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Kamiński B, Paczesny J. Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook. Pathogens 2024; 13:152. [PMID: 38392890 PMCID: PMC10893365 DOI: 10.3390/pathogens13020152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.
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Affiliation(s)
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
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2
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Watson DJ, Wiesner L, Matimela T, Beukes D, Meyers PR. Tandem LC-MS Identification of Antitubercular Compounds in Zones of Growth Inhibition Produced by South African Filamentous Actinobacteria. Molecules 2023; 28:molecules28114276. [PMID: 37298751 DOI: 10.3390/molecules28114276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Novel antitubercular compounds are urgently needed to combat drug-resistant Mycobacterium tuberculosis (Mtb). Filamentous actinobacteria have historically been an excellent source of antitubercular drugs. Despite this, drug discovery from these microorganisms has fallen out of favour due to the continual rediscovery of known compounds. To increase the chance of discovering novel antibiotics, biodiverse and rare strains should be prioritised. Subsequently, active samples need to be dereplicated as early as possible to focus efforts on truly novel compounds. In this study, 42 South African filamentous actinobacteria were screened for antimycobacterial activity using the agar overlay method against the Mtb indicator Mycolicibacterium aurum under six different nutrient growth conditions. Known compounds were subsequently identified through extraction and high-resolution mass spectrometric analysis of the zones of growth inhibition produced by active strains. This allowed the dereplication of 15 hits from six strains that were found to be producing puromycin, actinomycin D and valinomycin. The remaining active strains were grown in liquid cultures, extracted and submitted for screening against Mtb in vitro. Actinomadura napierensis B60T was the most active sample and was selected for bioassay-guided purification. This resulted in the identification of tetromadurin, a known compound, but which we show for the first time to have potent antitubercular activity, with the MIC90s within the range of 73.7-151.6 nM against M. tuberculosis H37RvTin vitro under different test conditions. This shows that South African actinobacteria are a good source of novel antitubercular compounds and warrant further screening. It is also revealed that active hits can be dereplicated by HPLC-MS/MS analysis of the zones of growth inhibition produced by the agar overlay technique.
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Affiliation(s)
- Daniel J Watson
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town 7700, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town 7700, South Africa
| | - Tlhalefo Matimela
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town 7700, South Africa
| | - Denzil Beukes
- School of Pharmacy, University of the Western Cape, Bellville 7535, South Africa
| | - Paul R Meyers
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7700, South Africa
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Hu M, Chen S, Ni Y, Wei W, Mao W, Ge M, Qian X. CRISPR/Cas9-mediated genome editing in vancomycin-producing strain Amycolatopsis keratiniphila. Front Bioeng Biotechnol 2023; 11:1141176. [PMID: 36937767 PMCID: PMC10020181 DOI: 10.3389/fbioe.2023.1141176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Amycolatopsis is an important source of diverse valuable bioactive natural products. The CRISPR/Cas-mediated gene editing tool has been established in some Amycolatopsis species and has accomplished the deletion of single gene or two genes. The goal of this study was to develop a high-efficient CRISPR/Cas9-mediated genome editing system in vancomycin-producing strain A. keratiniphila HCCB10007 and enhance the production of vancomycin by deleting the large fragments of ECO-0501 BGC. By adopting the promoters of gapdhp and ermE*p which drove the expressions of scocas9 and sgRNA, respectively, the all-in-one editing plasmid by homology-directed repair (HDR) precisely deleted the single gene gtfD and inserted the gene eGFP with the efficiency of 100%. Furthermore, The CRISPR/Cas9-mediated editing system successfully deleted the large fragments of cds13-17 (7.7 kb), cds23 (12.7 kb) and cds22-23 (21.2 kb) in ECO-0501 biosynthetic gene cluster (BGC) with high efficiencies of 81%-97% by selecting the sgRNAs with a suitable PAM sequence. Finally, a larger fragment of cds4-27 (87.5 kb) in ECO-0501 BGC was deleted by a dual-sgRNA strategy. The deletion of the ECO-0501 BGCs revealed a noticeable improvement of vancomycin production, and the mutants, which were deleted the ECO-0501 BGCs of cds13-17, cds22-23 and cds4-27, all achieved a 30%-40% increase in vancomycin yield. Therefore, the successful construction of the CRISPR/Cas9-mediated genome editing system and its application in large fragment deletion in A. keratiniphila HCCB10007 might provide a powerful tool for other Amycolatopsis species.
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Affiliation(s)
- Mengyi Hu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Ni
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Wenwei Mao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Xiuping Qian
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
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Nag A, Mehra S. Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator. Appl Microbiol Biotechnol 2022; 106:2175-2190. [PMID: 35194656 DOI: 10.1007/s00253-022-11837-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/05/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
Overexpression of efflux pumps represents a key mechanism of resistance in bacteria. Soil bacteria such as Streptomyces harbour a vast array of efflux genes that are transcriptionally silent under laboratory conditions. However, dissemination of many of these genes into clinical pathogens via horizontal gene transfer results in conferring resistance to multiple drugs. In this study, we have identified the role of a MFS transporter, SCO3366 from Streptomyces coelicolor, in governing multidrug resistance. Overexpression and knockout studies revealed that SCO3366 provides resistance to several structurally unrelated drugs including ciprofloxacin, chloramphenicol, rifampicin and EtBr, with rifampicin being the major substrate. Beyond multidrug resistance, SCO3366 was efficient in providing tolerance towards oxidative stress. A combinatorial mechanism of increased oxidative stress tolerance decreased intracellular drug levels and decreased permeability act synergistically to provide resistance towards rifampicin. Shedding light on the regulation of SCO3366, we find the pump to be directly regulated by the TetR regulator SCO3367 in a negative manner and the repression was found to be relieved in presence of different compounds recognized as substrates of SCO3366. KEY POINTS: • First reported rifampicin efflux pump in Streptomyces coelicolor • Resistance to rifampicin is the result of a synergistic action of increased efflux with increased oxidative stress tolerance and decreased permeability, which can potentially arise in clinically relevant bacteria • SCO3366-SCO3367 to be a novel system that operates to protect the bacteria under varied environmental stress conditions.
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Affiliation(s)
- Ankita Nag
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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George J. Metabolism and interactions of antileprosy drugs. Biochem Pharmacol 2020; 177:113993. [PMID: 32339493 DOI: 10.1016/j.bcp.2020.113993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/21/2020] [Indexed: 01/29/2023]
Abstract
Leprosy is a chronic infectious disease caused my Mycobacterium leprae that primarily affects peripheral nervous system and extremities and is prevalent in tropical countries. Treatment for leprosy with multidrug regimens is very effective compared to monotherapy especially in multibacillary cases. The three major antileprosy drugs currently in use are 4, 4'-diaminodiphenyl sulfone (DDS, dapsone), rifampicin, and clofazimine. During multidrug therapy, the potent antibiotic rifampicin induces the metabolism of dapsone, which results in decreased plasma half-life of dapsone and its metabolites. Furthermore, rifampicin induces its own metabolism and decreases its half-life during monotherapy. Rifampicin upregulates several hepatic microsomal drug-metabolizing enzymes, especially cytochrome P450 (CYP) family that in turn induce the metabolism of dapsone. Clofazimine lacks significant induction of any drug-metabolizing enzyme including CYP family and does not interact with dapsone metabolism. Rifampicin does not induce clofazimine metabolism during combination treatment. Administration of dapsone in the acetylated form (acedapsone) can release the drug slowly into circulation up to 75 days and could be useful for the effective treatment of paucibacillary cases along with rifampicin. This review summarizes the major aspects of antileprosy drug metabolism and drug interactions and the role of cytochrome P450 family of drug metabolizing enzymes, especially CYP3A4 during multidrug regimens for the treatment of leprosy.
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Affiliation(s)
- Joseph George
- Department of Biochemistry, Central Leprosy Teaching and Research Institute, Chengalpattu 603001, Tamil Nadu, India.
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Qi F, Lei C, Li F, Zhang X, Wang J, Zhang W, Fan Z, Li W, Tang GL, Xiao Y, Zhao G, Li S. Deciphering the late steps of rifamycin biosynthesis. Nat Commun 2018; 9:2342. [PMID: 29904078 PMCID: PMC6002545 DOI: 10.1038/s41467-018-04772-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/12/2018] [Indexed: 12/12/2022] Open
Abstract
Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C–O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families. The enzymes Rif15 and Rif16 are involved in the late steps of the biosynthesis of rifamycins, a group of antibiotics. Here, the authors characterized these two proteins and found that they catalyse unusual biochemical reactions.
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Affiliation(s)
- Feifei Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Chao Lei
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhen Fan
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
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Kumari R, Singh P, Lal R. Genetics and Genomics of the Genus Amycolatopsis. Indian J Microbiol 2016; 56:233-46. [PMID: 27407288 PMCID: PMC4920768 DOI: 10.1007/s12088-016-0590-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/23/2016] [Indexed: 02/06/2023] Open
Abstract
Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies.
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Affiliation(s)
- Rashmi Kumari
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
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Draft Genome Sequence of Rifamycin Derivatives Producing Amycolatopsis mediterranei Strain DSM 46096/S955. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00837-14. [PMID: 25125653 PMCID: PMC4132629 DOI: 10.1128/genomea.00837-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Amycolatopsis mediterranei DSM 46096 produces antibiotics of the rifamycin family, 27-demethoxy-27-hydroxyrifamycin B, 25-desacetyl-27-demethoxy-27-hydroxyrifamycin, and 27-demethoxy-27-hydroxyrifamycin SV, which are effective against Gram-negative bacteria. Here, we present the draft genome of A. mediterranei 46096 (approx. 10.2 Mbp) having 104 contigs with a GC content of 71.3% and 9,382 coding sequences.
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Draft Genome Sequence of Amycolatopsis mediterranei DSM 40773, a Tangible Antibiotic Producer. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00752-14. [PMID: 25081263 PMCID: PMC4118066 DOI: 10.1128/genomea.00752-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Amycolatopsis mediterranei DSM 40773 has been of special interest as successors of this strain are in use for the commercial production of rifamycin B. Here we present the draft genome sequence (~10 Mb) of this strain, which contains 108 contigs, 9,198 genes, and has a G+C content of 71.3%.
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