Abstract
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.
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Data Availability
The genome data available in the NCBI database under Bio-Project PRJNA800067.
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Acknowledgements
The authors thank the CSIR-National Chemical Laboratory, Pune, India, for the necessary facilities.
Funding
This work was financially supported by Council of Scientific and Industrial Research-Focused Basic Research (CSIR-FBR) scheme, New Delhi, India (Project No-MLP101126).
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All authors contributed to study conception and design. Data curation, data analysis, methodology, writing—original draft preparation, reviewing, and editing were performed by Amol Sawant. Data curation and formal editing were performed by Vishwambar Navale. Supervision, experiment design, resources, reviewing, editing, data analysis, and software were assigned to Dr. V. Koteswara Rao. All authors read and approved final manuscript.
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Sawant, A.M., Navale, V.D. & Vamkudoth, K.R. Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India. Int Microbiol (2024). https://doi.org/10.1007/s10123-024-00491-0
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DOI: https://doi.org/10.1007/s10123-024-00491-0