Enhancement of novel Endo-polygalacturonase expression in Rhodotorula mucilaginosa PY18: insights from mutagenesis and molecular docking

Pectinase is a particular type of enzyme that can break down pectin compounds and is extensively utilised in the agricultural field. In this study, twenty yeast isolates were isolated and assayed for pectinase activity. Molecular identification by PCR amplification and sequencing of internal transcribed spacer (ITS) regions of isolate no. 18 had the highest pectinase activity of 46.35 U/mg, was identified as Rhodotorula mucilaginosa PY18, and was submitted under accession no. (OM275426) in NCBI. Rhodotorula mucilaginosa PY18 was further enhanced through sequential mutagenesis, resulting in a mutant designated as Rhodotorula mucilaginosa E54 with a specific activity of 114.2 U/mg. Using Response Surface Methodology (RSM), the best culture conditions for the pectinase-producing yeast mutant Rhodotorula mucilaginosa E54 were pH 5, 72-h incubation, 2.5% xylose, and 2.5% malt extract, with a pectinase-specific activity of 156.55 U/mg. Then, the obtained sequences of the endo-polygalacturonase PGI gene from Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were isolated for the first time, sequenced, and submitted to NCBI accession numbers OQ283005 and OQ283006, respectively. The modelled 3D structure of the endo-PGI enzyme (485 residues) was validated using Ramachandran's plot, which showed 87.71, 85.56, and 91.57% in the most favourable region for template Rhodotorula mucilaginosa KR, strain Rhodotorula mucilaginosa PY18, and mutant Rhodotorula mucilaginosa E54, respectively. In molecular docking studies, the results of template Rhodotorula mucilaginosa KR endo-PG1 showed an interaction with an affinity score of - 6.0, - 5.9, and - 5.6 kcal/mol for active sites 1, 2, and 3, respectively. Rhodotorula mucilaginosa PY18 endo-PG1 showed an interaction affinity with a score of - 5.8, - 6.0, and - 5.0 kcal/mol for active sites 1, 2, and 3, respectively. Mutant Rhodotorula mucilaginosa E54 endo-PG1 showed an interaction affinity of - 5.6, - 5.5, - 5.5 and - 5.4 kcal/mol for active sites 1, 2, and 3, respectively. The endo-PGI genes of both the yeast strain Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were successfully cloned and expressed in E. coli DH5α, showing significantly higher endo-PG1 activity, which recorded 94.57 and 153.10 U/mg for recombinant Rhodotorula mucilaginosa pGEM-PGI-PY18 and recombinant mutant Rhotorula pGEM-PGI-E54, respectively.

A new strain of Aspergillus tubingensis for high-activity pectinase production

Pectinase is a general term for a class of enzymes that decompose pectin. To obtain a fungal strain with high-activity pectinase of potential commercial importance, we screened microorganisms from the soil of vineyards, performed mutation breeding by ultraviolet (UV) and nitrosoguanidine (NTG) mutagenesis, and performed comparisons to commercially available pectinases. We found that the derived pectinase-producing strain Rn14-88A had the highest pectinase activity of 8363.215 U/mL, and identified it using internal transcribed spacer sequence analysis as Aspergillus tubingensis. Rn14-88A was the original strain for UV mutagenesis, from which mutant strain R-7-2-4 had the highest pectinase enzyme activity (9198.68 U/mL), which was a 9.99% increase compared to that of Rn14-88A. Following NTG mutagenesis of R-7-2-4, mutant strain Y1-3-2-6 had a pectinase enzyme activity of 9843.34 U/mL, which reflects a 6.36% increase compared to the pectinase activity of R-7-2-4. Subsequently, another round of NTG mutagenesis was performed on Y1-3-2-6, and the mutagenic strain Y2-6-3-4 exhibited an improved enzyme activity of 21,864.34 U/mL, which was 161.44% higher than that of Rn14-88A. Through liquid fermentation experiments of A. tubingensis Y2-6-3-4, it was determined that pectinase activity was the highest at a fermentation time of 20 h. Therefore, we conclude that A. tubingensis Y2-6-3-4 has potential for use in commercial production.