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

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Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India
International Microbiology ( IF 2.3 ) Pub Date : 2024-02-22 , DOI: 10.1007/s10123-024-00491-0
Amol M Sawant _{1,

2} , Vishwambar D Navale _{1,

2} , Koteswara Rao Vamkudoth _{1,

2}

Affiliation

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.

中文翻译：

印度分离的产青霉素 V 的青霉菌菌株 BIONCL P45 的基因组测序和分析

背景

一种丝状真菌 Penicillium rubens 因以工业规模生产工业上重要的抗生素青霉素而被广泛认可。

目的

为了更好地理解，从印度分离出野生型 P. rubens 的遗传蓝图，以确定苯氧甲基青霉素（青霉素 V， PenV）和其他次生代谢物的遗传/生物合成途径。

方法

分离基因组 DNA （gDNA），并根据 Illumina 平台制备文库。根据 Illumina NovoSeq 平台进行全基因组测序（WGS）。此外，SOAPdenovo 用于组装由 Bowtie-2 和 SAMtools 包验证的短读长。使用 Glimmer 和 GeneMark 挖掘基因组中的总基因。预测蛋白质的功能注释由 NCBI 非冗余（NR）、 UniProt 、京都基因与基因组百科全书（KEGG）和基因本体论（GO）数据库进行。此外，通过 SignalP 4.1 和 TargetP v1.1 进行分泌组分析，通过 CAZy 数据库进行碳水化合物活性酶（CAZymes）和蛋白酶家族分析。使用 Mauve 2.4.0 进行比较基因组分析。寻找 P. rubens BIONCL P45 和 Penicillium chrysogenum Wisconsin 之间的基因组相关性的软件 54-1255;此外，通过 ParSNP 工具使用已知的青霉素生产菌株制备系统发育。

结果

红青霉BIONCL P45 菌株是从印度分离的，并且正在产生过量的 PenV。31.09 Mb 基因组组装在一起，参考基因组 P. chrysogenum Wis 54–1255 的覆盖率为 95.6%，具有 10687 个蛋白质编码基因，其中 3502 个基因在 NR、UniProt、KEGG 和 GO 数据库中具有同源物。此外，在基因组中发现了 358 个 CAZymes 和 911 个转运蛋白编码基因。基因组包含青霉素的完整通路、苯乙酸（PAA）分解代谢的匀浆通路、Andrastin A、山梨西林、Roquefortine C 和 Meleagrin。BIONCL P45 和 Wis 54-1255 的比较基因组分析显示，2952 个常见的 KEGG 直系同源蛋白质编码基因的覆盖率为 99.89%。系统发育分析显示，BIONCL P45 与 Fleming 的原始分离株 P. rubens IMI 15378 聚集。