitoxantrone metabolism, and may contribute to the cytotoxic effects of the drug in vivo. Based on the structural features of the proposed MH(2) oxidation products we elaborate on various biochemical mechanisms, which extend the understanding of mitoxantrone's pharmaceutical action and its clinical effectiveness with a particular focus on peroxidase-expressing solid tumors, such as breast carcinoma.

Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida.

Marine sediments and sponges may show steep variations in redox potential, providing niches for both aerobic and anaerobic microorganisms. Geodia spp. and sediment specimens from the Straits of Florida were fixed using paraformaldehyde and 95% ethanol (v/v) for fluorescence in situ hybridization (FISH). In addition, homogenates of sponge and sediment samples were incubated anaerobically on various cysteine supplemented agars. FISH analysis showed a prominent similarity of microbiota in sediments and Geodia spp. samples. Furthermore, the presence of sulfate-reducing and annamox bacteria as well as other obligate anaerobic microorganisms in both Geodia spp. and sediment samples were also confirmed. Anaerobic cultures obtained from the homogenates allowed the isolation of a variety of facultative anaerobes, primarily Bacillus spp. and Vibrio spp. Obligate anaerobes such as Desulfovibrio spp. and Clostridium spp. were also found. We also provide the first evidence for a culturable marine member of the Chloroflexi, which may enter into symbiotic relationships with deep-water sponges such as Geodia spp. Resuspended sediment particles, may provide a source of microorganisms able to associate or form a symbiotic relationship with sponges.

Comparative proteomic analysis of matched primary and metastatic melanoma cell lines.

Identification of the biochemical pathways involved in the transformation from primary to metastatic melanoma is an area under intense investigation. A 2DE proteomics approach has been applied herein to the matched patient primary and metastatic melanoma cell lines WM-115 and WM-266-4, respectively, to better understand the processes that underlie tumor progression. Image analysis between samples aligned 470 common gel spots. Quantitative gel analysis indicated 115 gel spots of greater intensity in the metastatic line compared with the primary one, leading to the identification of 131 proteins via database searching of nano-LC-ESI-Q-TOF-MS/MS data. This more than tripled the number of proteins previously shown to be of higher abundance during melanoma progression. Also observed were 22 gel spots to be of lesser intensity in the metastatic line with respect to the primary one. Of these gel spots 15 proteins could be identified. Numerous proteins from both groups had not been reported previously to participate in melanoma progression. Further analysis of one protein, cyclophilin A, confirmed that this protein is expressed at higher levels in metastatic melanoma compared with primary melanoma and normal fibroblasts. Overall, this study expands our knowledge of protein modulation during melanoma stages, and suggests new targets for inhibitor development.

Oxidation of mitoxantrone by lactoperoxidase.

The lactoperoxidase (LPO) catalysed oxidation of mitoxantrone, an anthraquinone type anti-cancer drug, was studied spectrophotometrically under turnover and single turnover conditions with a stopped flow apparatus. With Compound I and Compound II, mitoxantrone formed binding complexes that were deactivated with increasing substrate concentration. The productive second-order rate constants for reduction were 3.6 x 10(6) and 2.2 x 10(4) M(-1) s(-1) for Compound I and Compound II, respectively. Under turnover conditions, Compound II was the steady-state intermediate, but with increasing H2O2, Compound II reacted with H2O2 to form the catalytically inactive intermediate Compound III. Nitrite prevented formation of Compound III by reducing Compound II to the native state. It also modulated the pathway of mitoxantrone oxidation by increasing the level of oxidised metabolites such as MH2(2+) and the novel metabolite MH. The biological implication of drug activation by LPO with nitrite is discussed.