Design
Building upon the success of the chemical treatment method that significantly improved cellulose purity and fiber performance, we sought to address its environmental drawbacks, including high consumption of water and chemicals. To establish a more sustainable and environmentally friendly pretreatment process, we focused on developing a biological alternative leveraging the synergism of lignin-degrading enzymes. We selected two lignin-degrading enzymes, Laccase (Lac) lcc1 from Coriolopsis trogii and Versatile Peroxidase (VP) vpl2 from Pleurotus eryngii, along with an auxiliary enzyme, Lytic Polysaccharide Monooxygenase (LPMO) gh61-3 from Neurospora crassa. Their synergistic cooperation is designed to enhance residual lignin degradation efficiency: Laccase oxidizes phenolic subunits in lignin, generating radical intermediates that react with oxygen to produce hydrogen peroxide, which serves as the essential co-substrate for VP to cleave more recalcitrant lignin bonds. Simultaneously, LPMO acts as an electron sink for Lac and VP reactions and is activated by hydrogen peroxide to cleave hemicellulose and disrupt lignin-carbohydrate complexes(Ye et al., 2024). This coordinated action promotes thorough lignin removal and aids hemicellulose degradation, thereby purifying straw cellulose for spinning. Since these enzymes are prokaryotic-derived, we employed Pichia pastoris for secretory expression. To further enhance synergy, we engineered a synthetic multi-enzyme complex inspired by natural cellulosomes, utilizing a mini-scaffold protein containing three distinct cohesin domains from Acetivibrio thermocellus CipA, Clostridium cellulolyticum ScaB, and Clostridium cellulolyticum CipC, displayed on Saccharomyces cerevisiae surface. The enzymes, each fused to a specific dockerin domain, were secreted from P. pastoris and assembled onto the yeast-surface scaffold via mutually exclusive cohesin-dockerin interactions. Specifically, Lac was fused to a dockerin from Ruminiclostridium cellulolyticum for specific binding to the CipCcoh2 cohesin domain; VP was fused to a dockerin from Ruminococcus flavefaciens for binding to the ScaBcoh4 cohesin domain; and LPMO was fused to a dockerin from Acetivibrio thermocellus for binding to the CipAcoh2 cohesin domain(Ding et al., 2001, You et al., 2012, Pinheiro et al., 2008). This spatial co-localization creates a concentrated catalytic platform to maximize synergistic effects and minimize enzyme loss (Tian et al., 2019)
Figure 6. Enzymatic Purification of Cellulose from Straw.(A) Schematic of cellulose purification through enzymatic decomposition of straw. (B) An effective enzyme combination includes Laccase (Lac), Versatile Peroxidase (VP), and Lytic Polysaccharide Monooxygenase (LPMO). Specifically, laccase degrades lignin while generating hydrogen peroxide; VP simultaneously cleaves lignin by consuming hydrogen peroxide to produce radical electrons; and LPMO facilitates electron transfer between the two enzymes while additionally degrading hemicellulose.
Build
The plasmids for the three dockerin-fused enzymes (Lac, VP, LPMO) and the mini-scaffold were constructed using E. coli DH5α. For each enzyme, the gene sequences were cloned into P. pastoris expression vectors under the control of the AOX1 promoter with an α-factor signal peptide. The plasmids were linearized and transformed through electrotransformation into P. pastoris GS115. We then implemented an antibiotic-independent, phenotype-based screening strategy to identify high-expression clones (See Measurement for development and validation of this method). Transformants were selected on MM minimal medium plates where methanol replaced glucose as the carbon source, enabling direct induction of expression. The screening medium was supplemented with enzyme-specific cofactors and chromogenic substrates: for Lac screening, plates contained 0.5 mM ABTS and 1 mg/mL CuSO₄; for LPMO, 2.4 µM 2,6-DMP, 1 mg/mL CuSO₄, and 3 mM H₂O₂; and for VP, 2.4 µM 2,6-DMP, 1 mg/mL MnSO₄, 1 mg/mL CaCl₂, 3 mM H₂O₂, and 100 µg/mL hemin. To maintain induction, 1 mL of methanol was added daily to each plate. After two days of incubation, we successfully identified high-expression clones of Lac and LPMO by assessing color development intensity, though VP screening was compromised due to hemin-induced background coloration. Positive clones were further verified by colony PCR. For the mini-scaffold, the construct was transformed into S. cerevisiae EBY100, with transformants selected on SD/-Trp medium and expression induced in SG-CAA medium. For the mini-scaffold, the gene was cloned into a S. cerevisiae surface display vector and transformed into EBY100 competent cells. Transformants were selected on SD/-Trp medium, and scaffold expression was induced in SG-CAA medium. Protein expression was verified through SDS-PAGE and Western blot.
Test
To test protein expression, the transformed P. pastoris strains were cultured in a stepwise fermentation process. Selected clones were first grown in YPD medium overnight, then transferred to BMGY medium for 14-16 hours until the OD₆₀₀ reached 2-6. The cells were harvested by centrifugation and resuspended in BMMY induction medium containing 0.5% methanol. The cultures were maintained at 30°C with shaking for 120 hours, with additional methanol added every 24 hours to maintain a final concentration of 0.5%. Culture samples were collected at 24-hour intervals, and the supernatants were analyzed by SDS-PAGE. The results showed only very faint bands at the expected molecular weights for all three enzymes, indicating extremely low secretion levels into the culture medium (Figure 7C).
Meanwhile, analysis of S. cerevisiae lysates expressing the mini-scaffold confirmed successful protein expression. We used NetNGlyc 1.0 to predict N-glycosylation sites on the mini-scaffold and identified seven potential modification sites. Given that S. cerevisiae typically mediates substantial glycosylation, SDS-PAGE alone could not accurately determine the protein's molecular size. Therefore, after lysing the mini-scaffold expression strains with 5× SDS loading buffer, we utilized the V5 tag fused to the mini-scaffold and performed Western blot analysis, which clearly detected the target protein expression (Figure 7D).
Figure 7. Expression of Three Enzymes in Pichia pastoris. (A) The three enzymes were secreted extracellularly via the α-mating factor secretion signal and fused with distinct dockerin domains. (B) These dockerin domains specifically interact with cohesin modules displayed on mini-scaffold proteins expressed by engineered Saccharomyces cerevisiae, forming stable enzyme complexes.(C) SDS-PAGE analysis of yeast fermentation supernatant confirmed protein expression, though the bands were barely detectable.(D) Expression of the mini-scaffold proteins was verified by both SDS-PAGE and Western blot analysis.
Learn
We successfully confirmed the expression of the mini-scaffold in S. cerevisiae. However, the extremely weak bands on the SDS-PAGE gel indicated that the secretion expression of all three enzymes in P. pastoris was insufficient using the original α-factor signal peptide. This low yield of enzymes would severely limit the assembly efficiency and catalytic performance of our designed multi-enzyme complex, thus enhancing the secretion efficiency of the enzymes was the critical next step. We decided to systematically optimize the signal peptides to address this bottleneck.