Synthesis of an antiviral drug precursor from chitin using a saprophyte as a whole-cell catalyst

Life History and Population Dynamics of Green Crabs (Carcinus maenas)

Carcinus maenas (the “shore crab” or “European green crab”) is a very proficient invader (considered to be one of the world’s 100 worst invaders by the IUCN) due to its phenotypic plasticity, wide temperature and salinity tolerance, and an extensive omnivorous diet. Native to Atlantic Europe, it has established two well-studied nonindigenous populations in the northwestern Atlantic and northeastern Pacific and less-studied populations in Australia, Argentina and South Africa. Green crabs are eurythermal and euryhaline as adults, but they are limited to temperate coastlines due to more restrictive temperature requirements for breeding and larval development. They cannot tolerate wave-swept open shores so are found in wave-protected sheltered bays, estuaries and harbors. Carcinus maenas has been the subject of numerous papers, with over 1000 published in the past decade. This review provides an up-to-date account of the current published information on the life history and population dynamics of this very important species, including genetic differentiation, habitat preferences, physical parameter tolerances, reproduction and larval development, sizes of crabs, densities of populations, sex ratios, ecosystem dynamics and ecological impacts in the various established global populations of green crabs.

Potential role of N-acetyl glucosamine in Aspergillus fumigatus-assisted Chlorella pyrenoidosa harvesting

BACKGROUND

Algal harvesting is a major cost which increases biofuel production cost. Algal biofuels are widely studied as third-generation biofuel. However, they are yet not viable because of its high production cost which is majorly contributed by energy-intensive biomass harvesting techniques. Biological harvesting method like fungal-assisted harvesting of microalgae is highly efficient but poses a challenge due to its slow kinetics and poorly understood mechanism.

RESULTS

In this study, we investigate Aspergillus fumigatus-Chlorella pyrenoidosa attachment resulting in a harvesting efficiency of 90% within 4 h. To pinpoint the role of extracellular metabolite, several experiments were performed by eliminating the C. pyrenoidosa or A. fumigatus spent medium from the C. pyrenoidosa-A. fumigatus mixture. In the absence of A. fumigatus spent medium, the harvesting efficiency dropped to 20% compared to > 90% in the control, which was regained after addition of A. fumigatus spent medium. Different treatments of A. fumigatus spent medium showed drop in harvesting efficiency after periodate treatment (≤ 20%) and methanol-chloroform extraction (≤ 20%), indicating the role of sugar-like moiety. HR-LC-MS (high-resolution liquid chromatography-mass spectrometry) results confirmed the presence of N-acetyl-d-glucosamine (GlcNAc) and glucose in the spent medium. When GlcNAc was used as a replacement of A. fumigatus spent medium for harvesting studies, the harvesting process was significantly faster (p < 0.05) till 4 h compared to that with glucose. Further experiments indicated that metabolically active A. fumigatus produced GlcNAc from glucose. Concanavalin A staining and FTIR (Fourier transform infrared spectroscopy) analysis of A. fumigatus spent medium- as well as GlcNAc-incubated C. pyrenoidosa cells suggested the presence of GlcNAc on its cell surface indicated by dark red dots and GlcNAc-specific peaks, while no such characteristic dots or peaks were observed in normal C. pyrenoidosa cells. HR-TEM (High-resolution Transmission electron microscopy) showed the formation of serrated edges on the C. pyrenoidosa cell surface after treatment with A. fumigatus spent medium or GlcNAc, while Atomic force microscopy (AFM) showed an increase in roughness of the C. pyrenoidosa cells surface upon incubation with A. fumigatus spent medium.

CONCLUSIONS

Results strongly suggest that GlcNAc present in A. fumigatus spent medium induces surface changes in C. pyrenoidosa cells that mediate the attachment to A. fumigatus hyphae. Thus, this study provides a better understanding of the A. fumigatus-assisted C. pyrenoidosa harvesting process.

Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model

Background

Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies on intracellular metabolic and regulatory mechanisms would expedite development of bioprocessing applications.

Results

In this study, our goal was to characterize the metabolic profile of S. marcescens to provide insight for metabolic engineering applications and fundamental biological studies. Hereby, we constructed a constraint-based genome-scale metabolic model (iSR929) including 929 genes, 1185 reactions and 1164 metabolites based on genomic annotation of S. marcescens Db11. The model was tested by comparing model predictions with experimental data and analyzed to identify essential aspects of the metabolic network (e.g. 138 essential genes predicted). The model iSR929 was refined by integrating RNAseq data of S. marcescens growth on three different carbon sources (glucose, N-acetylglucosamine, and glycerol). Significant differences in TCA cycle utilization were found for growth on the different carbon substrates, For example, for growth on N-acetylglucosamine, S. marcescens exhibits high pentose phosphate pathway activity and nucleotide synthesis but low activity of the TCA cycle.

Conclusions

Our results show that S. marcescens model iSR929 can provide reasonable predictions and can be constrained to fit with experimental values. Thus, our model may be used to guide strain designs for metabolic engineering to produce chemicals such as 2,3-butanediol, N-acetylneuraminic acid, and n-butanol using S. marcescens.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2826-1) contains supplementary material, which is available to authorized users.

Cloning and characterization of a chitinase from Thermobifida fusca reveals Tfu_0580 as a thermostable and acidic endochitinase

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A Thermobifida fusca chitinase Tfu_0580 is characterized for its function.

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Tfu_0580 is the first reported as a functional chitinase that can degrade colloidal chitin.

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Enzymatic characterization shows Tfu_0580 as a thermostable and acidic endochitinase.

Being capable of hydrolyzing chitin, chitinases have various applications such as production of N-acetylchitooligosaccharides (COSs) and N-acetylglucosamine (GlcNAc), degrading chitin as a consolidated bioprocessing, and bio-control of fungal phytopathogens. Here, a putative chitinase in Thermobifida fusca, Tfu_0580, is characterized. Tfu_0580 was purified by homogeneity with a molecular weight of 44.9 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Tfu_0580 displayed a clear activity against colloidal chitin, which is comparable to a commercial Streptomyces griseus chitinase. Enzyme activities against p-nitrophenyl β-D-N,N′,N′′-triacetylchitotriose (p-NP-(GlcNAc)₃), N,N′-diacetyl-β-D-chitobioside (p-NP-(GlcNAc)₂) and p-nitrophenyl N-acetyl-β-D-glucosaminide (p-NP-(GlcNAc)) showed that Tfu_0580 exhibited highest activity against p-NP-(GlcNAc)₃. Further optimization of the enzyme activity conditions showed: 1) an optimum catalytic activity at pH 6.0 and 30 °C; 2) activity over broad pH (4.8–7.5) and temperature (20–55 °C); 3) stimulation of activity by the metallic ions Ca²⁺ and Mn²⁺.

Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei

More than 70 years ago, the filamentous ascomycete Trichoderma reesei was isolated on the Solomon Islands due to its ability to degrade and thrive on cellulose containing fabrics. This trait that relies on its secreted cellulases is nowadays exploited by several industries. Most prominently in biorefineries which use T. reesei enzymes to saccharify lignocellulose from renewable plant biomass in order to produce biobased fuels and chemicals. In this review we summarize important milestones of the development of T. reesei as the leading production host for biorefinery enzymes, and discuss emerging trends in strain engineering. Trichoderma reesei has very recently also been proposed as a consolidated bioprocessing organism capable of direct conversion of biopolymeric substrates to desired products. We therefore cover this topic by reviewing novel approaches in metabolic engineering of T. reesei.

Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.

High-throughput ion exchange purification of positively charged recombinant protein in the presence of negatively charged dextran sulfate

Product quality analyses are critical for developing cell line and bioprocess producing therapeutic proteins with desired critical product quality attributes. To facilitate these analyses, a high-throughput small-scale protein purification (SSP) is required to quickly purify many samples in parallel. Here we develop an SSP using ion exchange resins to purify a positively charged recombinant growth factor P1 in the presence of negatively charged dextran sulfate supplemented to improve the cell culture performance. The major challenge in this work is that the strong ionic interaction between P1 and dextran sulfate disrupts interaction between P1 and chromatography resins. To solve this problem, we develop a two-step SSP using Q Sepharose Fast Flow (QFF) and SP Sepharose XL (SPXL) resins to purify P1. The overall yield of this two-step SSP is 78%. Moreover, the SSP does not affect the critical product quality attributes. The SSP was critical for developing the cell line and process producing P1.