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Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose–xylose mixture (50 g·L−1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.

The moss Physcomitrium patens is an advantageous host for the production of biopharmaceutical proteins, particularly due to the ease of glyco-engineering. However, the ability to produce proteins with paucimannosidic (MM) glycans in this species currently depends solely on the nature of the product. MM glycans offer benefits for some therapeutic proteins by facilitating their import into target cells via a presumed mannose receptor. Here, we describe the use of Spodoptera frugiperda enzymes expressed in moss to produce recombinant human lysosomal acid α-glucosidase with mainly MM glycans. We tested the expression of mannosidase type III and a hexosaminidase by varying the promoter strength and protein localization. The parental line produced recombinant α-glucosidase with no detectable MM glycans at all, whereas the weak expression of mannosidase type III targeted to the medial Golgi produced 4% MM glycans. The strong expression of a hexosaminidase targeted to the extracellular space increased the MM glycan content to 43.5%. Unlike previous attempts to express proteins with MM glycans in plants, neither of our introduced modifications interfered with growth or recombinant protein production. Our data confirm that the finely tuned expression and cellular localization of the glycosylation machinery can improve the efficiency of glyco-engineering. We also exploit the assembly of DNA fragments in vivo , which overcomes the limitations of traditional knock-in methods and facilitates the screening of different genetic elements. Our combined methods therefore represent the first straightforward approach allowing the production of recombinant proteins with abundant MM glycans.

Long-chain cuticular hydrocarbons (CHC) are key components of chemical communication in many insects. The parasitoid jewel wasps from the genus Nasonia use their CHC profile as sex pheromone and for species recognition. The standard analytical tool to analyze CHC is gas chromatography coupled with mass spectrometric detection (GC/MS). This method reliably identifies short- to long-chain alkanes and alkenes, but CHC with more than 40 carbon atoms are usually not detected. Here, we applied two laser mass spectrometry (MS) techniques, namely direct laser desorption/ionization (d)LDI and silver-assisted (Ag-)LDI MS, respectively, to analyze CHC profiles of N. vitripennis, N. giraulti, and N. longicornis directly from the cuticle or extracts. Furthermore, we applied direct analysis in real-time (DART) MS as another orthogonal technique for extracts. The three methods corroborated previous results based on GC/MS, i.e., the production of CHC with carbon numbers between C25 and C40. However, we discovered a novel series of long-chain CHC ranging from C41 to C51/C52. Additionally, several previously unreported singly and doubly unsaturated alkenes in the C31-C39 range were found. Use of principal component analysis (PCA) revealed that the composition of the newly discovered CHC varies significantly between species, sex, and age of the animals. Our study adds to the growing literature on the presence of very long-chain CHC in insects and hints at putative roles in insect communication.

Most drugs that target the complement system are designed to inhibit the complement pathway at either the proximal or terminal levels. The use of a natural complement regulator such as factor H (FH) could provide a superior treatment option by restoring the balance of an overactive complement system while preserving its normal physiological functions. Until now, the systemic treatment of complement-associated disorders with FH has been deemed unfeasible, primarily due to high production costs, risks related to FH purified from donors’ blood, and the challenging expression of recombinant FH in different host systems. We recently demonstrated that a moss-based expression system can produce high yields of properly folded, fully functional, recombinant FH. However, the half-life of the initial variant (CPV-101) was relatively short. Here we show that the same polypeptide with modified glycosylation (CPV-104) achieves a pharmacokinetic profile comparable to that of native FH derived from human serum. The treatment of FH-deficient mice with CPV-104 significantly improved important efficacy parameters such as the normalization of serum C3 levels and the rapid degradation of C3 deposits in the kidney compared to treatment with CPV-101. Furthermore, CPV-104 showed comparable functionality to serum-derived FH in vitro , as well as similar performance in ex vivo assays involving samples from patients with atypical hemolytic uremic syndrome, C3 glomerulopathy and paroxysomal nocturnal hematuria. CPV-104 – the human FH analog expressed in moss – will therefore allow the treatment of complement-associated human diseases by rebalancing instead of inhibiting the complement cascade.

Pyrrolizidine alkaloids (PAs) are toxic secondary metabolites that are found in several distantly related families of the angiosperms. The first specific step in PA biosynthesis is catalyzed by homospermidine synthase (HSS), which has been recruited several times independently by duplication of the gene encoding deoxyhypusine synthase, an enzyme involved in the posttranslational activation of the eukaryotic initiation factor 5A. HSS shows highly diverse spatiotemporal gene expression in various PA-producing species. In comfrey (Symphytum officinale; Boraginaceae), PAs are reported to be synthesized in the roots, with HSS being localized in cells of the root endodermis. Here, we show that comfrey plants activate a second site of HSS expression when inflorescences start to develop. HSS has been localized in the bundle sheath cells of specific leaves. Tracer feeding experiments have confirmed that these young leaves express not only HSS but the whole PA biosynthetic route. This second site of PA biosynthesis results in drastically increased PA levels within the inflorescences. The boost of PA biosynthesis is proposed to guarantee optimal protection especially of the reproductive structures.

Microbial production of fuels and chemicals from lignocellulosic biomass provides promising bio-renewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. While industrial Escherichia coli strains efficiently utilize glucose, their ability to utilize xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94 % of a glucose-xylose mixture (50 g L-1 each) was utilized in mineral salt media that led to a 50 % increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild-type, suggesting its potential wide application in industrial E. coli biocatalysts.

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet. Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla. The genomics of uncultured microbes Currently available genome sequences give us a narrow view of the remarkable diversity of microorganisms because the vast majority of them have never been cultivated in pure culture. Here Tanja Woyke and colleagues use single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats. This information reveals numerous intra- and inter-phylum relationships and a number of unexpected metabolic features. On the basis of the new data the authors propose taxonomic revisions to the archaeal and bacterial domains, including a proposal to reorganizing the Archaea into three superphyla.

IntroductionSuccessful outcomes have been reported for the treatment of lower urinary tract symptoms (LUTS) with the prostatic urethral lift (PUL) in a number of clinical investigations. Our aim was to investigate PUL outcomes in patients treated in a day-to-day clinical setting without the rigid exclusion criteria of clinical studies.Materials and methodsWe investigated the outcome of the PUL procedure at five German departments during the initial period when PUL was approved for the clinic (10/2012–06/2014). All candidates for transurethral resection of the prostate (TURP) received PUL information and were given the choice of procedures. The only exclusion criterion was an obstructive median lobe. No patients were excluded because of high post-void residual volume (PVR), prostate size, retention history or LUTS oral therapy. Maximum urinary flow (Qmax), PVR, International Prostate Symptom Score (IPSS) and Quality of Life (QOL) were assessed at baseline, 1, 6, 12, and 24 months after surgery.ResultsOf 212 TURP candidates, 86 choose PUL. A mean of 3.8 (2–7) UroLift implants were implanted in patients of 38–85 years with a prostate size of 17–111 ml over 57 (42–90) min under general or local anesthesia. Thirty-eight (38.4%) patients had severe BPH obstruction and would have been denied PUL utilizing previously reported study criteria. Within 1 month 74 (86%) reported substantial symptom relief with significant improvements in Qmax, PVR, IPSS, and QOL (p < 0.001) that was maintained within the follow-up. Sexual function including ejaculation was unchanged or improved. No Clavien–Dindo Grad ≥ 2 was reported postoperatively. Eleven (12.8%) patients were retreated over 2 years. Twelve (86%) of 14 patients presenting with chronic urinary retention were catheter free at last follow-up.ConclusionPUL is a promising surgical technique that may alleviate LUTS, even in patients with severe obstruction.

Direct air capture (DAC) is increasingly recognized as a necessary puzzle piece to achieve the Paris climate targets. However, the current high cost and energy intensity of DAC act as a barrier. Short-term strategies for initial deployment, technology improvement, and cost reduction are needed to enable large-scale deployment. We assess and compare two near-term pathways leading to the same installed DAC capacity and thus yielding the same cost reductions: its combination with CO2 storage as direct air carbon capture and storage, or its deployment for CO2 utilization as direct air carbon capture and utilization e.g. for synthetic fuels, chemicals, and materials; we characterize these as Direct and Spillover pathways. Drawing on the Multi-level Perspective on Technological Transition as a heuristic, we examine both technical and immaterial factors needed to scale up DAC under the two pathways, in order to assess the pathways’ relative advantages and to identify possible short-term bottlenecks. We find neither pathway to be clearly better: the Direct pathway offers technical advantages but faces regulatory barriers that need to be resolved before deployment, while the Spillover pathway offers market and governance advantages but faces challenges related to hydrogen production and increasing resource needs as it scales up. There may be reasons for policymakers to therefore pursue both approaches in a dynamic manner. This could involve prioritizing the Spillover pathway in the short term due to possibly fewer short-term regulatory barriers and its ability to produce net-zero emission products for existing and accessible markets. Once short-term governance obstacles have been addressed, however, the Direct pathway may allow for more efficient scaling of DAC capacity and cost reductions, especially if by then the needed infrastructure and institutions are in place.