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.

Biosynthesis of gold nanoparticles by Penicillium rubens and catalytic detoxification of ochratoxin A and organic dye pollutants / Biosíntesis de nanopartículas de oro por Penicillium rubens y desintoxicación catalítica de ocratoxina A y contaminantes colorantes orgánicos

The environmental pollution caused by chemical dyes is a growing concern nowadays. Limitations of traditional methods opened the route for nanotechnology; owing to the versatile properties of nanomaterials, gold nanoparticles (AuNPs) became a potential strategy for different applications. In the present study, biosynthesis of gold nanoparticles (BioAuNPs) was carried out by reacting chloroauric acid (HAuCl4) with cell-free filtrate of Penicillium rubens sp. nov. NCIM 1937. The AuNPs were then characterized by UV–visible spectroscopy, HR-TEM, FTIR, and DLS analysis to further examine their efficacious biosynthesis and morphological properties including size, shape, and stability. The biogenic AuNPs are polydisperse in nature, with a mean size of 14.92 ± 5 nm. These AuNPs exhibited promising antimicrobial activity against Escherichia coli NCIM-2065, Bacillus subtilis NCIM-2010, and Penicillium verrucosum MTCC 4935. In vitro quantitative HPLC results revealed that BioAuNPs significantly inhibited the biosynthesis of ochratoxin A (OTA). Microbial fuel cells (MFCs) are intriguing for power generation and wastewater treatment since they can directly transform chemical energy stored in organic matter to electricity by extracellular electron transfer (EET) via membrane proteins. AuNPs also showed excellent potential for dye degradation of organic pollutants, viz., methylene blue (MB), phenol red (PR), bromothymol blue (BTB), Congo red (CR), and 4-nitrophenol (4-NP). All dye removal efficiencies were estimated and fitted to pseudo-first-order processes using kinetic rate constants (Ka).The present study reveals a simple, original, and eco-friendly method for the synthesis of multifunctional biogenic AuNPs that could be effective in OTA detoxification in food products and organic pollutant removal during wastewater treatment for a sustainable environment.(AU)

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

Beta (ß)-lactam antibiotic is an industrially important molecule produced by Penicillium chrysogenum/rubens. Penicillin is a building block for 6-aminopenicillanic acid (6-APA), an important active pharmaceutical intermediate (API) used for semi-synthetic antibiotics biosynthesis. In this investigation, we isolated and identified Penicillium chrysogenum, P. rubens, P. brocae, P. citrinum, Aspergillus fumigatus, A. sydowii, Talaromyces tratensis, Scopulariopsis brevicaulis, P. oxalicum, and P. dipodomyicola using the internal transcribed spacer (ITS) region and the ß-tubulin (BenA) gene for precise species identification from Indian origin. Furthermore, the BenA gene distinguished between complex species of P. chrysogenum and P. rubens to a certain extent which partially failed by the ITS region. In addition, these species were distinguished by metabolic markers profiled by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Secalonic acid, Meleagrin, and Roquefortine C were absent in P. rubens. The crude extract evaluated for PenV production by antibacterial activities by well diffusion method against Staphylococcus aureus NCIM-2079. A high-performance liquid chromatography (HPLC) method was developed for simultaneous detection of 6-APA, phenoxymethyl penicillin (PenV), and phenoxyacetic acid (POA). The pivotal objective was the development of an indigenous strain portfolio for PenV production. Here, a library of 80 strains of P. chrysogenum/rubens was screened for PenV production. Results showed 28 strains capable of producing PenV in a range from 10 to 120 mg/L when 80 strains were screened for its production. In addition, fermentation parameters, precursor concentration, incubation period, inoculum size, pH, and temperature were monitored for the improved PenV production using promising P. rubens strain BIONCL P45. In conclusion, P. chrysogenum/rubens strains can be explored for the industrial-scale PenV production.

Genetic diversity of toxigenic Fusarium verticillioides associated with maize grains, India.

In the present investigation, prevalence, genetic diversity, and mycotoxin producing potential of Fusarium species associated with maize grain samples were studied from different geographical regions of India. The highest prevalence of Fusarium verticillioides was recorded as 88.52%, followed by F. coffeatum, F. foetens, and F. euwallaceae, 6.55%, 3.27%, and 1.63%, respectively. We isolated 54 strains of F. verticillioides, and their genetic diversity was studied by inter simple sequence repeats (ISSR). The ISSR fingerprints (AG) 8C and (AG) 8G showed 252 and 368 microsatellite sites in the genome of F. verticillioides and resulted in 99-100% repeatability and reproducibility. The Simpson (SID) and Shannon (H) indices (0.78 and 2.36) suggest that F. verticillioides strains exhibit moderate to high diversity. Molecular detection of fumonisin B1 (FB1) biosynthetic genes (FUM1 and FUM13) involved in FB1 production in F. verticillioides was confirmed by polymerase chain reaction (PCR). Furthermore, 91% of the strains were positive for FB1 production, which was affirmed by liquid chromatography with tandem mass spectrometry (LC-MS-MS). In-vitro appurtenance of F. verticillioides spores exhibited a high to moderate effect on the growth and development of the maize. The current finding demonstrated that most F. verticillioides strains showed a wide range of genetic diversity with varied toxigenic and pathogenic potentials. In conclusion, for the first time, F. coffeatum, F. foetens, and F. euwallaceae species were reported from maize grain samples in India. They were positive for FB1 and negatively affecting grain quality, which is a major concern in food safety.

Biosynthesis of gold nanoparticles by Penicillium rubens and catalytic detoxification of ochratoxin A and organic dye pollutants.

The environmental pollution caused by chemical dyes is a growing concern nowadays. Limitations of traditional methods opened the route for nanotechnology; owing to the versatile properties of nanomaterials, gold nanoparticles (AuNPs) became a potential strategy for different applications. In the present study, biosynthesis of gold nanoparticles (BioAuNPs) was carried out by reacting chloroauric acid (HAuCl4) with cell-free filtrate of Penicillium rubens sp. nov. NCIM 1937. The AuNPs were then characterized by UV-visible spectroscopy, HR-TEM, FTIR, and DLS analysis to further examine their efficacious biosynthesis and morphological properties including size, shape, and stability. The biogenic AuNPs are polydisperse in nature, with a mean size of 14.92 ± 5 nm. These AuNPs exhibited promising antimicrobial activity against Escherichia coli NCIM-2065, Bacillus subtilis NCIM-2010, and Penicillium verrucosum MTCC 4935. In vitro quantitative HPLC results revealed that BioAuNPs significantly inhibited the biosynthesis of ochratoxin A (OTA). Microbial fuel cells (MFCs) are intriguing for power generation and wastewater treatment since they can directly transform chemical energy stored in organic matter to electricity by extracellular electron transfer (EET) via membrane proteins. AuNPs also showed excellent potential for dye degradation of organic pollutants, viz., methylene blue (MB), phenol red (PR), bromothymol blue (BTB), Congo red (CR), and 4-nitrophenol (4-NP). All dye removal efficiencies were estimated and fitted to pseudo-first-order processes using kinetic rate constants (Ka).The present study reveals a simple, original, and eco-friendly method for the synthesis of multifunctional biogenic AuNPs that could be effective in OTA detoxification in food products and organic pollutant removal during wastewater treatment for a sustainable environment.

Assembly, Annotation, and Comparative Whole Genome Sequence of Fusarium verticillioides Isolated from Stored Maize Grains.

Fusarium verticillioides is a plant pathogenic fungus affecting a wide range of crops worldwide due to its toxigenic properties. F. verticillioides BIONCL4 strain was isolated from stored maize grain samples in India, and produces high amount of fumonisin B1 (FB1). We report a comparative genomic analysis of F. verticillioides, covering the basic genome information, secretome, and proteins involved in host-pathogen interactions and mycotoxin biosynthesis. Whole-genome sequencing (WGS) was performed using the Illumina platform with an assembly size of 42.91 Mb, GC content of 48.24%, and 98.50% coverage with the reference genome (GCA000149555). It encodes 15,053 proteins, including 2058 secretory proteins, 676 classical secretory proteins, and 569 virulence and pathogenicity-related proteins. There were also 1447 genes linked to carbohydrate active enzymes (CaZymes) and 167 genes related to mycotoxin production. Furthermore, F. verticillioides genome comparison revealed information about the species' evolutionary history. The overall study helps in disease prevention and management of mycotoxins to ensure food safety.

Biosynthetic process and strain improvement approaches for industrial penicillin production.

Penicillins and cephalosporins are the most important class of beta (ß) lactam antibiotics, accounting for 65% total antibiotic market. Penicillins are produced by Penicillium rubens (popularly known as P. chrysogenum) were used to synthesize the active pharmaceutical intermediate (API), 6-aminopenicillinic acid (6-APA) employed in semisynthetic antibiotic production. The wild strains produce a negligible amount of penicillin (Pen). High antibiotic titre-producing P. chrysogenum strains are necessitating for industrial Pen production to meet global demand at lower prices. Classical strain improvement (CSI) approaches such as random mutagenesis, medium engineering, and fermentation are the cornerstones for high-titer Pen production. Since, Sir Alexander Fleming Discovery of Pen, great efforts are expanded to develop at a commercial scale antibiotics producing strains. Breakthroughs in genetic engineering, heterologous expression and CRISPR/Cas9 genome editing tools opened a new window for Pen production at a commercial scale to assure health crisis. The current state of knowledge, limitations of CSI and genetic engineering approaches to Pen production are discussed in this review.

Process Development for 6-Aminopenicillanic Acid Production Using Lentikats-Encapsulated Escherichia coli Cells Expressing Penicillin V Acylase.

Penicillin V acylase (PVA, EC 3.5.1.11) hydrolyzes the side chain of phenoxymethylpenicillin (Pen V) and finds application in the manufacture of the pharmaceutical intermediate 6-aminopenicillanic acid (6-APA). Here, we report the scale-up of cultivation of Escherichia coli whole cells expressing a highly active PVA from Pectobacterium atrosepticum and their encapsulation in polyvinyl alcohol-poly(ethylene glycol) Lentikats hydrogels. A biocatalytic process for the hydrolysis of 2% (w/v) Pen V was set up in a 2 L reactor using the Lentikats-immobilized whole cells, with a customized setup to enable continuous downstream processing of the reaction products. The biocatalytic reaction afforded complete conversion of Pen V for 10 reaction cycles, with an overall 90% conversion up to 50 cycles. The bioprocess was further scaled up to the pilot-scale at 10 L, enabling complete conversion of Pen V to 6-APA for 10 cycles. The 6-APA and phenoxy acetic acid products were recovered from downstream processing with isolated yields of 85-90 and 87-92%, respectively. Immobilization in Lentikats beads improved the stability of the whole cells on storage, maintaining 90-100% activity and similar conversion efficiency after 3 months at 4 °C. The robust PVA biocatalyst can be employed in a continuous process to provide a sustainable route for bulk 6-APA production from Pen V.