ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction

Allosteric ribozyme-driven crRNA switch for the amplification-free detection of biomolecules

Currently, CRISPR-mediated biosensors are concentrating on the design of the crRNA or the activator strand to regulate the trans-cleavage activity of Cas12a. Herein, we report an allosteric ribozyme-driven crRNA switch-regulated CRISPR/Cas12a sensor for amplification-free detection of biomolecules. An allosteric ribozyme is meticulously engineered to connect the target recognition sequence with the 5' binding arm of the hammerhead ribozyme, resulting in the formation of a hairpin structure through complementary hybridization. The presence of target induces the conformational change in the allosteric module and disrupts the hairpin structure, restoring multiple-turnover cleavage RNA activity of ribozyme. Then, the activated ribozyme specifically cuts the cleavage site of the substrate-locked crRNA and releases the native crRNA to initiate CRISPR/Cas12a functions for signal reporting. The reported biosensor exhibited high sensitivity and excellent specificity for miR-155 and adenosine triphosphate (ATP) detection, giving the detection limits of 256 fM and 160 nM, respectively. For clinical validation, our proposed strategy can quantify miR-155 expression levels in cells and serum of cancer patients. Furthermore, we also demonstrate that the allosteric ribozyme-driven crRNA switch can be easily compatible with lateral flow assays, realizing visualization and the portable monitoring of target. Hence, the biosensor not only has outstanding potential in point-of-care testing, but also enables the detection of various biomolecules by flexibly substituting target recognition sequences for molecular diagnosis in the clinic.

A CRISPR-Cas9 system for knock-out and knock-in of high molecular weight DNA enables module-swapping of the pikromycin synthase in its native host

BACKGROUND

Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA.

RESULTS

We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI-pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin.

CONCLUSION

Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.

Bidirectional effects of melanoidins derived from thermal Maillard reaction on polyhydroxyalkanoates synthesis by mixed culture: Transient and long-term responses

The synthesis of polyhydroxyalkanoates (PHA) by mixed microbial culture (MMC) using thermal hydrolyzed sludge is a promising strategy. However, the thermal hydrolysis by-product melanoidins may disturb PHA synthesis. In this study, transient-cycle experiments revealed bidirectional effects of melanoidins on PHA production: low concentrations (≤400 mg/L) promoted, high concentrations (≥800 mg/L) inhibited. Low melanoidins induced hormesis response and improved electron transfer, with energy metabolism increasing by 45 % and 15 % at 200 and 400 mg/L compared with no melanoidins. Reversely, high melanoidins caused cytotoxicity, with cell death ratio 4.5 times higher at 2000 mg/L than blank. In long-term operation, the promoting effect of low melanoidins diminished or turned inhibitory, possibly due to more PHA degraded. The melanoidins-tolerant genera such as Hydrogenophaga and Pannonibacter might alter MMC enrichment and PHA-producing capacity. These findings highlight the concentration-dependent effects of melanoidins on PHA synthesis, offering an insight into optimizing sludge-to-PHA recycling.

Upcycling food waste digestate into single-cell microalgae protein through a mixotrophic cultivation approach

The effective use of digestate remains a significant challenge in adopting anaerobic digestion technology for sustainable urban food waste management. This study investigates the potential of converting food waste-derived digestate (FWD) into single-cell protein through mixotrophic cultivation of Chlorella sorokiniana UTEX 1230. The liquid fraction of the digestate (LD) was diluted to 10 % to maintain ammonium-nitrogen (NH4+-N) levels within tolerable ranges (up to 250 mg/L) and enriched with macro- and micronutrients such as magnesium, calcium, sulfur, phosphorus, and trace elements to enhance microalgae growth. Glucose and acetate were tested at different organic carbon-to-nitrogen (Organic-C/N) ratios to assess their effects on biomass production, protein content, and NH4+-N removal. Results indicated that increasing the Organic-C/N ratios to 5 (glucose) or 10 (acetate) enhanced biomass concentration and NH4+-N removal rates. Although protein content declined with higher Organic-C/N ratios, total protein production still increased. Glucose at an Organic-C/N ratio of 5 achieved the highest biomass yield (up to 2.5 g/L), while acetate required an Organic-C/N ratio of 10 to reach comparable levels, pointing to its lower metabolic efficiency. Additionally, biomass protein content under glucose supplementation (40-41 %) surpassed that obtained with acetate (34-36 %). Combining acetate with 60-80 % glucose at a constant Organic-C/N ratio of 5 improved biomass production, but did not match the protein levels observed with glucose alone. Overall, the mixotrophic cultivation approach achieved higher biomass, superior NH4+-N removal rates, and over 40 % protein content, confirming its effectiveness in converting FWD into single-cell protein.

Effect of Heterologous Expression of Key Enzymes Involved in Astaxanthin and Lipid Synthesis on Lipid and Carotenoid Production in Aurantiochytrium sp

Aurantiochytrium sp., a heterotrophic microorganism, has received increasing attention for its high production of polyunsaturated fatty acids and has been widely applied in various industries. This study intended to optimize the carotenoid synthesis pathway in Aurantiochytrium sp. by metabolic engineering to increase the carotenoid content. Multi-sourced key enzyme genes involved in lipid synthesis (LPAAT and DGAT) and astaxanthin synthesis (crtZ and crtW) were selected to construct single-gene expression vectors and transformed into Aurantiochytrium sp. The results showed that the overexpression of LPAAT of Phaeodactylum tricornutum in Aurantiochytrium sp. caused an increase of 39.3% in astaxanthin, 424.7% in β-carotene, 901.8% in canthaxanthin, and 575.9% in lutein, as well as a down-regulation of 15.3% in the fatty acid content. Transcriptomics analysis revealed enhanced expression of genes involved in purine and amino acid metabolism in the transformed strains, and the down-regulation of the citric acid cycle led to an increase in the source of acetyl coenzyme A for the production of fatty acids. This study provides strong experimental evidence to support the application of increasing carotenoid levels in Aurantiochytrium sp.

A CRISPR-Cas9 System for Knock-out and Knock-in of High Molecular Weight DNA Enables Module-Swapping of the Pikromycin Synthase in its Native Host

Background

Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA.

Results

We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI-pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin.

Conclusion

Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.

Laser-assisted thermoelectric-enhanced hydrogen peroxide biosensors based on Ag2Se nanofilms for sensitive detection of bacterial pathogens

Thermoelectric (TE) materials can convert the heat produced during biochemical reactions into electrical signals, enabling the self-powered detection of biomarkers. In this work, we design and fabricate a simple Ag2Se nanofilm-based TE biosensor to precisely quantify hydrogen peroxide (H2O2) levels in liquid samples. A chemical reaction involving horseradish peroxidase, ABTS and H2O2 in the specimens produces a photothermal agent-ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) free radical, which triggers the heat fluctuations at the TE sensor through the photo-thermal effect, eventually enabling the sensing of H2O2. Consequently, the constructed sensor can achieve a detection limit of 0.26 μM by a three-leg TE device design. Further investigations suggest that the application of our TE sensor can be extended in testing H2O2 in beverages (including milk, soda water, and lemonade) and evaluating the load of bacterial pathogens relevant to dental diseases and infections including Streptococcus sanguinis and Methicillin-resistant Staphylococcus aureus with high analytical accuracy. This strategy utilizes the combination of high thermoelectric performance with chemical reactions to realize a straightforward and accurate biomarker detection method, making it suitable for applications in medical diagnostics, personalized health monitoring, and the food industry.