Degradation of polyphosphates by polyphosphate kinases from Ruegeria pomeroyi

Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov., isolated from seawater of the Yellow Sea

Two novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacteria, designated as WL0004T and XHP0148T, were isolated from seawater samples collected from the coastal areas of Nantong and Lianyungang, PR China, respectively. Both strains were found to grow at 10-42 °C (optimum, 37 °C) and with 2.0-5.0 % (w/v) NaCl (optimum, 3.0 %). Strain WL0004T grew at pH 6.0-9.0 (optimum, pH 7.0-8.0), while XHP0148T grew at pH 6.0-10.0 (optimum, pH 7.0-8.0). The major cellular fatty acids (>10 %) of both strains included summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c). In addition, strain WL0004T contained 11-methyl C18 : 1  ω7c and strain XHP0148T contained C12 : 0 3-OH. The respiratory quinone of both strains was ubiquinone-10. The G+C content of genomic DNA of strains WL0004T and XHP0148T were 62.5 and 63.0 mol%, respectively. Strains WL0004T and XHP0148T showed the highest 16S rRNA gene sequence similarity to Ruegeria pomeroyi DSS-3T (99.4 and 99.0 %, respectively), and the 16S rRNA gene-based phylogenetic analysis indicated that the two strains were closely related to members of the genus Ruegeria. The average nucleotide identity and digital DNA-DNA hybridization values among the two strains and type strains of the genus Ruegeria were all below 95 and 70 %, respectively, and the phylogenetic tree reconstructed from the bac120 gene set indicated that the two strains are distinct from each other and the members of the genus Ruegeria. Based on this phenotypic and genotypic characterization, strains WL0004T (=MCCC 1K07523T=JCM 35565T=GDMCC 1.3083T) and XHP0148T (=MCCC 1K07543T=JCM 35569T=GDMCC 1.3089T) should be recognized as representing two novel species of the genus Ruegeria and the names Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov. are proposed, respectively.

Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose

Cell-free production systems are increasingly used for the synthesis of industrially relevant chemicals and biopharmaceuticals. Cell-free systems often utilize cell lysates, but biocatalytic cascades based on recombinant enzymes have emerged as a promising alternative strategy. However, implementing efficient enzyme cascades is a non-trivial task and mathematical modeling and optimization has become a key tool to improve their performance. In this work, we introduce a generic framework for the model-based optimization of cell-free enzyme cascades based on a given kinetic model of the system. We first formulate and systematize seven optimization problems relevant in the context of cell-free production processes including, for example, the maximization of productivity or product yield and the minimization of overall costs. We then present an approach that accounts for parameter uncertainties, not only during model calibration and model analysis but also when performing the actual optimization. After constructing a kinetic model of the enzyme cascade, experimental data are used to generate an ensemble of kinetic parameter sets reflecting their variabilities. For every parameter set, systems optimization is then performed and the resulting solution subsequently cross-validated for all other parameterizations to identify the solution with the highest overall performance under parameter uncertainty. We exemplify our approach for the cell-free synthesis of GDP-fucose, an important sugar nucleotide with various applications. We selected and solved three optimization problems based on a constructed dynamic model and validated two of them experimentally leading to significant improvements of the process (e.g., 50% increase of titer under identical total enzyme load). Overall, our results demonstrate the potential of model-driven optimization for the rational design and improvement of cell-free production systems. The developed approach for systems optimization under parameter uncertainty could also be relevant for the metabolic design of cell factories.

Non-canonical nucleosides: Biomimetic triphosphorylation, incorporation into mRNA and effects on translation and structure

Recent advances in mRNA therapeutics demand efficient toolkits for the incorporation of nucleoside analogues into mRNA suitable for downstream applications. Herein, we report the application of a versatile enzyme cascade for the triphosphorylation of a broad range of nucleoside analogues, including unprotected nucleobases containing chemically labile moieties. Our biomimetic system was suitable for the preparation of nucleoside triphosphates containing adenosine, cytidine, guanosine, uridine and non-canonical core structures, as determined by capillary electrophoresis coupled to mass spectrometry. This enabled us to establish an efficient workflow for transcribing and purifying functional mRNA containing these nucleoside analogues, combined with mass spectrometric verification of analogue incorporation. Our combined methodology allows for analyses of how incorporation of nucleoside analogues that are commercially unavailable as triphosphates affect mRNA properties: The translational fidelity of the produced mRNA was demonstrated in analyses of how incorporated adenosine analogues impact translational recoding. For the SARS-CoV-2 frameshifting site, analyses of the mRNA pseudoknot structure using circular dichroism spectroscopy allowed insight into how the pharmacologically active 7-deazaadenosine destabilises RNA secondary structure, consistent with observed changes in recoding efficiency.

Metabolic turnover rate, digestive enzyme activities, and bacterial communities in the white shrimp Litopenaeus vannamei under compensatory growth

The present work aimed to evaluate the effects promoted by a phase of compensatory growth on metabolic turnover rate, digestive enzyme activity, and bacterial biota of the Pacific white shrimp Litopenaeus vannamei kept under different feeding regimes. Three treatments were evaluated as follows: 70% feed restriction during 3 (T3) and 6 (T6) days, followed by a period of feeding to satiety, and a control treatment without restriction periods. The results showed a full compensatory growth in treatments T3 and T6 by day 35 of the bioassay. A significant increase in trypsin and lipase (T6) activities was observed during compensatory growth, whereas specific amylase activity was significantly lower in treatment T6 compared to T3 but not significantly different from the control group. To determine the metabolic turnover rate of nitrogen in muscle tissue, an analysis of nitrogen isotope values (δ¹⁵N) at natural abundance levels was performed. At the end of the experimental period, shrimp under feed restriction had lower metabolic turnover rates and longer nitrogen residence times (t ₅₀) in muscle tissue, as compared to individuals in the control treatment. Regarding the changes in the bacterial communities in shrimp gut, no significant differences were observed at the phylum level, with Proteobacteria being the most abundant bacteria, followed by Actinobacteria. At family taxa level, Rhodobacteraceae presented the highest relative abundance in all treatments, whereas a decrease in Vibrionaceae was observed in treatments T3 and T6 when compared to control shrimps during compensatory growth. At the genus level, a decrease in Celeribacter, Catenococcus, and Epibacterium, and an increase in Ruegeria and Shimia, were identified in shrimp subjected to feed restriction when compared to control organisms during compensatory growth (day 14). At the end of the experimental period, the evaluated parameters showed similar results as those observed in the control treatment, suggesting a normalization of the metabolism and the physiological state. The present findings contribute to a better understanding on the physiological effects produced during compensatory growth in shrimp, which in turn could assist in the development of improved feeding strategies in benefit of the aquaculture industry.

Ruegeria alba sp. nov., Isolated from a Tidal Flat Sediment

A novel Gram-staining-negative, aerobic, rod-shaped, and white-colored bacterium designated as 1NDH52C^T was isolated from a tidal flat sediment and its taxonomic position was determined using a polyphasic taxonomic approach. The microorganism was found to grow at 10-37 °C, pH 6.0-9.0, and in the presence of 0-2% (w/v) NaCl, and to hydrolyze gelatin and aesculin. The major cellular fatty acid of strain 1NDH52C^T was summed feature 8 (C_19:1 ω7c and/or C_18:1 ω6c); the polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, and a lipid; the respiratory quinone was ubiquinone-10. The 16S rRNA gene-based phylogenetic analysis showed that strain 1NDH52C^T was closely related to members of the genus Ruegeria with the identity of 98.2% to the type strain Ruegeria pomeroyi DSM 15711^T. The genome DNA G + C content of strain 1NDH52C^T was 63.6%. The phylogenomic analysis indicated that strain 1NDH52C^T formed an independent branch distinct from reference type strains of species within this genus. Digital DNA-DNA hybridization and average nucleotide identity values between strain 1NDH52C^T and reference strains were, respectively, 19.1-41.5% and 78.3-91.3%, which are far below the thresholds of 70% and 95-96% for species definition, respectively, indicating that strain 1NDH52C^T represents a novel genospecies of the genus Ruegeria. Based on phenotypic and genotypic data, strain 1NDH52C^T is concluded to represent a novel species of the genus Ruegeria, for which the name Ruegeria alba sp. nov., is proposed. The type strain of the species is 1NDH52C^T (= GDMCC 1.2382^T = KCTC 82664^T).

Combined toxic effects of thiamethoxam on intestinal flora, transcriptome and physiology of Pacific white shrimp Litopenaeus vannamei

The environmental accumulation of thiamethoxam has increasingly become a risk for the health of aquatic animals, especially crustacean species in the same phylum as the target pests. The lack of knowledge on the toxicity of thiamethoxam to crustaceans motivates our research to study the acute and chronic toxicity of decapod crustaceans Litopenaeus vannamei, exposed to thiamethoxam. A 28-day chronic toxicity test followed a 96 h acute toxicity test. Thiamethoxam induced oxidative stress and decreased growth performance in shrimp. In addition, thiamethoxam has led to a substantial imbalance of the micro-ecosystem in the intestine. The composition of the intestinal flora changed significantly, and the balance of the interaction network in genera was broken. The competitive interaction of many bacteria becomes an unstable cooperative interaction. Transcriptomic analysis showed that the numbers of up- and down-regulated differentially expressed genes (DEGs) increased in a dose-dependent manner. These DEGs were significantly enriched in pathways related to detoxification, and the expression of most detoxification genes was upregulated. DEGs related to detoxification were positively correlated with Shimia and negatively correlated with Pseudoalteromonas. This study provides evidence for the first time on the toxic effects of thiamethoxam on the growth, biochemistry, intestinal flora, and transcriptome in crustaceans.

Toxic effects of ammonia and thermal stress on the intestinal microbiota and transcriptomic and metabolomic responses of Litopenaeus vannamei

Ammonia and thermal stress frequently have harmful effects on aquatic animals. The intestine is an important barrier allowing the body to defend against stress. In this study, we investigated the intestinal microbiota and transcriptomic and metabolomic responses of Litopenaeus vannamei subjected to individual and combined ammonia and thermal stress. The results showed that obvious variation in the intestinal microbiota was observed after stress exposure, with increased levels of Firmicutes and decreased levels of Bacteroidetes and Planctomycetes. Several genera of putatively beneficial bacteria (Demequina, Weissella and Bacteroides) were abundant, while Formosa, Kriegella, Ruegeria, Rhodopirellula and Lutimonas were decreased; pathogenic bacteria of the genus Vibrio were increased under individual stress but decreased under combined stress. The intestinal transcriptome revealed several immune-related differentially expressed genes associated with the peritrophic membrane and antimicrobial processes in contrasting accessions. Haemolymph metabolomic analysis showed that stress exposure disturbed the metabolic processes of the shrimp, especially amino acid metabolism. This study provides insight into the underlying mechanisms associated with the intestinal microbiota, immunity and metabolism of L.vannamei in response to ammonia and thermal stress; ten stress-related metabolite markers were identified, including L-lactic acid, gulonic acid, docosahexaenoic acid, l-lysine, gamma-aminobutyric acid, methylmalonic acid, trans-cinnamate, N-acetylserotonin, adenine, and dihydrouracil.

Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability

Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using ¹³C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant ¹³C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant ¹³C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.

Effects of Microcystis aeruginosa and microcystin-LR on intestinal histology, immune response, and microbial community in Litopenaeus vannamei

Microcystis aeruginosa (MA) is a primary hazardous cyanobacteria species in aquatic ecosystems that can produce microcystin-LR (MC-LR), which harms aquatic animals. The intestine is an important target tissue for MA and MC-LR. In this study, we investigated the effects of MA and MC-LR exposure on the intestinal microbiota variation and immune responses of Litopenaeus vannamei. Shrimp were experimentally exposed to MA and MC-LR for 72 h. The results showed that both MA and MC-LR exposure caused marked histological variation and apoptosis characteristics and increased oxidative stress in the intestine. Furthermore, the relative expression levels of antimicrobial peptide genes (ALF, Crus, Pen-3) decreased, while those of pro-inflammatory cytokines (MyD88, Rel, TNF-a), a pattern-recognition receptor (TLR4) and a mediator of apoptosis (Casp-3) increased. MA and MC-LR exposure also caused intestinal microbiota variation, including decreasing microbial diversity and disturbing microbial composition. Specifically, the relative abundance of Proteobacteria decreased in the two stress groups; that of Bacteroidetes decreased in the MA group but increased in the MC-LR group, while Tenericutes varied inversely with Bacteroidetes. Our results indicate that MA and MC-LR exposure causes intestinal histopathological and microbiota variations and induces oxidative stress and immune responses in L. vannamei. In conclusion, this study reveals the negative effects of MA and MC-LR on the intestinal health of shrimp, which should be considered in aquaculture.

Osmotic stress induces gut microbiota community shift in fish

Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.

Changes in the intestine microbial, digestion and immunity of Litopenaeus vannamei in response to dietary resistant starch

Resistant starch (RS) is a constituent of dietary fibre that has beneficial effects on the intestine physiological function of animals. However, the roles of RS on shrimp intestine health is unknown. In this study, we investigated the the effects of dietary RS on the microbial composition, and digestive and immune-related indices in the intestine of Litopenaeus vannamei. The shrimp were fed with diets containing different levels of RS: 0 g/kg (Control), 10 g/kg (RS1), 30 g/kg (RS2) and 50 g/kg (RS3) for 56 days. The results showed that dietary RS improved the morphology of the intestine mucosa. RS also increased the activity of digestive enzymes (AMS, LPS, Tryp, and Pep) and immune enzymes (PO, T-AOC, T-NOS, and NO), and the expression levels of immune-related genes (proPO, ALF, Lys, HSP70, Trx, Muc-1, Muc-2, Muc-5AC, Muc-5B, and Muc-19). A microbiome analysis indicated that dietary RS increased the short-chain fatty acids (SCFAs) contents and altered the composition of the intestine microbial. Specifically, RS increased the abundances of Proteobacteria and decreased the abundance of Bacteroidetes. At the genus level, the beneficial bacteria (Lutimonas, Ruegeria, Shimia, Mesoflavibacter, and Mameliella) were enriched, which might be involved in degrading toxins and producing beneficial metabolites; while potential pathogens (Formosa and Pseudoalteromonas) were decreased in response to dietary RS. Our results revealed that dietary RS could improve the intestine health of L. vannamei, probably via modulating the intestine microbial composition and SCFAs contents, and enhancing the digestion and immunity of the shrimp.

Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine

In spite of huge endeavors in cell line engineering to produce glycoproteins with desired and uniform glycoforms, it is still not possible in vivo. Alternatively, in vitro glycoengineering can be used for the modification of glycans. However, in vitro glycoengineering relies on expensive nucleotide sugars, such as uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) which serves as GlcNAc donor for the synthesis of various glycans. In this work, we present a systematic study for the cell-free de novo synthesis and regeneration of UDP-GlcNAc from polyphosphate, UMP and GlcNAc by a cascade of five enzymes (N-acetylhexosamine kinase (NahK), Glc-1P uridyltransferase (GalU), uridine monophosphate kinase (URA6), polyphosphate kinase (PPK3), and inorganic diphosphatase (PmPpA). All enzymes were expressed in E. coli BL21 Gold (DE3) and purified using immobilized metal affinity chromatography (IMAC). Results from one-pot experiments demonstrate the successful production of UDP-GlcNAc with a yield approaching 100%. The highest volumetric productivity of the cascade was about 0.81 g L^-1  h^-1 of UDP-GlcNAc. A simple model based on mass action kinetics was sufficient to capture the dynamic behavior of the multienzyme pathway. Moreover, a design equation based on metabolic control analysis was established to investigate the effect of enzyme concentration on the UDP-GlcNAc flux and to demonstrate that the flux of UDP-GlcNAc can be controlled by means of the enzyme concentrations. The effect of temperature on the UDP-GlcNAc flux followed an Arrhenius equation and the optimal co-factor concentration (Mg²⁺) for high UDP-GlcNAc synthesis rates depended on the working temperature. In conclusion, the study covers the entire engineering process of a multienzyme cascade, i.e. pathway design, enzyme expression, enzyme purification, reaction kinetics and investigation of the influence of basic parameters (temperature, co-factor concentration, enzyme concentration) on the synthesis rate. Thus, the study lays the foundation for future cascade optimization, preparative scale UDP-GlcNAc synthesis and for in situ coupling of the network with UDP-GlcNAc transferases to efficiently regenerate UDP-GlcNAc. Hence, this study provides a further step towards cost-effective in vitro glycoengineering of antibodies and other glycosylated proteins.

Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis

The polyphosphate kinase 2 (PPK2) from the intracellular pathogen Francisella tularensis has been characterized by a range of biochemical methods and X-ray crystallography. The antibiotic sensitivity of a deletion mutant lacking the gene encoding PPK2 is also reported.

The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using ³¹P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors.