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Sawant AM, Navale VD, Vamkudoth KR. Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India. Int Microbiol 2024:10.1007/s10123-024-00491-0. [PMID: 38388812 DOI: 10.1007/s10123-024-00491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
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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Affiliation(s)
- Amol M Sawant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishwambar D Navale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Koteswara Rao Vamkudoth
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Liu X, Wang X, Zhou F, Xue Y, Liu C. Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments. BMC Genomics 2024; 25:4. [PMID: 38166640 PMCID: PMC10759354 DOI: 10.1186/s12864-023-09921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments. RESULTS Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain's adaptation to its environmental niche. CONCLUSIONS Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Xinran Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China.
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Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals (Basel) 2023; 16:1615. [PMID: 38004480 PMCID: PMC10675245 DOI: 10.3390/ph16111615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.
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Affiliation(s)
- Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11437, Saudi Arabia;
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Mohammad Aatif
- Department of Public Health, College of Applied Medical Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
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Shaaban R, Elnaggar MS, Khalil N, Singab ANB. A comprehensive review on the medicinally valuable endosymbiotic fungi Penicillium chrysogenum. Arch Microbiol 2023; 205:240. [PMID: 37195521 DOI: 10.1007/s00203-023-03580-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/20/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023]
Abstract
Recently, it has been shown that metabolites derived from endosymbiotic fungi attracted high attention, since plenty of them have promising pharmaceutical applications. The variation of metabolic pathways in fungi is considered an optimistic source for lead compounds. Among these classes are terpenoids, alkaloids, polyketides, and steroids, which have proved several pharmacological activities, including antitumor, antimicrobial, anti-inflammatory, and antiviral actions. This review concludes the major isolated compounds from different strains of Penicillium chrysogenum during the period 2013-2023, together with their reported pharmacological activities. From literature surveys, 277 compounds have been identified from P. chrysogenum, which has been isolated as an endosymbiotic fungus from different host organisms, with specific attention paid to those showing marked biological activities that could be useful in the pharmaceutical industry in the future. This review represents documentation for a valuable reference for promising pharmaceutical applications or further needed studies on P. chrysogenum.
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Affiliation(s)
- Rawan Shaaban
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo, 11835, Egypt
| | - Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Cairo, 11566, Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University, Cairo, 11566, Egypt
| | - Noha Khalil
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo, 11835, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Cairo, 11566, Egypt.
- Center of Drug Discovery Research and Development, Ain-Shams University, Cairo, 11566, Egypt.
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Wingfield LK, Jitprasitporn N, Che-alee N. Isolation and characterization of halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. PLoS One 2023; 18:e0281623. [PMID: 36780513 PMCID: PMC9925087 DOI: 10.1371/journal.pone.0281623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
The present study explored culturable halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. A total of 24 fungal isolates were discovered and characterized using morphological and molecular identification. Production of extracellular enzymes, secondary metabolites and mycoviruses was examined. Growth was observed in salinity and temperature ranges between 0%-20% and 28-40°C, respectively. Growth in different environmental conditions confirmed the halophilic or halotolerant nature of some strains. Fungal isolates were phylogenetically classified into seven different genera belonging to Aspergillus, Cladosporium, Curvularia, Diaporthe, Ectophoma, Fusarium and Penicillium. An enzymatic production test revealed that thirteen isolates could produce proteases and amylases at different levels. The presence of mycoviruses was detected in three isolates. Seventeen of the 24 isolates produced antimicrobial metabolites. The majority of these active isolates were identified as Aspergillus and Penicillium species. Crude extracts of the fungal mycelia and culture broths from these isolates had an inhibitory effect on both Gram-positive and Gram-negative bacteria and human pathogenic fungi. Research into fungi from saline environments could reveal fungal strains of biotechnological and industrial interest.
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Affiliation(s)
- Lakkhana Kanhayuwa Wingfield
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- * E-mail:
| | - Ninadia Jitprasitporn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Nureeda Che-alee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Zhou YQ, Yao SC, Wang J, Xie XY, Tan XM, Huang RS, Yang XF, Tan Y, Yu LY, Fu P. Cultivable endophytic fungal community associated with the karst endemic plant Nervilia fordii and their antimicrobial activity. Front Microbiol 2022; 13:1063897. [PMID: 36504825 PMCID: PMC9730403 DOI: 10.3389/fmicb.2022.1063897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Endophytic fungi from medicinal plants with specific pharmacological functions attract much attention to provide the possibility of discovering valuable natural drugs with novel structures and biological activities. Nervilia fordii is a rare and endangered karst endemic plant that is used as medicine and food homology in Guangxi, China. These plants have been reported to have antimicrobial, antitumor, antiviral, and anti-inflammatory activities. However, few studies have focused on the diversity and antibacterial activity of endophytic fungi from N. fordii. In the present study, 184 endophytic fungi were isolated from the healthy tissues of N. fordii, and their molecular diversity and antimicrobial activities were analyzed for the first time. These fungi were categorized into 85 different morphotypes based on the morphological characteristics and the similarity between the target sequence and the reference sequence in the GenBank database. With the exception of 18 unidentified fungi, the fungal isolates belonged to at least 2 phyla, 4 classes, 15 orders, 45 known genera, and 45 different species, which showed high abundance, rich diversity, and obvious tissue specificity. All isolates were employed to screen for their antimicrobial activities via the agar diffusion method against Escherichia coli, Staphylococcus aureus, and Candida tropicalis. Among these endophytes, eight strains (9.41%) displayed inhibitory activity against E. coli, 11 strains (12.94%) against S. aureus, and two strains (2.35%) against C. tropicalis, to some extent. In particular, our study showed for the first time that the fungal agar plugs of Penicillium macrosclerotiorum 1151# exhibited promising antibacterial activity against E. coli and S. aureus. Moreover, the ethyl acetate (EA) extract of P. macrosclerotiorum 1151# had antibacterial effects against E. coli and S. aureus with a minimum inhibitory concentration (MIC) of 0.5 mg ml-1. Further research also confirmed that one of the antimicrobial compounds of P. macrosclerotiorum 1151# was methyl chloroacetate and exhibited excellent antibacterial activity against E. coli and S. aureus up to 1.71-fold and 1.13-fold compared with tetracycline (TET) (5 mg ml-1), respectively. Taken together, the present data suggest that various endophytic fungi of N. fordii could be exploited as sources of novel natural antimicrobial agents.
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Affiliation(s)
- Ya-Qin Zhou
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Conservation and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Shao-Chang Yao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Jie Wang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Zhuang Yao Key Laboratory of Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Xin-Yi Xie
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiao-Ming Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Rong-Shao Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Xin-Feng Yang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Yong Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
| | - Li-Ying Yu
- Guangxi Key Laboratory of Medicinal Resources Conservation and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Peng Fu
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Zhuang Yao Key Laboratory of Medicine, Guangxi University of Chinese Medicine, Nanning, China
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Nasution AK, Wijaya SH, Gao P, Islam RM, Huang M, Ono N, Kanaya S, Altaf-Ul-Amin M. Prediction of Potential Natural Antibiotics Plants Based on Jamu Formula Using Random Forest Classifier. Antibiotics (Basel) 2022; 11:antibiotics11091199. [PMID: 36139978 PMCID: PMC9495033 DOI: 10.3390/antibiotics11091199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Jamu is the traditional Indonesian herbal medicine system that is considered to have many benefits such as serving as a cure for diseases or maintaining sound health. A Jamu medicine is generally made from a mixture of several herbs. Natural antibiotics can provide a way to handle the problem of antibiotic resistance. This research aims to discover the potential of herbal plants as natural antibiotic candidates based on a machine learning approach. Our input data consists of a list of herbal formulas with plants as their constituents. The target class corresponds to bacterial diseases that can be cured by herbal formulas. The best model has been observed by implementing the Random Forest (RF) algorithm. For 10-fold cross-validations, the maximum accuracy, recall, and precision are 91.10%, 91.10%, and 90.54% with standard deviations 1.05, 1.05, and 1.48, respectively, which imply that the model obtained is good and robust. This study has shown that 14 plants can be potentially used as natural antibiotic candidates. Furthermore, according to scientific journals, 10 of the 14 selected plants have direct or indirect antibacterial activity.
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Affiliation(s)
- Ahmad Kamal Nasution
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
- Correspondence: (A.K.N.); (M.A.-U.-A.)
| | - Sony Hartono Wijaya
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Pei Gao
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - Rumman Mahfujul Islam
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - Ming Huang
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - Naoaki Ono
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - Shigehiko Kanaya
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
| | - Md. Altaf-Ul-Amin
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0101, Japan
- Correspondence: (A.K.N.); (M.A.-U.-A.)
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