Isolation and Molecular Characterization of Indigenous Penicillium chrysogenum/rubens Strain Portfolio for Penicillin V Production

Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India

BACKGROUND

A filamentous fungus Penicillium rubens is widely recognized for producing industrially important antibiotic, penicillin at industrial scale.

OBJECTIVE

To better comprehend, the genetic blueprint of the wild-type P. rubens was isolated from India to identify the genetic/biosynthetic pathways for phenoxymethylpenicillin (penicillin V, PenV) and other secondary metabolites.

METHOD

Genomic DNA (gDNA) was isolated, and library was prepared as per Illumina platform. Whole genome sequencing (WGS) was performed according to Illumina NovoSeq platform. Further, SOAPdenovo was used to assemble the short reads validated by Bowtie-2 and SAMtools packages. Glimmer and GeneMark were used to dig out total genes in genome. Functional annotation of predicted proteins was performed by NCBI non-redundant (NR), UniProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Moreover, secretome analysis was performed by SignalP 4.1 and TargetP v1.1 and carbohydrate-active enzymes (CAZymes) and protease families by CAZy database. Comparative genome analysis was performed by Mauve 2.4.0. software to find genomic correlation between P. rubens BIONCL P45 and Penicillium chrysogenum Wisconsin 54-1255; also phylogeny was prepared with known penicillin producing strains by ParSNP tool.

RESULTS

Penicillium rubens BIONCL P45 strain was isolated from India and is producing excess PenV. The 31.09 Mb genome was assembled with 95.6% coverage of the reference genome P. chrysogenum Wis 54-1255 with 10687 protein coding genes, 3502 genes had homologs in NR, UniProt, KEGG, and GO databases. Additionally, 358 CAZymes and 911 transporter coding genes were found in genome. Genome contains complete pathways for penicillin, homogentisate pathway of phenyl acetic acid (PAA) catabolism, Andrastin A, Sorbicillin, Roquefortine C, and Meleagrin. Comparative genome analysis of BIONCL P45 and Wis 54-1255 revealed 99.89% coverage with 2952 common KEGG orthologous protein-coding genes. Phylogenetic analysis revealed that BIONCL P45 was clustered with Fleming's original isolate P. rubens IMI 15378.

CONCLUSION

This genome can be a helpful resource for further research in developing fermentation processes and strain engineering approaches for high titer penicillin production.

An Adsorption Based Downstream Processing Approach for Penicillin V from a Penicillium chrysogenum BIONCL I22 Culture Filtrate

Penicillin V (phenoxy methyl penicillin) is highly sought after among natural penicillins because of its exceptional acid stability and effectiveness against common skin and respiratory infections. Given its wide-ranging therapeutic uses, there is a need to establish a greener method for its maximum recovery to reduce the carbon footprint. Here, we have identified and validated optimized operational conditions for resin-based penicillin V recovery. It was observed that Amberlite XAD4 had the highest penicillin V hydrophobic adsorption capacity among the other screened resins. Kinetic and isothermal studies using linear and nonlinear regression analysis showed that the adsorption process well fitted with pseudo-second-order kinetics (R 2 = 0.9816) and the Freundlich adsorption isotherm model (R 2 = 0.9871). Adsorption equilibrium was attained within 4 h, while maximum adsorption was observed at 3 mg/mL penicillin V concentration. Furthermore, the optimized extraction protocol was compared with the conventional butyl acetate-based downstream processing. Under optimum conditions resin-based penicillin V recovery was 2-fold higher as compared to the solvent extraction method and the resin could be reused for over six cycles without compromising the yield. These findings signify substantial progress toward the development of an environmentally sustainable approach for penicillin V recovery and a potentially viable method for extractive fermentation.