1
|
Perez JV, Serrano L, Viteri R, Sosa D, Romero CA, Diez N. Antarctic Streptomyces: Promising biocontrol agents for combating Fusarium oxysporum f. sp. cubense. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 43:e00852. [PMID: 39282660 PMCID: PMC11402157 DOI: 10.1016/j.btre.2024.e00852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024]
Abstract
Fusarium wilt of Banana (FWB) caused by Fusarium oxysporum f. sp. cubense (Foc) poses a significant threat to the banana industry, with current inadequate control measures. This study evaluated the antifungal potential of nine Streptomyces strains isolated from Antarctic soil samples, using Casein-Starch media to stimulate the production of antifungal compounds. The inhibition spectrum against Foc was assessed under laboratory conditions using the well diffusion on Mueller-Hinton agar, with antifungal activity measured in arbitrary units (AU/mL) and minimum inhibitory concentration (MIC) tested using ethyl acetate extracts. Among the nine isolates, K6 and E7 were closely related to Streptomyces polyrhachis and Streptomyces fildesensis, exhibited significant antifungal activity, with K6 and E7 showing 320 and 80 AU/mL, and MIC values of 250 and >500 ppm, respectively. These findings highlight K6 and E7 as potential biocontrol agents against Foc, offering new avenues for sustainable Fusarium wilt management in banana cultivation.
Collapse
Affiliation(s)
- Jeffrey Vargas Perez
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Lizette Serrano
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Rafael Viteri
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Daynet Sosa
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida (FCV), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Christian A Romero
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Universidad Bolivariana del Ecuador, UBE, Carrera de Enfermería, Km 5.5 vía Durán-Yaguachi, Durán, Ecuador
| | - Nardy Diez
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador (CIBE), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida (FCV), Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| |
Collapse
|
2
|
Ghareeb A, Fouda A, Kishk RM, El Kazzaz WM. Unlocking the therapeutic potential of bioactive exopolysaccharide produced by marine actinobacterium Streptomyces vinaceusdrappus AMG31: A novel approach to drug development. Int J Biol Macromol 2024; 276:133861. [PMID: 39029838 DOI: 10.1016/j.ijbiomac.2024.133861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/27/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Acidic exopolysaccharide (EPS) was produced by a marine actinobacterium Streptomyces vinaceusdrappus strain AMG31 with the highest yield of 10.6 g/l. The synthesized EPS has an average molecular weight of 5.1 × 104 g/mol and contains arabinose, glucose, galacturonic acid (0.5:2:2 M ratio), with 39.77 % uronic acid residues and 18.8 % sulfate detected. EPS exhibited antioxidant activities with 93.8 % DPPH radical scavenging and 344.7 μg/mg total antioxidant capacity. It displayed anti-inflammatory effects by inhibiting 5-LOX and COX-2. Regarding the cytotoxic activity, the IC50 values are 301.6 ± 11.8, 260.8 ± 12.2, 29.4 ± 13.5, 351.3 ± 11.2, 254.1 ± 9.8, and 266.5 ± 10.4 μg/ml for PC-3, HEP-2, MCF-7, HCT-116, A-549, HepG-2 respectively, which indicate that the produced EPS does not have strong cytotoxic activities. Moreover, the EPS showed anti-Alzheimer activity via inhibition of the Butyrylcholinesterase enzyme, with the highest percentage of 84.5 % at 100 μg/ml. Interestingly, the EPS showed superior anti-obesity activity by inhibiting lipase enzyme with a rate of 95.3 % compared to orlistat as a positive control (96.8 %) at a concentration of 1000 μg/ml. Additionally, the produced EPS displayed the highest anti-diabetic properties by inhibiting α-amylase (IC50 31.49 μg/ml) and α-glucosidase (IC50 6.48 μg/ml), suggesting antidiabetic potential analogous to acarbose. EPS exhibited promising antibacterial and antibiofilm activity against a wide range of Gram-positive and Gram-negative pathogenic bacteria.
Collapse
Affiliation(s)
- Ahmed Ghareeb
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Amr Fouda
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt; School of Nuclear Science and Technology, University of South China, Heng Yang, China.
| | - Rania M Kishk
- Microbiology and Immunology Department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Waleed M El Kazzaz
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| |
Collapse
|
3
|
Anjum MS, Khaliq S, Ashraf N, Anwar MA, Akhtar K. Bioactive Streptomycetes: A Powerful Tool to Synthesize Diverse Nanoparticles With Multifarious Properties. J Basic Microbiol 2024; 64:e2400129. [PMID: 38922954 DOI: 10.1002/jobm.202400129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Nanobiotechnology has gained significant attention due to its capacity to generate substantial benefits through the integration of microbial biotechnology and nanotechnology. Among microbial organisms, Actinomycetes, particularly the prominent genus Streptomycetes, have garnered attention for their prolific production of antibiotics. Streptomycetes have emerged as pivotal contributors to the discovery of a substantial number of antibiotics and play a dominant role in combating infectious diseases on a global scale. Despite the noteworthy progress achieved through the development and utilization of antibiotics to combat infectious pathogens, the prevalence of infectious diseases remains a prominent cause of mortality worldwide, particularly among the elderly and children. The emergence of antibiotic resistance among pathogens has diminished the efficacy of antibiotics in recent decades. Nevertheless, Streptomycetes continue to demonstrate their potential by producing bioactive metabolites for the synthesis of nanoparticles. Streptomycetes are instrumental in producing nanoparticles with diverse bioactive characteristics, including antiviral, antibacterial, antifungal, antioxidant, and antitumor properties. Biologically synthesized nanoparticles have exhibited a meaningful reduction in the impact of antibiotic resistance, providing resources for the development of new and effective drugs. This review succinctly outlines the significant applications of Streptomycetes as a crucial element in nanoparticle synthesis, showcasing their potential for diverse and enhanced beneficial applications.
Collapse
Affiliation(s)
- Muhammad Sultan Anjum
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- Institute of Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, Albert-Ludwig University of Freiburg, Freiburg im Breisgau, Germany
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| |
Collapse
|
4
|
Tang LF, Jihuo WL, Shi PD, Mei CX, Zhao ZK, Chen Y, Di YT, Hao XJ, Cao M, Zhao Y, Che YY. Cytotoxic glutarimide-containing polyketides isolated from Streptomyces sp. JCM 4793. J Antibiot (Tokyo) 2024; 77:627-633. [PMID: 38816449 DOI: 10.1038/s41429-024-00743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Glutarimide-containing polyketides usually exhibit anti-fungi activity, which was well exampled by cycloheximide. In our work, three new polyketide structures, 12-amidestreptimidone (1), 12-carboxylstreptimidone (2) and 3-(5S,8R)-(2-amino-2-oxoethyl-2'-methoxy-2'-oxoethyl)-8,10-dimethyl-7-oxododeca-5-hydroxy-9E,11-diolefin (3) were isolated from Streptomyces sp. JCM 4793. 3 without the glutarimide moiety is not active against fungi as expected, while 1 bearing the amide moiety is much more active than its carboxylic form 2. Here we report the isolation, structural elucidation, antifungal activity, and proposed biosynthesis pathway of 1-3.
Collapse
Affiliation(s)
- Lin-Fang Tang
- Faculty of Pharmacy, Yunnan University of TCM, Kunming, Yunnan, 650500, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Wu-Lai Jihuo
- Faculty of Pharmacy, Yunnan University of TCM, Kunming, Yunnan, 650500, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Pei-Dong Shi
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Cui-Xuan Mei
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Zi-Kang Zhao
- Faculty of Pharmacy, Yunnan University of TCM, Kunming, Yunnan, 650500, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yuan Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ying-Tong Di
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Mingming Cao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Yi Zhao
- Faculty of Pharmacy, Yunnan University of TCM, Kunming, Yunnan, 650500, China.
| | - Yan-Yun Che
- Faculty of Pharmacy, Yunnan University of TCM, Kunming, Yunnan, 650500, China.
| |
Collapse
|
5
|
Mispelaere M, De Rop AS, Hermans C, De Maeseneire SL, Soetaert WK, De Mol ML, Hulpiau P. Whole genome-based comparative analysis of the genus Streptomyces reveals many misclassifications. Appl Microbiol Biotechnol 2024; 108:453. [PMID: 39212721 PMCID: PMC11364561 DOI: 10.1007/s00253-024-13290-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species. KEY POINTS: • Evaluation of taxonomic classification methods for Streptomyces species. • Whole genome analysis, specifically FastANI, has been chosen as preferred method. • Various reclassifications are proposed within the Streptomyces genus.
Collapse
Affiliation(s)
- Marieke Mispelaere
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium
| | - Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Cedric Hermans
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim K Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Maarten L De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.Be), Department of Biotechnology, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Paco Hulpiau
- Bioinformatics Knowledge Center (BiKC), Cluster Life Sciences, Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200, Brugge, Belgium.
| |
Collapse
|
6
|
Jansen Z, Alameri A, Wei Q, Kulhanek DL, Gilmour AR, Halper S, Schwalm ND, Thyer R. A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation. Appl Environ Microbiol 2024; 90:e0034024. [PMID: 39082821 PMCID: PMC11337820 DOI: 10.1128/aem.00340-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/29/2024] [Indexed: 08/22/2024] Open
Abstract
Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.
Collapse
Affiliation(s)
- Zachary Jansen
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Abdulaziz Alameri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Qiyao Wei
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Devon L. Kulhanek
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Andrew R. Gilmour
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Sean Halper
- DEVCOM Army Research Laboratory, Adelphi, Maryland, USA
| | | | - Ross Thyer
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| |
Collapse
|
7
|
Al Mamun A, Alam K, Koly FA, Showline Chaity F, Ferdous J, Islam S. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in Streptomyces bacteria. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-14. [PMID: 39140768 DOI: 10.1080/10286020.2024.2390510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are a novel category of bioactive natural products (NPs). Streptomyces bacteria are a potential source of many bioactive NPs. Limited opportunities are available to characterize all the bioactive NP gene clusters. In this study, 410 sequences of Streptomyces were analyzed for RiPPs through genome mining using the National Center for Biotechnology Information (NCBI), by combining BAGEL and anti-SMASH. A total of 4098 RiPPs were found; including both classified (lanthipeptide, RiPP-like, bacteriocin, LAPs, lassopeptide, thiopeptides) and nonclassified RiPPs. Soil was identified as a rich habitat for RiPPs. These data may offer alternative future remedies for various health issues.
Collapse
Affiliation(s)
- Abdullah Al Mamun
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Khorshed Alam
- Bangladesh Standards and Testing Institution (BSTI), Dhaka, Bangladesh
| | - Farjana Akter Koly
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Farjana Showline Chaity
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Jannatul Ferdous
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| |
Collapse
|
8
|
Rodríguez M, Cuervo L, Prado‐Alonso L, González‐Moreno MS, Olano C, Méndez C. The role of Streptomyces to achieve the United Nations sustainable development goals. Burning questions in searching for new compounds. Microb Biotechnol 2024; 17:e14541. [PMID: 39096299 PMCID: PMC11297445 DOI: 10.1111/1751-7915.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 08/05/2024] Open
Affiliation(s)
- Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Lorena Cuervo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Laura Prado‐Alonso
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - María Soledad González‐Moreno
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A)Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria de Asturias (ISPA)OviedoSpain
| |
Collapse
|
9
|
Krysenko S, Wohlleben W. Role of Carbon, Nitrogen, Phosphate and Sulfur Metabolism in Secondary Metabolism Precursor Supply in Streptomyces spp. Microorganisms 2024; 12:1571. [PMID: 39203413 PMCID: PMC11356490 DOI: 10.3390/microorganisms12081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds.
Collapse
Affiliation(s)
- Sergii Krysenko
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
10
|
Louviot F, Abdelrahman O, Abou-Mansour E, L'Haridon F, Allard PM, Falquet L, Weisskopf L. Oligomycin-producing Streptomyces sp. newly isolated from Swiss soils efficiently protect Arabidopsis thaliana against Botrytis cinerea. mSphere 2024; 9:e0066723. [PMID: 38864637 PMCID: PMC11288007 DOI: 10.1128/msphere.00667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/05/2024] [Indexed: 06/13/2024] Open
Abstract
Botrytis cinerea is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been developed to control this disease, resulting in the rise of fungicide-resistance B. cinerea strains. The aim of this study was to identify Streptomyces strains showing antagonistic activity against B. cinerea to contribute to plant protection in an environmentally friendly way. We isolated 15 Actinomycete strains from 9 different Swiss soils. The culture filtrates of three isolates showing antifungal activity inhibited spore germination and delayed mycelial growth of B. cinerea. Infection experiments showed that Arabidopsis thaliana plants were more resistant to this pathogen after leaf treatment with the Streptomyces filtrates. Bioassay-guided isolation of the active compounds revealed the presence of germicidins A and B as well as of oligomycins A, B, and E. While germicidins were mostly inactive, oligomycin B reduced the mycelial growth of B. cinerea significantly. Moreover, all three oligomycins inhibited this fungus' spore germination, suggesting that these molecules might contribute to the Streptomyces's ability to protect plants against infection by the broad host-pathogen Botrytis cinerea. IMPORTANCE This study reports the isolation of new Streptomyces strains with strong plant-protective potential mediated by their production of specialized metabolites. Using the broad host range pathogenic fungus Botrytis cinerea, we demonstrate that the cell-free filtrate of selected Streptomyces isolates efficiently inhibits different developmental stages of the fungus, including mycelial growth and the epidemiologically relevant spore germination. Beyond in vitro experiments, the strains and their metabolites also efficiently protected plants against the disease caused by this pathogen. This work further identifies oligomycins as active compounds involved in the observed antifungal activity of the strains. This work shows that we can harness the natural ability of soil-borne microbes and of their metabolites to efficiently fight other microbes responsible for significant crop losses. This opens the way to the development of environmentally friendly health protection measures for crops of agronomical relevance, based on these newly isolated strains or their metabolic extracts containing oligomycins.
Collapse
Affiliation(s)
- Fanny Louviot
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ola Abdelrahman
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Food Research and Innovation Centre, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
11
|
Sekurova ON, Zehl M, Predl M, Hunyadi P, Rattei T, Zotchev SB. Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism. Microb Cell Fact 2024; 23:201. [PMID: 39026318 PMCID: PMC11256431 DOI: 10.1186/s12934-024-02479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Ethanol shock significantly affects expression of over 1200 genes in Streptomyces venezuelae NRRL B-65,442, including those involved in secondary metabolite biosynthesis and a cryptic gene pepX, which encodes a 19-amino acid peptide with an unknown function. RESULTS To establish a possible correlation between the PepX peptide and secondary metabolism in S. venezuelae, its gene was deleted, followed by analyses of the transcriptome and secondary metabolome of the mutant. Although the secondary metabolome of the pepX mutant was not strongly affected, pepX deletion, similar to ethanol shock, mostly resulted in downregulated expression of secondary metabolite biosynthesis gene clusters (BGCs). At the same time, there was a reverse correlation between the expression of certain extracytoplasmic function sigma factors (ECFs) and several BGCs. Individual deletions of three selected ECF-coding genes conserved in Streptomyces that were upregulated upon both pepX deletion and ethanol shock, had a profound positive effect on the expression of BGCs, which also correlated with the overproduction of specific secondary metabolites. Deletion of one such ECF-coding gene in a marine sponge-derived Streptomyces sp. also significantly altered the secondary metabolite profile, suggesting an important role of this ECF in the regulation of secondary metabolism. CONCLUSIONS These findings pave the way for the activation or upregulation of BGCs in Streptomyces bacteria harboring genes for ECFs homologous to those identified in this study, hereby assisting in the discovery of novel bioactive secondary metabolites.
Collapse
Affiliation(s)
- Olga N Sekurova
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, 1090, Austria
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Michael Predl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, 1030, Austria
| | - Peter Hunyadi
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, 1030, Austria
| | - Sergey B Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, 1090, Austria.
| |
Collapse
|
12
|
Mazumdar R, Thakur D. Antibacterial activity and biosynthetic potential of Streptomyces sp. PBR19, isolated from forest rhizosphere soil of Assam. Braz J Microbiol 2024:10.1007/s42770-024-01454-3. [PMID: 38985434 DOI: 10.1007/s42770-024-01454-3] [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: 03/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
An Actinomycetia isolate, designated as PBR19, was derived from the rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate, identified as Streptomyces sp., shares a sequence similarity of 93.96% with its nearest type strain, Streptomyces atrovirens. This finding indicates the potential classification of PBR19 as a new taxon within the Actinomycetota phylum. PBR19 displayed notable antibacterial action against some ESKAPE pathogens. The ethyl acetate extract of PBR19 (EtAc-PBR19) showed the lowest minimum inhibitory concentration (MIC) of ≥ 0.195 µg/mL against Acinetobacter baumannii ATCC BAA-1705. A lower MIC indicates higher potency against the tested pathogen. Scanning electron microscope (SEM) findings revealed significant changes in the cytoplasmic membrane structure of the pathogen. This suggests that the antibacterial activity may be linked to the disruption of the microbial membrane. The predominant chemical compound detected in the EtAc-PBR19 was identified as phenol, 3,5-bis(1,1-dimethylethyl), comprising 48.59% of the area percentage. Additionally, PBR19 was found to contain the type II polyketide synthases (PKS type II) gene associated with antibiotic synthesis. The predicted gene product of PKSII was identified as the macrolide antibiotic Megalomicin A. The taxonomic distinctiveness, potent antibacterial effects, and the presence of a gene associated with antibiotic synthesis suggest that PBR19 could be a valuable candidate for further exploration in drug development and synthetic biology. The study contributes to the broader understanding of microbial diversity and the potential for discovering bioactive compounds in less-explored environments.
Collapse
Affiliation(s)
- Rajkumari Mazumdar
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Debajit Thakur
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India.
| |
Collapse
|
13
|
Wang R, Li B, Cai S, Ding Y, Shi M, Jin T, Lin W, Liu P. Genetic Diversity of Ralstonia solanacearum Causing Tobacco Bacterial Wilt in Fujian Province and Identification of Biocontrol Streptomyces sp. PLANT DISEASE 2024; 108:1946-1958. [PMID: 38499975 DOI: 10.1094/pdis-08-23-1604-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Tobacco bacterial wilt is a highly destructive soilborne disease caused by the Ralstonia solanacearum species complex, exhibiting a significant risk to global flue-cured tobacco cultivation and resulting in substantial economic loss. In this study, 77 isolates were collected from three prominent flue-cured tobacco cultivation areas in Fujian, China (Nanping, Sanming, and Longyan), in 2021 and 2022. The isolated strains were classified through phylotype-specific multiplex polymerase chain reaction (Pmx-PCR) and physiological tests. The analysis showed that all the strains were associated with phylotype I, race 1, and biovar III. Subsequent phylogenetic analysis using partial egl gene sequences classified the 77 isolates into 5 distinct sequevars: 13, 15, 16, 17, and 34. Notably, a remarkable predominance of sequevar 15 was observed in Fujian Province, while sequevar 16 was first reported on tobacco in China, which was identified in other plants, expanding the understanding of its host range and distribution in the country. In addition, a Streptomyces strain extracted from the rhizosphere soil of tobacco was found to inhibit the growth of multiple sequevars of tobacco R. solanacearum, indicating its broad-spectrum antagonistic properties. Furthermore, pot experiments showed that the strain St35 effectively controlled tobacco bacterial wilt. The isolate St35 was conclusively identified as Streptomyces gancidicus according to the morphological and genetic features. In summary, the present study demonstrated the genetic diversity and distribution of tobacco R. solanacearum strains in the Fujian province of China, as well as the identification of a candidate biological control agent for the management of tobacco bacterial wilt.
Collapse
Affiliation(s)
- Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Benjin Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Songling Cai
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yingfu Ding
- Nanping Branch, Fujian Tobacco Company, Nanping 353000, China
| | - Mingyue Shi
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Ting Jin
- Xiamen Chanke Bioengineering Co., Ltd., Xiamen 361000, China
| | - Wei Lin
- Nanping Branch, Fujian Tobacco Company, Nanping 353000, China
| | - Peiqing Liu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| |
Collapse
|
14
|
Cerna-Chávez E, Rodríguez-Rodríguez JF, García-Conde KB, Ochoa-Fuentes YM. Potential of Streptomyces avermitilis: A Review on Avermectin Production and Its Biocidal Effect. Metabolites 2024; 14:374. [PMID: 39057697 PMCID: PMC11278826 DOI: 10.3390/metabo14070374] [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: 04/18/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Secondary metabolites produced by the fermentation of Streptomyces avermitilis bacterium are powerful antiparasitic agents used in animal health, agriculture and human infection treatments. Avermectin is a macrocyclic lactone with four structural components (A1, A2, B1, B2), each of them containing a major and a minor subcomponent, out of which avermectin B1a is the most effective parasitic control compound. Avermectin B1a produces two homologue avermectins (B1 and B2) that have been used in agriculture as pesticides and antiparasitic agents, since 1985. It has a great affinity with the Cl-channels of the glutamate receptor, allowing the constant flow of Cl- ions into the nerve cells, causing a phenomenon of hyperpolarization causing death by flaccid paralysis. The purpose of this work was to gather information on the production of avermectins and their biocidal effects, with special emphasis on their role in the control of pests and phytopathogenic diseases. The literature showed that S. avermitilis is an important producer of macrocyclic lactones with biocidal properties. In addition, avermectin contributes to the control of ectoparasites and endoparasites in human health care, veterinary medicine and agriculture. Importantly, avermectin is a compound that is harmless to the host (no side effects), non-target organisms and the environment.
Collapse
Affiliation(s)
- Ernesto Cerna-Chávez
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Calzada Antonio Narro 1923, Saltillo 25315, Coahuila, Mexico;
| | - José Francisco Rodríguez-Rodríguez
- Estudiante de Postgrado en Ciencias en Parasitología Agrícola, Universidad Autónoma Agraria Antonia Narro, Calzada Antonio Narro 1923, Saltillo 25315, Coahuila, Mexico;
| | - Karen Berenice García-Conde
- Estudiante de Postgrado en Ciencias en Parasitología Agrícola, Universidad Autónoma Agraria Antonia Narro, Calzada Antonio Narro 1923, Saltillo 25315, Coahuila, Mexico;
| | - Yisa María Ochoa-Fuentes
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Calzada Antonio Narro 1923, Saltillo 25315, Coahuila, Mexico;
| |
Collapse
|
15
|
Liu T, Gui X, Zhang G, Luo L, Zhao J. Streptomyces-Fungus Co-Culture Enhances the Production of Borrelidin and Analogs: A Genomic and Metabolomic Approach. Mar Drugs 2024; 22:302. [PMID: 39057412 PMCID: PMC11278061 DOI: 10.3390/md22070302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The marine Streptomyces harbor numerous biosynthetic gene clusters (BGCs) with exploitable potential. However, many secondary metabolites cannot be produced under laboratory conditions. Co-culture strategies of marine microorganisms have yielded novel natural products with diverse biological activities. In this study, we explored the metabolic profiles of co-cultures involving Streptomyces sp. 2-85 and Cladosporium sp. 3-22-derived from marine sponges. Combining Global Natural Products Social (GNPS) Molecular Networking analysis with natural product database mining, 35 potential antimicrobial metabolites annotated were detected, 19 of which were exclusive to the co-culture, with a significant increase in production. Notably, the Streptomyces-Fungus interaction led to the increased production of borrelidin and the discovery of several analogs via molecular networking. In this study, borrelidin was first applied to combat Saprolegnia parasitica, which caused saprolegniosis in aquaculture. We noted its superior inhibitory effects on mycelial growth with an EC50 of 0.004 mg/mL and on spore germination with an EC50 of 0.005 mg/mL compared to the commercial fungicide, preliminarily identifying threonyl-tRNA synthetase as its target. Further analysis of the associated gene clusters revealed an incomplete synthesis pathway with missing malonyl-CoA units for condensation within this strain, hinting at the presence of potential compensatory pathways. In conclusion, our findings shed light on the metabolic changes of marine Streptomyces and fungi in co-culture, propose the potential of borrelidin in the control of aquatic diseases, and present new prospects for antifungal applications.
Collapse
Affiliation(s)
- Tan Liu
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
| | - Xi Gui
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
| | - Gang Zhang
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361005, China; (G.Z.); (L.L.)
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361005, China; (G.Z.); (L.L.)
| | - Jing Zhao
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
| |
Collapse
|
16
|
Mažylytė R, Kailiuvienė J, Mažonienė E, Orola L, Kaziūnienė J, Mažylytė K, Lastauskienė E, Gegeckas A. The Co-Inoculation Effect on Triticum aestivum Growth with Synthetic Microbial Communities (SynComs) and Their Potential in Agrobiotechnology. PLANTS (BASEL, SWITZERLAND) 2024; 13:1716. [PMID: 38931148 PMCID: PMC11207813 DOI: 10.3390/plants13121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
The use of rhizospheric SynComs can be a new and sustainable strategy in the agrobiotechnology sector. The objective of this study was to create the most appropriate SynCom composition; examine the ability to dissolve natural rock phosphate (RP) from Morocco in liquid-modified NBRIP medium; determine organic acids, and phytohormones; and verify plant growth promoting and nutrition uptake effect in the pot experiments of winter wheat (Triticum aestivum). A total of nine different microorganisms were isolated, which belonged to three different genera: Bacillus, Pseudomonas, and Streptomyces. Out of the 21 treatments tested, four SynComs had the best phosphate-dissolving properties: IJAK-27+44+91 (129.17 mg L-1), IIBEI-32+40 (90.95 µg mL-1), IIIDEG-45+41 (122.78 mg L-1), and IIIDEG-45+41+72 (120.78 mg L-1). We demonstrate that these SynComs are capable of producing lactic, acetic, gluconic, malic, oxalic, citric acids, and phytohormones such as indole-3-acetic acid, zeatin, gibberellic acid, and abscisic acid. In pot experiments with winter wheat, we also demonstrated that the designed SynComs were able to effectively colonize the plant root rhizosphere and contributed to more abundant plant growth characteristics and nutrient uptake as uninoculated treatment or uninoculated treatment with superphosphate (NPK 0-19-0). The obtained results show that the SynCom compositions of IJAK-27+44+91, IIBEI-32+40, IIIDEG-45+41, and IIIDEG-45+41+72 can be considered as promising candidates for developing biofertilizers to facilitate P absorption and increase plant nutrition.
Collapse
Affiliation(s)
- Raimonda Mažylytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania; (K.M.); (E.L.); (A.G.)
| | | | - Edita Mažonienė
- Roquette Amilina, LT-35101 Panevezys, Lithuania; (J.K.); (E.M.)
| | - Liana Orola
- Faculty of Chemistry, University of Latvia, LV-1004 Riga, Latvia;
| | - Justina Kaziūnienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Akademija, Lithuania;
| | - Kamilė Mažylytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania; (K.M.); (E.L.); (A.G.)
| | - Eglė Lastauskienė
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania; (K.M.); (E.L.); (A.G.)
| | - Audrius Gegeckas
- Life Sciences Center, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania; (K.M.); (E.L.); (A.G.)
| |
Collapse
|
17
|
Coskun FS, Toprak E. Streptomyces use umbrella toxins to gently compete with kin. Cell Host Microbe 2024; 32:779-781. [PMID: 38870893 DOI: 10.1016/j.chom.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 06/15/2024]
Abstract
In a recent issue of Nature, Zhao et al. have demonstrated that Streptomyces spp. produce "umbrella"-shaped polymorphic toxin particles, a novel class of non-lethal toxins that gently inhibit competitors by arresting hyphal growth in closely related bacteria, unveiling a unique bacterial defense strategy in microbial ecological interactions.1.
Collapse
Affiliation(s)
- Fatma Sevde Coskun
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Erdal Toprak
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390; Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.
| |
Collapse
|
18
|
Nainangu P, Mothilal SN, Subramanian K, Thanigaimalai M, Kandasamy R, Srinivasan GP, Gopal S, Shaik MR, Kari ZA, Guru A, Antonyraj APM. Characterization and antibacterial evaluation of Eco-friendly silver nanoparticles synthesized by halophilic Streptomyces rochei SSCM102 isolated from mangrove sediment. Mol Biol Rep 2024; 51:730. [PMID: 38864973 DOI: 10.1007/s11033-024-09666-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Antimicrobial resistance has surged due to widespread antimicrobial drug use, prompting interest in biosynthesizing nanoparticles from marine-derived actinomycetes extracellular metabolites, valued for their diverse bioactive compounds. This approach holds promise for addressing the urgent need for novel antimicrobial agents. The current study aimed to characterize novel bioactive compounds from unexplored biodiversity hotspots, halophilic Streptomyces sp. isolated from mangrove sediment in the Pichavaram region, India. METHODS AND RESULTS Streptomyces rochei SSCM102 was conclusively identified through morphological and molecular characterization. Synthesis of silver nanoparticles (AgNPs) from Streptomyces rochei SSCM102 was characterized using various techniques, including UV-Vis, XRD, SEM, EDX, and FT-IR. The UV-Vis spectrum of the reduced AgNPs exhibited a prominent peak at 380 nm, confirming the AgNPs. The UV-Vis spectrum confirmed the synthesis of AgNP, and SEM analysis revealed a cubic morphology with sizes ranging from 11 to 21 nm. The FTIR spectrum demonstrated a shift in frequency widths between 626 cm-1 and 3432 cm-1. The EDX analysis substantiated the presence of metallic silver, evident from a strong band at 1.44 keV. The synthesized AgNPs exhibited antibacterial efficacy against human pathogens Escherichia coli (64 ± 0.32 µg/ml), Klebsiella pneumoniae (32 ± 0.16 µg/ml), and Pseudomonas aeruginosa (16 ± 0.08 µg/ml) by MIC and MBC values of 128 ± 0.64 (µg/ml), 64 ± 0.32 (µg/ml) and 32 ± 0.16 (µg/ml), respectively. Additionally, at a concentration of 400 µg/ml, the AgNPs displayed a 72% inhibition of DPPH radicals, indicating notable antioxidant capacity. The LC50 value of 130 µg/mL indicates that the green-synthesized AgNPs have lower toxicity by Brine Shrimp Larvae assay. CONCLUSION The study's novel approach to synthesizing eco-friendly silver nanoparticles using Halophilic Streptomyces rochei SSCM102 contributes significantly to the field of biomedical research and drug development. By demonstrating potent antibacterial properties and aligning with sustainability goals, these nanoparticles offer promising avenues for novel antibacterial therapies.
Collapse
Affiliation(s)
- Prasannabalaji Nainangu
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, Kanchipuram, Tamil Nadu, 631561, India
| | | | - Kumaran Subramanian
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, Kanchipuram, Tamil Nadu, 631561, India
| | - Murugan Thanigaimalai
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, Kanchipuram, Tamil Nadu, 631561, India
| | - Rajesh Kandasamy
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, Kanchipuram, Tamil Nadu, 631561, India
| | - Guru Prasad Srinivasan
- Centre for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College, Saveetha University, Chennai, India
| | - Suresh Gopal
- PG & Research Department of Microbiology, Sri Sankara Arts and Science College, Kanchipuram, Tamil Nadu, 631561, India
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Zulhisyam Abdul Kari
- Department of Agricultural Sciences, Faculty of Agro‑Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Malaysia
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro‑Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Malaysia
| | - Ajay Guru
- Department of Cariology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Saveetha University, Chennai, India.
| | - Anahas Perianaika Matharasi Antonyraj
- Department of Research Analytics, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospital, Saveetha University, Poonamallee, Chennai, Tamil Nadu, 600 077, India.
| |
Collapse
|
19
|
Dayma P, Choudhary N, Ali D, Alarifi S, Dudhagara P, Luhana K, Yadav VK, Patel A, Patel R. Exploring the Potential of Halotolerant Actinomycetes from Rann of Kutch, India: A Study on the Synthesis, Characterization, and Biomedical Applications of Silver Nanoparticles. Pharmaceuticals (Basel) 2024; 17:743. [PMID: 38931410 PMCID: PMC11206697 DOI: 10.3390/ph17060743] [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: 04/12/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
A tremendous increase in the green synthesis of metallic nanoparticles has been noticed in the last decades, which is due to their unique properties at the nano dimension. The present research work deals with synthesis mediated by the actinomycete Streptomyces tendae of silver nanoparticles (AgNPs), isolated from Little and Greater Rann of Kutch, India. The confirmation of the formation of AgNPs by the actinomycetes was carried out by using a UV-Vis spectrophotometer where an absorbance peak was obtained at 420 nm. The X-ray diffraction pattern demonstrated five characteristic diffraction peaks indexed at the lattice plane (111), (200), (231), (222), and (220). Fourier transform infrared showed typical bands at 531 to 1635, 2111, and 3328 cm-1. Scanning electron microscopy shows that the spherical-shaped AgNPs particles have diameters in the range of 40 to 90 nm. The particle size analysis displayed the mean particle size of AgNPs in aqueous medium, which was about 55 nm (±27 nm), bearing a negative charge on their surfaces. The potential of the S. tendae-mediated synthesized AgNPs was evaluated for their antimicrobial, anti-methicillin-resistant Staphylococcus aureus (MRSA), anti-biofilm, and anti-oxidant activity. The maximum inhibitory effect was observed against Pseudomonas aeruginosa at (8 µg/mL), followed by Escherichia coli and Aspergillus niger at (32 µg/mL), and against Candida albicans (64 µg/mL), whereas Bacillus subtilis (128 µg/mL) and Staphylococcus aureus (256 µg/mL) were much less sensitive to AgNPs. The biosynthesized AgNPs displayed activity against MRSA, and the free radical scavenging activity was observed with an increase in the dosage of AgNPs from 25 to 200 µg/mL. AgNPs in combination with ampicillin displayed inhibition of the development of biofilm in Pseudomonas aeruginosa and Streptococcus pneumoniae at 98% and 83%, respectively. AgNPs were also successfully coated on the surface of cotton to prepare antimicrobial surgical cotton, which demonstrated inhibitory action against Bacillus subtilis (15 mm) and Escherichia coli (12 mm). The present research integrates microbiology, nanotechnology, and biomedical science to formulate environmentally friendly antimicrobial materials using halotolerant actinomycetes, evolving green nanotechnology in the biomedical field. Moreover, this study broadens the understanding of halotolerant actinomycetes and their potential and opens possibilities for formulating new antimicrobial products and therapies.
Collapse
Affiliation(s)
- Paras Dayma
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, Gujarat, India; (P.D.); (P.D.)
| | - Nisha Choudhary
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, Gujarat, India;
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, Gujarat, India; (P.D.); (P.D.)
| | - Kuldeep Luhana
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan 384265, Gujarat, India;
| | - Virendra Kumar Yadav
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashish Patel
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, Gujarat, India; (P.D.); (P.D.)
| |
Collapse
|
20
|
Veilumuthu P, Nagarajan T, Magar S, Sundaresan S, Moses LJ, Theodore T, Christopher JG. Genomic insights into an endophytic Streptomyces sp. VITGV156 for antimicrobial compounds. Front Microbiol 2024; 15:1407289. [PMID: 38887720 PMCID: PMC11180775 DOI: 10.3389/fmicb.2024.1407289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024] Open
Abstract
Endophytic Streptomyces sp. are recognized as a potential resource for valuable natural products but are less explored. This study focused on exploring endophytic Streptomyces species residing within tomato plants (Solanum lycopersicum) harboring genes for the production of a novel class of antibiotics. Our research involved the isolation and characterization of Streptomyces sp. VITGV156, a newly identified endophytic Streptomyces species that produces antimicrobial products. VITGV156 harbors a genome of 8.18 mb and codes 6,512 proteins, of which 4,993 are of known function (76.67%) and 1,519 are of unknown function (23.32%). By employing genomic analysis, we elucidate the genome landscape of this microbial strain and shed light on various BGCs responsible for producing polyketide antimicrobial compounds, with particular emphasis on the antibiotic kendomycin. We extended our study by evaluating the antibacterial properties of kendomycin. Overall, this study provides valuable insights into the genome of endophytic Streptomyces species, particularly Streptomyces sp. VITGV156, which are prolific producers of antimicrobial agents. These findings hold promise for further research and exploitation of pharmaceutical compounds, offering opportunities for the development of novel antimicrobial drugs.
Collapse
Affiliation(s)
- Pattapulavar Veilumuthu
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - T. Nagarajan
- Department of Biological Sciences, SRM University-AP, Amaravathi, India
| | - Sharayu Magar
- Department of Biological Sciences, SRM University-AP, Amaravathi, India
| | - Sasikumar Sundaresan
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Lenus Joy Moses
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Thomas Theodore
- School of Chemical Engineering, Vellore Institute of Technology, Vellore, India
| | - John Godwin Christopher
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| |
Collapse
|
21
|
Sudheer NS, Biju IF, Balasubramanian CP, Panigrahi A, Kumar TS, Kumar S, Mandal B, Das S, De D. Probiotic potential of a novel endophytic Streptomyces griseorubens CIBA-NS1 isolated from Salicornia sp. against Vibrio campbellii infection in shrimp. Microb Pathog 2024; 191:106677. [PMID: 38705217 DOI: 10.1016/j.micpath.2024.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/07/2024]
Abstract
A novel endophytic Streptomyces griseorubens CIBA-NS1 was isolated from a salt marsh plant Salicornia sp. The antagonistic effect of S. griseorubens against Vibrio campbellii, was studied both in vitro and in vivo. The strain was validated for its endophytic nature and characterized through scanning electron microscopy, morphological and biochemical studies and 16SrDNA sequencing. The salinity tolerance experiment has shown that highest antibacterial activity was at 40‰ (16 ± 1.4 mm) and lowest was at 10 ‰ salinity (6.94 ± 0.51 mm). In vivo exclusion of Vibrio by S. griseorubens CIBA-NS1 was studied in Penaeus indicus post larvae and evaluated for its ability to improve growth and survival of P. indicus. After 20 days administration of S. griseorubens CIBA-NS1, shrimps were challenged with V. campbellii. The S. griseorubens CIBA-NS1 reduced Vibrio population in test group when compared to control, improved survival (60.5 ± 6.4%) and growth, as indicated by weight gain (1.8 ± 0.05g). In control group survival and growth were 48.4 ± 3.5% and 1.4 ± 0.03 g respectively. On challenge with V. campbellii, the S. griseorubens CIBA-NS1 administered group showed better survival (85.6 ± 10%) than positive control (64.3 ± 10%). The results suggested that S. griseorubens CIBA-NS1 is antagonistic to V. campbellii, reduce Vibrio population in the culture system and improve growth and survival. This is the first report on antagonistic activity of S. griseorubens isolated from salt marsh plant Salicornia sp, as a probiotic candidate to prevent V. campbellii infection in shrimps.
Collapse
Affiliation(s)
- N S Sudheer
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India.
| | - I F Biju
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - C P Balasubramanian
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - A Panigrahi
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - T Sathish Kumar
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - Sujeet Kumar
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - Babita Mandal
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - S Das
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - D De
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| |
Collapse
|
22
|
Kalaba MH, El-Sherbiny GM, Darwesh OM, Moghannem SA. A statistical approach to enhance the productivity of Streptomyces baarensis MH-133 for bioactive compounds. Synth Syst Biotechnol 2024; 9:196-208. [PMID: 38385149 PMCID: PMC10876617 DOI: 10.1016/j.synbio.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The goal of this study was to use statistical optimization to change the nutritional and environmental conditions so that Streptomyces baarensis MH-133 could make more active metabolites. Twelve trials were used to screen for critical variables influencing productivity using the Placket-Burman Design method. S. baarensis MH-133 is significantly influenced by elicitation, yeast extract, inoculum size, and incubation period in terms of antibacterial activity. A total of 27 experimental trials with various combinations of these factors were used to carry out the response surface technique using the Box-Behnken design. The analyses revealed that the model was highly significant (p < 0.001), with a lack-of-fit of 0.212 and a coefficient determination (R2) of 0.9224. Additionally, the model predicted that the response as inhibition zone diameter would reach a value of 27 mm. Under optimal conditions, S. baarensis MH-133 produced 18.0 g of crude extract to each 35L and was purified with column chromatography. The active fraction exhibiting antibacterial activity was characterized using spectroscopic analysis. The MIC and MBC values varied between 37.5 and 300 μg/ml and 75 and 300 μg/ml, respectively. In conclusion, the biostatistical optimization of the active fraction critical variables, including environmental and nutritional conditions, enhances the production of bioactive molecules by Streptomyces species.
Collapse
Affiliation(s)
- Mohamed H. Kalaba
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Gamal M. El-Sherbiny
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Osama M. Darwesh
- Agricultural Microbiology Department, National Research Centre, Dokki, Cairo, Egypt
| | - Saad A. Moghannem
- Botany and Microbiology Department, Faculty of Science (Boys), Al-Azhar University, Cairo 11884, Egypt
| |
Collapse
|
23
|
Wang Z, Dai Q, Su D, Zhang Z, Tian Y, Tong J, Chen S, Yan C, Yang J, Cui X. Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing. Front Microbiol 2024; 15:1377782. [PMID: 38873161 PMCID: PMC11169695 DOI: 10.3389/fmicb.2024.1377782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.
Collapse
Affiliation(s)
- Zongneng Wang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Qingzhong Dai
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Daifa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | | | - Yunxia Tian
- Kunming Academy of Agricultural Science, Kunming, China
| | - Jiangyun Tong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Shanyan Chen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Congwen Yan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Junyu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- Yunnan International Joint Laboratory of Virology and Immunology, Kunming, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| |
Collapse
|
24
|
Bataeva Y, Delegan Y, Bogun A, Shishkina L, Grigoryan L. Whole Genome Analysis and Assessment of the Metabolic Potential of Streptomyces carpaticus SCPM-O-B-9993, a Promising Phytostimulant and Antiviral Agent. BIOLOGY 2024; 13:388. [PMID: 38927268 PMCID: PMC11200584 DOI: 10.3390/biology13060388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
This work aimed to study the genome organization and the metabolic potential of Streptomyces carpaticus strain SCPM-O-B-9993, a promising plant-protecting and plant-stimulating strain isolated from brown semi-desert soils with very high salinity. The strain genome contains a linear chromosome 5,968,715 bp long and has no plasmids. The genome contains 5331 coding sequences among which 2139 (40.1%) are functionally annotated. Biosynthetic gene clusters (BGCs) of secondary metabolites exhibiting antimicrobial properties (ohmyungsamycin, pellasoren, naringenin, and ansamycin) were identified in the genome. The most efficient period of SCPM-O-B-9993 strain cultivation was 72 h: during this period, the culture went from the exponential to the stationary growth phase as well as exhibited excellent phytostimulatory properties and antiviral activity against the cucumber mosaic virus in tomatoes under laboratory conditions. The Streptomyces carpaticus SCPM-OB-9993 strain is a biotechnologically promising producer of secondary metabolites exhibiting antiviral and phytostimulatory properties.
Collapse
Affiliation(s)
- Yulia Bataeva
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Russia; (Y.D.); (A.B.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Russia; (Y.D.); (A.B.)
| | - Lidiya Shishkina
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia;
| | - Lilit Grigoryan
- Department of Biology, Tatishchev Astrakhan State University, 414056 Astrakhan, Russia;
| |
Collapse
|
25
|
Klumbys E, Xu W, Koduru L, Heng E, Wei Y, Wong FT, Zhao H, Ang EL. Discovery, characterization, and engineering of an advantageous Streptomyces host for heterologous expression of natural product biosynthetic gene clusters. Microb Cell Fact 2024; 23:149. [PMID: 38790014 PMCID: PMC11127301 DOI: 10.1186/s12934-024-02416-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Streptomyces is renowned for its robust biosynthetic capacity in producing medically relevant natural products. However, the majority of natural products biosynthetic gene clusters (BGCs) either yield low amounts of natural products or remain cryptic under standard laboratory conditions. Various heterologous production hosts have been engineered to address these challenges, and yet the successful activation of BGCs has still been limited. In our search for a valuable addition to the heterologous host panel, we identified the strain Streptomyces sp. A4420, which exhibited rapid initial growth and a high metabolic capacity, prompting further exploration of its potential. RESULTS We engineered a polyketide-focused chassis strain based on Streptomyces sp. A4420 (CH strain) by deleting 9 native polyketide BGCs. The resulting metabolically simplified organism exhibited consistent sporulation and growth, surpassing the performance of most existing Streptomyces based chassis strains in standard liquid growth media. Four distinct polyketide BGCs were chosen and expressed in various heterologous hosts, including the Streptomyces sp. A4420 wild-type and CH strains, alongside Streptomyces coelicolor M1152, Streptomyces lividans TK24, Streptomyces albus J1074, and Streptomyces venezuelae NRRL B-65442. Remarkably, only the Streptomyces sp. A4420 CH strain demonstrated the capability to produce all metabolites under every condition outperforming its parental strain and other tested organisms. To enhance visualization and comparison of the tested strains, we developed a matrix-like analysis involving 15 parameters. This comprehensive analysis unequivocally illustrated the significant potential of the new strain to become a popular heterologous host. CONCLUSION Our engineered Streptomyces sp. A4420 CH strain exhibits promising attributes for the heterologous expression of natural products with a focus on polyketides, offering an alternative choice in the arsenal of heterologous production strains. As genomics and cloning strategies progress, establishment of a diverse panel of heterologous production hosts will be crucial for expediting the discovery and production of medically relevant natural products derived from Streptomyces.
Collapse
Affiliation(s)
- Evaldas Klumbys
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Wei Xu
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, #04-01, Nanos, Singapore, 138669, Republic of Singapore.
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
| |
Collapse
|
26
|
Diab MK, Mead HM, Ahmad Khedr MM, Abu-Elsaoud AM, El-Shatoury SA. Actinomycetes are a natural resource for sustainable pest control and safeguarding agriculture. Arch Microbiol 2024; 206:268. [PMID: 38762847 DOI: 10.1007/s00203-024-03975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024]
Abstract
Actinomycetes, a diverse group of bacteria with filamentous growth characteristics, have long captivated researchers and biochemists for their prolific production of secondary metabolites. Among the myriad roles played by actinomycete secondary metabolites, their historical significance in the field of biocontrol stands out prominently. The fascinating journey begins with the discovery of antibiotics, where renowned compounds like streptomycin, tetracycline, and erythromycin revolutionized medicine and agriculture. The history of biocontrol traces its roots back to the early twentieth century, when scientists recognized the potential of naturally occurring agents to combat pests and diseases. The emergence of synthetic pesticides in the mid-twentieth century temporarily overshadowed interest in biocontrol. However, with growing environmental concerns and the realization of the negative ecological impacts of chemical pesticides, the pendulum swung back towards exploring sustainable alternatives. Beyond their historical role as antibiotics, actinomycete-produced secondary metabolites encompass a rich repertoire with biopesticide potential. The classification of these compounds based on chemical structure and mode of action is highlighted, demonstrating their versatility against both plant pathogens and insect pests. Additionally, this review provides in-depth insights into how endophytic actinomycete strains play a pivotal role in biocontrol strategies. Case studies elucidate their effectiveness in inhibiting Spodoptera spp. and nematodes through the production of bioactive compounds. By unraveling the multifunctional roles of endophytic actinomycetes, this review contributes compelling narrative knowledge to the field of sustainable agriculture, emphasizing the potential of these microbial allies in crafting effective, environmentally friendly biocontrol strategies for combating agricultural pests.
Collapse
Affiliation(s)
- Mohamed Khaled Diab
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt.
| | - Hala Mohamed Mead
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Mohamad M Ahmad Khedr
- Agricultural Research Center, Cotton Leafworm Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | | | - Sahar Ahmed El-Shatoury
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| |
Collapse
|
27
|
Lazic J, Filipovic V, Pantelic L, Milovanovic J, Vojnovic S, Nikodinovic-Runic J. Late-stage diversification of bacterial natural products through biocatalysis. Front Bioeng Biotechnol 2024; 12:1351583. [PMID: 38807651 PMCID: PMC11130421 DOI: 10.3389/fbioe.2024.1351583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/18/2024] [Indexed: 05/30/2024] Open
Abstract
Bacterial natural products (BNPs) are very important sources of leads for drug development and chemical novelty. The possibility to perform late-stage diversification of BNPs using biocatalysis is an attractive alternative route other than total chemical synthesis or metal complexation reactions. Although biocatalysis is gaining popularity as a green chemistry methodology, a vast majority of orphan sequenced genomic data related to metabolic pathways for BNP biosynthesis and its tailoring enzymes are underexplored. In this review, we report a systematic overview of biotransformations of 21 molecules, which include derivatization by halogenation, esterification, reduction, oxidation, alkylation and nitration reactions, as well as degradation products as their sub-derivatives. These BNPs were grouped based on their biological activities into antibacterial (5), antifungal (5), anticancer (5), immunosuppressive (2) and quorum sensing modulating (4) compounds. This study summarized 73 derivatives and 16 degradation sub-derivatives originating from 12 BNPs. The highest number of biocatalytic reactions was observed for drugs that are already in clinical use: 28 reactions for the antibacterial drug vancomycin, followed by 18 reactions reported for the immunosuppressive drug rapamycin. The most common biocatalysts include oxidoreductases, transferases, lipases, isomerases and haloperoxidases. This review highlights biocatalytic routes for the late-stage diversification reactions of BNPs, which potentially help to recognize the structural optimizations of bioactive scaffolds for the generation of new biomolecules, eventually leading to drug development.
Collapse
Affiliation(s)
- Jelena Lazic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | | |
Collapse
|
28
|
Somphong A, Polyiam W, Suriyachadkun C, Sripreechasak P, Harunari E, Igarashi Y, Tanasupawat S, Phongsopitanun W. Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl. Int J Syst Evol Microbiol 2024; 74. [PMID: 38713186 DOI: 10.1099/ijsem.0.006364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Abstract
Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07-26.80 %, 81.24-82.01 % and 86.82-86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70-31.70 %, 84.09-85.31 % and 88.02-88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).
Collapse
Affiliation(s)
- Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Wetchasart Polyiam
- Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani 12120, Thailand
| | - Paranee Sripreechasak
- Office of Educational Affairs, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
29
|
Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
Collapse
Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
| |
Collapse
|
30
|
Zhao D, Zhang W, Cui J. Microbial community structure and carbon transformation characteristics of different aggregates in black soil. PeerJ 2024; 12:e17269. [PMID: 38699178 PMCID: PMC11064869 DOI: 10.7717/peerj.17269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
Background Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification. Methods In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2-5, 1-2, 0.5-1, 0.25-0.5, <0.25 mm, and bulk soil. Results The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25-0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25-0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil's ability to fix carbon and nitrogen. Discussion There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25-0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.
Collapse
Affiliation(s)
- Danqi Zhao
- College of Resources and Environment, Jilin Agricultural University, Changchun, Jilin, China
| | - Wei Zhang
- College of Modern Agriculture, Chang Chun Polytschnic, Changchun, Jilin, China
| | - Juntao Cui
- College of Resources and Environment, Jilin Agricultural University, Changchun, Jilin, China
| |
Collapse
|
31
|
Olano C, Rodríguez M. Actinomycetes Associated with Arthropods as a Source of New Bioactive Compounds. Curr Issues Mol Biol 2024; 46:3822-3838. [PMID: 38785506 PMCID: PMC11119530 DOI: 10.3390/cimb46050238] [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: 03/28/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Antimicrobial resistance is one of the main global threats to human health in the 21st century due to the rapid appearance of bacterial resistance and the lack of novel bioactive compounds. Natural products, especially from Actinomycetes, remain the best source to refill the drug industry pipeline. Different strategies have been pursued to increase the chances of discovering new molecules, such as studying underexplored environments like arthropod symbionts, which represent a relevant reservoir for active metabolites. This review summarizes recent research on the identification of bioactive molecules produced by Actinomycetes associated with arthropods' microbiome. The metabolites have been categorized based on their structural properties and host, highlighting that multidisciplinary approaches will be the key to fully understanding this complex relationship.
Collapse
Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| |
Collapse
|
32
|
Firrincieli A, Tornatore E, Piacenza E, Cappelletti M, Saiano F, Pavia FC, Alduina R, Zannoni D, Presentato A. The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion. CHEMOSPHERE 2024; 354:141712. [PMID: 38484991 DOI: 10.1016/j.chemosphere.2024.141712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
The effects of oxyanions selenite (SeO32-) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized.
Collapse
Affiliation(s)
- Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via San Camillo de Lellis snc, 01100, Viterbo, Italy.
| | - Enrico Tornatore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Filippo Saiano
- Department of Agricultural, Food and Forestry Sciences (SAAF), University of Palermo, Viale delle Scienze Ed. 4, 90128, Palermo, Italy.
| | - Francesco Carfì Pavia
- Department of Engineering, University of Palermo, Viale delle Scienze Ed. 8, 90128, Palermo, Italy.
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| |
Collapse
|
33
|
Wannawong T, Mhuantong W, Macharoen P, Niemhom N, Sitdhipol J, Chaiyawan N, Umrung S, Tanasupawat S, Suwannarach N, Asami Y, Kuncharoen N. Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers. FRONTIERS IN PLANT SCIENCE 2024; 15:1346574. [PMID: 38601305 PMCID: PMC11004387 DOI: 10.3389/fpls.2024.1346574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
A novel endophytic actinomycete, strain MEP2-6T, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6T is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H6) was the predominant menaquinone, whereas iso-C16:0 and iso-C15:0 were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6T was closely related to Amycolatopsis lexingtonensis NRRL B-24131T (99.4%), A. pretoriensis DSM 44654T (99.3%), and A. eburnea GLM-1T (98.9%). Notably, strain MEP2-6T displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653T (=NRRL B-24131T), A. eburnea GLM-1T, and A. pretoriensis DSM 44654T, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6T could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6T (=JCM 36309T = TBRC 17632T = NBRC 116395T). Amycolatopsis solani MEP2-6T was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6T to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6T is a promising candidate as a novel biocontrol agent and antibiotic producer.
Collapse
Affiliation(s)
- Thippawan Wannawong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Wuttichai Mhuantong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pipat Macharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Nantawan Niemhom
- Microbiological and Molecular Biological Laboratory, Scientific Instruments Center, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Jaruwan Sitdhipol
- Biodiversity Research Centre, Research and Development Group for Bio-Industries, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Neungnut Chaiyawan
- Biodiversity Research Centre, Research and Development Group for Bio-Industries, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Sarinna Umrung
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Nakarin Suwannarach
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Yukihiro Asami
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
34
|
Kum E, İnce E. Metabolomics Approach to Explore Bioactive Natural Products Derived From Plant-Root-Associated Streptomyces. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04905-7. [PMID: 38512549 DOI: 10.1007/s12010-024-04905-7] [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] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Streptomyces, a prominent genus within the Actinomycetota phylum, is responsible for over 60% of clinically relevant antibiotics. Streptomyces strains inhabiting plant roots possess the potential to synthesize bioactive natural products, conferring defense and resilience to plants against pathogenic microorganisms. However, this potential remains largely unexplored. This study aims to screen for bioactive metabolites produced by Streptomyces strains in the plant rhizosphere.Six Streptomyces isolates were cultivated using three modified media to induce the production of diverse metabolites, employing the One Strain Many Compounds (OSMAC) approach. The metabolites present in extracts from fermentation broths were examined through a non-targeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) approach coupled with Global Natural Products Social Molecular Networking (GNPS MN). The antimicrobial activity of the extracts was assessed using the disc diffusion method.The strains demonstrated a wide-ranging antimicrobial efficacy against all examined organisms. The GNPS molecular network analyses reveal that metabolite profiles in extracts can exhibit variations based on the medium and solvent system employed. Notably, the ethyl acetate and dichloromethane extracts from Streptomyces sp. CAH29, cultivated in Glucose-Yeast Extract Medium (GYM), exhibited inhibition diameters of up to 30 mm against both Staphylococcus aureus and Candida albicans. Within the metabolomes of these strains, the antibiotics spiramycin and actinomycin were detected. Additionally, lyngbatoxin, a tumor promoter, and potential new analogs were identified. Significantly, a considerable portion of the produced metabolites did not align with any known compounds, indicating the existence of unidentified metabolites generated by these strains. This suggests the possibility of introducing novel chemical entities.Our study illustrated that Streptomyces strains associated with plant roots could be considered a valuable source of bioactive secondary metabolites. Furthermore, the metabolomics approach utilized in this study serves as a rapid and valuable tool for the screening of microorganisms capable of producing bioactive metabolites.
Collapse
Affiliation(s)
- Ekrem Kum
- The Institute of Natural and Applied Science, Dicle University, Diyarbakır, Turkey
| | - Ebru İnce
- Department of Biology, Faculty of Science, Dicle University, Diyarbakır, Turkey.
| |
Collapse
|
35
|
Hua HM, Xu JF, Huang XS, Zimin AA, Wang WF, Lu YH. Low-Toxicity and High-Efficiency Streptomyces Genome Editing Tool Based on the Miniature Type V-F CRISPR/Cas Nuclease AsCas12f1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5358-5367. [PMID: 38427033 DOI: 10.1021/acs.jafc.3c09101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Genome editing tools based on SpCas9 and FnCpf1 have facilitated strain improvements for natural product production and novel drug discovery in Streptomyces. However, due to high toxicity, their editing requires high DNA transformation efficiency, which is unavailable in most streptomycetes. The transformation efficiency of an all-in-one editing tool based on miniature Cas nuclease AsCas12f1 was significantly higher than those of SpCas9 and FnCpf1 in tested streptomycetes, which is due to its small size and weak DNA cleavage activity. Using this tool, in Streptomyces coelicolor, we achieved 100% efficiency for single gene or gene cluster deletion and 46.7 and 40% efficiency for simultaneous deletion of two genes and two gene clusters, respectively. AsCas12f1 was successfully extended to Streptomyces hygroscopicus SIPI-054 for efficient genome editing, in which SpCas9/FnCpf1 does not work well. Collectively, this work offers a low-toxicity, high-efficiency genome editing tool for streptomycetes, particularly those with low DNA transformation efficiency.
Collapse
Affiliation(s)
- Hui-Min Hua
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jia-Feng Xu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xue-Shuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Andrei A Zimin
- G.K. Scriabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino 142290, Russia
| | - Wen-Fang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| |
Collapse
|
36
|
Xiao Z, Zha J, Yang X, Huang T, Huang S, Liu Q, Wang X, Zhong J, Zheng J, Liang R, Deng Z, Zhang J, Lin S, Dai S. A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D. Nat Commun 2024; 15:2128. [PMID: 38459030 PMCID: PMC10923870 DOI: 10.1038/s41467-024-46363-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/23/2024] [Indexed: 03/10/2024] Open
Abstract
Modulation of protein function through allosteric regulation is central in biology, but biomacromolecular systems involving multiple subunits and ligands may exhibit complex regulatory mechanisms at different levels, which remain poorly understood. Here, we discover an aldo-keto reductase termed AKRtyl and present its three-level regulatory mechanism. Specifically, by combining steady-state and transient kinetics, X-ray crystallography and molecular dynamics simulation, we demonstrate that AKRtyl exhibits a positive synergy mediated by an unusual Monod-Wyman-Changeux (MWC) paradigm of allosteric regulation at low concentrations of the cofactor NADPH, but an inhibitory effect at high concentrations is observed. While the substrate tylosin binds at a remote allosteric site with positive cooperativity. We further reveal that these regulatory mechanisms are conserved in AKR12D subfamily, and that substrate cooperativity is common in AKRs across three kingdoms of life. This work provides an intriguing example for understanding complex allosteric regulatory networks.
Collapse
Affiliation(s)
- Zhihong Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jinyin Zha
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shuxin Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qi Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jie Zhong
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China.
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shaobo Dai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| |
Collapse
|
37
|
Rana B, Chandola R, Sanwal P, Joshi GK. Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing. Sci Rep 2024; 14:4031. [PMID: 38369518 PMCID: PMC10874962 DOI: 10.1038/s41598-024-53350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.
Collapse
Affiliation(s)
- Babita Rana
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Renu Chandola
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India
| | - Pankaj Sanwal
- Department of Biochemical Engineering, BTKIT, Dwarahat, Uttarakhand, India
| | - Gopal Krishna Joshi
- Department of Biotechnology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, India.
| |
Collapse
|
38
|
Kumar M, Parveen, Raj N, Khatoon S, Fakhri KU, Kumar P, Alamri MA, Kamal M, Manzoor N, Harsha, Solanki R, Elossaily GM, Asiri YI, Hassan MZ, Kapur MK. In-silico and in-vitro evaluation of antifungal bioactive compounds from Streptomyces sp. strain 130 against Aspergillus flavus. J Biomol Struct Dyn 2024:1-19. [PMID: 38319066 DOI: 10.1080/07391102.2024.2313167] [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: 07/17/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024]
Abstract
Streptomyces spp. are considered excellent reservoirs of natural bioactive compounds. The study evaluated the bioactive potential of secondary metabolites from Streptomyces sp. strain 130 through PKS-I and NRPS gene-clusters screening. GC-MS analysis was done for metabolic profiling of bioactive compounds from strain 130 in the next set of experiments. Identified antifungal compounds underwent ADMET analyses to screen their toxicity. All compounds' molecular docking was done with the structural gene products of the aflatoxin biosynthetic pathway of Aspergillus flavus. MD simulations were utilized to evaluate the stability of protein-ligand complexes under physiological conditions. Based on the in-silico studies, compound 2,4-di-tert butyl-phenol (DTBP) was selected for in-vitro studies against Aspergillus flavus. Simultaneously, bioactive compounds were extracted from strain 130 in two different solvents (ethyl-acetate and methanol) and used for similar assays. The MIC value of DTBP was found to be 314 µg/mL, whereas in ethyl-acetate extract and methanol-extract, it was 250 and 350 µg/mL, respectively. A mycelium growth assay was done to analyze the effect of compounds/extracts on the mycelium formation of Aspergillus flavus. In agar diffusion assay, zone of inhibitions in DTBP, ethyl-acetate extract, and methanol extract were observed with diameters of 11.3, 13.3, and 7.6 mm, respectively. In the growth curve assay, treated samples have delayed the growth of fungi, which signified that the compounds have a fungistatic nature. Spot assay has determined the fungal sensitivity to a sub-minimum inhibitory concentration of antifungal compounds. The study's results suggested that DTBP can be exploited for antifungal-drug development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Munendra Kumar
- Department of Zoology, Rajiv Gandhi University, Doimukh, India
| | - Parveen
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Nafis Raj
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shabana Khatoon
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Prateek Kumar
- Department of Zoology, University of Allahabad, Prayagraj, India
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Nikhat Manzoor
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Harsha
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, India New Delhi
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Gehan M Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohd Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Monisha Khanna Kapur
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, India New Delhi
| |
Collapse
|
39
|
Kumar P, Parveen, Raj N, Kumar M, Fakhri KU, Kumar S, Khan AA, Alanazi AM, Solanki R, Harsha, Manzoor N, Kapur MK. Natural products from Streptomyces spp. as potential inhibitors of the major factors (holoRdRp and nsp13) for SARS-CoV-2 replication: an in silico approach. Arch Microbiol 2024; 206:88. [PMID: 38305873 DOI: 10.1007/s00203-023-03820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024]
Abstract
The COVID-19 pandemic caused unprecedented damage to humanity, and while vaccines have been developed, they are not fully effective against the SARS-CoV-2 virus. Limited targeted drugs, such as Remdesivir and Paxlovid, are available against the virus. Hence, there is an urgent need to explore and develop new drugs to combat COVID-19. This study focuses on exploring microbial natural products from soil-isolated bacteria Streptomyces sp. strain 196 and RI.24 as a potential source of new targeted drugs against SARS-CoV-2. Molecular docking studies were performed on holoRdRp and nsp13, two key factors responsible for virus replication factor. Our in silico studies, K-252-C aglycone indolocarbazole alkaloid (K252C) and daunorubicin were found to have better binding affinities than the respective control drugs, with K252C exhibiting binding energy of - 9.1 kcal/mol with holoRdRp and - 9.2 kcal/mol with nsp13, and daunorubicin showing binding energy at - 8.1 kcal/mol with holoRdRp and - 9.3 kcal/mol with nsp13. ADMET analysis, MD simulation, and MM/GBSA studies indicated that K252C and daunorubicin have the potential to be developed as targeted drugs against SARS-CoV-2. The study concludes that K252C and daunorubicin are potential lead compounds that might suppress the inhibition of SARS-CoV-2 replication among the tested microbial compounds and could be developed as targeted drugs against COVID-19. In the future, further in vitro studies are required to validate these findings.
Collapse
Affiliation(s)
- Prateek Kumar
- Department of Zoology, University of Allahabad, Uttar Pradesh, Prayagraj, 211 002, India.
| | - Parveen
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Nafis Raj
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Munendra Kumar
- Department of Zoology, Rajiv Gandhi University, Doimukh, 791112, Arunachal Pradesh, India
| | - Khalid Umar Fakhri
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sugandh Kumar
- School of Medicine, University of San Francisco California (UCSF), San Francisco, CA, 95115, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, 110 078, India
| | - Harsha
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, New Delhi, 110 019, India
| | - Nikhat Manzoor
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Monisha Khanna Kapur
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, New Delhi, 110 019, India.
| |
Collapse
|
40
|
Solomon S, Babu DT, Gopalakrishnan S, Augustine D, Kachiprath B, Kesavan D, Sarasan M, Philip R. Marine actinomycete Streptomyces variabilis S26 as a biocontrol agent for vibriosis in shrimp larval rearing systems. J Basic Microbiol 2024; 64:e2300225. [PMID: 37906111 DOI: 10.1002/jobm.202300225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/02/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Indiscriminate use of antibiotics has led to the emergence of antibiotic-resistant microbes and the loss of natural flora in aquaculture systems necessitating the ban of many of these chemotherapeutants in aquaculture. Actinobacteria play a profound role in the biogeochemical cycling in the marine environment and represent the principal source of secondary metabolites with antimicrobial property. In the present study, 98 marine-derived actinomycete isolates were screened for antimicrobial activity against the common aquatic pathogens. A potent actinomycete isolate S26, identified as Streptomyces variabilis based on 16 S ribosomal RNA (rRNA) gene sequencing was then checked for the production of antibiotic in five different fermentation media and the one which showed maximum production was chosen for further study. Optimization of the fermentation medium for secondary metabolite production was carried out by response surface methodology (RSM) using DESIGN EXPERT. The analysis of variance (ANOVA) of the quadratic regression model demonstrated that the model was highly significant for the response concerned that is, antimicrobial activity as evident from the Fisher's F- test with a very low probability value [(P model>F) = 0.0001]. Of the 10 different solutions suggested by the software, the most suitable composition was found to be starch, 1.38%; soy powder, 0.88%; ammonium sulfate, 0.16% and salinity, 27.76‰. S. variabilis S26 cultured in the optimized production medium was applied in the Penaeus monodon larval rearing system and the total Vibrio count and survival rate were estimated. S. variabilis S26 treatment showed a significant reduction in vibrios and conferred better protection to P. monodon in culture system compared with control.
Collapse
Affiliation(s)
- Solly Solomon
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
- Fishery Survey of India, Cochin Zonal Base, Kochi, Kerala, India
| | - Divya T Babu
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Sumitha Gopalakrishnan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Deepthi Augustine
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Bhavya Kachiprath
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Dhanya Kesavan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Manomi Sarasan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| | - Rosamma Philip
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Kerala, India
| |
Collapse
|
41
|
Yan YS, Zou LS, Wei HG, Yang MY, Yang YQ, Li XF, Xia HY. An atypical two-component system, AtcR/AtcK, simultaneously regulates the biosynthesis of multiple secondary metabolites in Streptomyces bingchenggensis. Appl Environ Microbiol 2024; 90:e0130023. [PMID: 38112424 PMCID: PMC10807435 DOI: 10.1128/aem.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Streptomyces bingchenggensis is an industrial producer of milbemycins, which are important anthelmintic and insecticidal agents. Two-component systems (TCSs), which are typically situated in the same operon and are composed of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Here, an atypical TCS, AtcR/AtcK, in which the encoding genes (sbi_06838/sbi_06839) are organized in a head-to-head pair, was demonstrated to be indispensable for the biosynthesis of multiple secondary metabolites in S. bingchenggensis. With the null TCS mutants, the production of milbemycin and yellow compound was abolished but nanchangmycin was overproduced. Transcriptional analysis and electrophoretic mobility shift assays showed that AtcR regulated the biosynthesis of these three secondary metabolites by a MilR3-mediated cascade. First, AtcR was activated by phosphorylation from signal-triggered AtcK. Second, the activated AtcR promoted the transcription of milR3. Third, MilR3 specifically activated the transcription of downstream genes from milbemycin and yellow compound biosynthetic gene clusters (BGCs) and nanR4 from the nanchangmycin BGC. Finally, because NanR4 is a specific repressor in the nanchangmycin BGC, activation of MilR3 downstream genes led to the production of yellow compound and milbemycin but inhibited nanchangmycin production. By rewiring the regulatory cascade, two strains were obtained, the yield of nanchangmycin was improved by 45-fold to 6.08 g/L and the production of milbemycin was increased twofold to 1.34 g/L. This work has broadened our knowledge on atypical TCSs and provided practical strategies to engineer strains for the production of secondary metabolites in Streptomyces.IMPORTANCEStreptomyces bingchenggensis is an important industrial strain that produces milbemycins. Two-component systems (TCSs), which consist of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Coupled encoding genes of TCSs are typically situated in the same operon. Here, TCSs with encoding genes situated in separate head-to-head neighbor operons were labeled atypical TCSs. It was found that the atypical TCS AtcR/AtcK played an indispensable role in the biosynthesis of milbemycin, yellow compound, and nanchangmycin in S. bingchenggensis. This atypical TCS regulated the biosynthesis of specialized metabolites in a cascade mediated via a cluster-situated regulator, MilR3. Through rewiring the regulatory pathways, strains were successfully engineered to overproduce milbemycin and nanchangmycin. To the best of our knowledge, this is the first report on atypical TCS, in which the encoding genes of RR and HK were situated in separate head-to-head neighbor operons, involved in secondary metabolism. In addition, data mining showed that atypical TCSs were widely distributed in actinobacteria.
Collapse
Affiliation(s)
- Yu-Si Yan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Li-Sha Zou
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - He-Geng Wei
- Zhejiang Yongtai Technology Co., LTD., Taizhou, Zhejiang, China
| | - Meng-Yao Yang
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Yun-Qi Yang
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Xiao-Fang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| | - Hai-Yang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, Zhejiang, China
| |
Collapse
|
42
|
Tunvongvinis T, Jaitrong W, Samung Y, Tanasupawat S, Phongsopitanun W. Diversity and antimicrobial activity of the tropical ant-derived actinomycetes isolated from Thailand. AIMS Microbiol 2024; 10:68-82. [PMID: 38525037 PMCID: PMC10955170 DOI: 10.3934/microbiol.2024005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 03/26/2024] Open
Abstract
Antibiotic resistance is one of the most important global healthcare challenges and is responsible for the mortality of millions of people worldwide every year. It is a crisis attributed to misuse of antibiotics and a lack of new drug development. Actinomycetes constitute a group of Gram-positive bacteria known for their distinctive high guanine-cytosine (G+C) content in their genomic DNA. These microorganisms are widely recognized for their capability to generate a wide range of secondary metabolites with diverse biological activities. These versatile microorganisms are ubiquitous in diverse ecosystems, including soil, freshwater, marine sediments, and within the bodies of insects. A recent study has demonstrated that social insects, such as ants, host a diverse array of these bacteria. In this study, we involved the isolation and characterization of a total of 72 actinomycete strains obtained from 18 distinct ant species collected from various regions across Thailand. Utilizing 16S rRNA gene analysis, these isolated actinomycetes were classified into four distinct genera: Amycolatopsis (2 isolates), Micromonospora (1 isolate), Nocardia (8 isolates), and Streptomyces (61 isolates). Among the Streptomyces strains, 23 isolates exhibited antimicrobial activity against a panel of Gram-positive bacteria, including Bacillus subtilis ATCC 6633, Staphylococcus epidermidis ATCC 12228, Staphylococcus aureus ATCC 25923, Kocuria rhizophila ATCC 9341, and Methicillin-resistant Staphylococcus aureus (MRSA) DMST 20646. Additionally, two isolates displayed antifungal activity against Candida albicans TISTR 5554. Based on 16S rRNA gene sequence similarity studies, these two isolates, ODS25 and ODS28, were demonstrated to be closely related to Streptomyces lusitanus NBRC 13464T (98.07%) and Streptomyces haliclonae DSM 41970T (97.28%), respectively. The level of 16S rRNA gene sequence similarity below 98.65% cutoff indicates its potential as a novel actinomycete species. These findings underscore the potential of actinomycetes sourced from ants as a valuable reservoir of novel antimicrobials.
Collapse
Affiliation(s)
- Tuangrat Tunvongvinis
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
| | - Weeyawat Jaitrong
- Office of Natural Science Research, National Science Museum, 39, Moo 3, Khlong 5, Khlong Luang, Pathum Thani 12120, Thailand
| | - Yudthana Samung
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences. Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Units (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
43
|
Singh N, Patil S, Shahnawaz M, Rai V, Patil A, Tripathi CKM, Wen F, Dong S, Cai D. Green extraction of puromycin-based antibiotics from Streptomyces albofaciens (MS38) for sustainable biopharmaceutical applications. Front Chem 2024; 11:1326328. [PMID: 38264123 PMCID: PMC10803528 DOI: 10.3389/fchem.2023.1326328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Background: Microbial secondary metabolites have shown promise as a source of novel antimicrobial agents. In this study, we aimed to isolate, characterize, and evaluate the antimicrobial activity of compound from a novel Streptomyces albofaciens strain MS38. The objective was to identify a potential bioactive compound with broad-spectrum antimicrobial properties. Methods: The isolated strain MS38 on starch casein agar was characterized using morphological, physiological, and molecular identification techniques. The compound was obtained from the fermented broth through extraction with n-butanol and further purification using silica gel column chromatography and high-performance liquid chromatography (HPLC). Structural elucidation was conducted using Ultraviolet (UV), Infrared (IR), nuclear magnetic resonance (NMR), and mass spectrometry (MS) techniques. The antimicrobial activity was evaluated using the agar well diffusion method and the microplate Alamar blue assay (MABA). Results: The isolated strain MS38 was identified as novel S. albofaciens based on morphological characteristics and confirmed by 16S sequences analysis and MALDI-TOF MS. The compound obtained from the fermented broth exhibited substantial antimicrobial activity against a variety of pathogenic bacteria and fungi. Structural analysis revealed a complex chemical structure with characteristic functional groups indicative of potential antimicrobial properties. The compound demonstrated strong activity against both Gram-positive (Staphylococcus Spp.) and Gram-negative (Klebsiella pneumoniae and Escherichia coli) bacteria, as well as fungi, including Candida albicans and Trichophyton rubrum. Conclusion: This study successfully isolated and characterized a bioactive compound from a novel S. albofaciens MS38. The compound exhibited significant antimicrobial activity against a range of pathogenic microorganisms. These findings underscore the importance of exploring microbial biodiversity for the discovery of novel antimicrobial agents. This study contributes to the growing knowledge of microbial secondary metabolites with potential therapeutic value.
Collapse
Affiliation(s)
- Neha Singh
- Biochemistry and Microbiology Laboratory, School of Studies in Life Sciences, Pt. Ravishankar Shukla University, Raipur, India
- Virology Lab, Department of Microbiology, Pandit Jawahar Lal Nehru Memorial Medical College, Raipur, Chhattisgarh, India
| | - Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Mohd. Shahnawaz
- Department of Botany, University of Ladakh, Ladakh UT, India
| | - Vibhuti Rai
- Biochemistry and Microbiology Laboratory, School of Studies in Life Sciences, Pt. Ravishankar Shukla University, Raipur, India
| | - Abhinandan Patil
- Division of Pharmacy, Dr. DY Patil University, Kolhapur, Maharashtra, India
| | - C. K. M. Tripathi
- Fermentation Technology Division, Central Drug Research Institute, CSIR, Lucknow, India
| | - Feiqiu Wen
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Shaowei Dong
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Defeng Cai
- Clinical Laboratory (Pathology) Centre, South China Hospital of Shenzhen University, Shenzhen, Guangdong, China
| |
Collapse
|
44
|
Qiu S, Yang B, Li Z, Li S, Yan H, Xin Z, Liu J, Zhao X, Zhang L, Xiang W, Wang W. Building a highly efficient Streptomyces super-chassis for secondary metabolite production by reprogramming naturally-evolved multifaceted shifts. Metab Eng 2024; 81:210-226. [PMID: 38142854 DOI: 10.1016/j.ymben.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Streptomyces has an extensive array of bioactive secondary metabolites (SMs). Nevertheless, devising a framework for the heterologous production of these SMs remains challenging. We here reprogrammed a versatile plug-and-play Streptomyces super-chassis and established a universal pipeline for production of diverse SMs via understanding of the inherent pleiotropic effects of ethanol shock on jadomycin production in Streptomyces venezuelae. We initially identified and characterized a set of multiplex targets (afsQ1, bldD, bldA, and miaA) that contribute to SM (jadomycin) production when subjected to ethanol shock. Subsequently, we developed an ethanol-induced orthogonal amplification system (EOAS), enabling dynamic and precise control over targets. Ultimately, we integrated these multiplex targets into functional units governed by the EOAS, generating a universal and plug-and-play Streptomyces super-chassis. In addition to achieving the unprecedented titer and yield of jadomycin B, we also evidenced the potential of this super-chassis for production of diverse heterologous SMs, including antibiotic oxytetracycline, anticancer drug doxorubicins, agricultural herbicide thaxtomin A, and plant growth regulator guvermectin, all with the yields of >10 mg/g glucose in a simple mineral medium. Given that the production of SMs all required complexed medium and the cognate yields were usually much lower, our achievement of using a universal super-chassis and engineering pipeline in a simple mineral medium is promising for convenient heterologous production of SMs.
Collapse
Affiliation(s)
- Shiwen Qiu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bowen Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingfang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuejin Zhao
- State Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, 200237, China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
45
|
Cuebas‐Irizarry MF, Grunden AM. Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste. Microb Biotechnol 2024; 17:e14258. [PMID: 37017414 PMCID: PMC10832569 DOI: 10.1111/1751-7915.14258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.
Collapse
Affiliation(s)
- Mara F. Cuebas‐Irizarry
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
| | - Amy M. Grunden
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
| |
Collapse
|
46
|
Dhillon B, Chakrabarti S. Draft genome sequence of Streptomyces murinus strain SPC1 with antimicrobial potential against fungal pathogens of palms. Microbiol Resour Announc 2023; 12:e0082623. [PMID: 38014990 PMCID: PMC10871060 DOI: 10.1128/mra.00826-23] [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: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Streptomyces murinus strain SPC1, isolated from foxtail palm seeds, exhibited antimicrobial activity against fungal pathogens of palms. The assembled genome was 8.3 Mb, with 71.96% GC content, and contained 37 secondary metabolite clusters (SMCs). A complete SMC for antifungal metabolite pentamycin (fungichromin) biosynthesis was identified in SPC1 genome.
Collapse
Affiliation(s)
- Braham Dhillon
- Department of Plant Pathology, University of Florida, Fort Lauderdale Research and Education Center, Davie, Florida, USA
| | - Seemanti Chakrabarti
- Department of Plant Pathology, University of Florida, Fort Lauderdale Research and Education Center, Davie, Florida, USA
| |
Collapse
|
47
|
Saadoun I, Mahasneh A, Odat JD, Al-Joubori B, Elsheikh E. Cloning, sequencing, and characterizing of soil antibiotic active-producing Streptomyces species-specific DNA markers. Saudi J Biol Sci 2023; 30:103854. [PMID: 38020227 PMCID: PMC10651690 DOI: 10.1016/j.sjbs.2023.103854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Association of the antibiotic activity of the soil Streptomyces isolates to their genetic profiles analyzed through RAPD-PCR fingerprints prompted us here in this study to use the most common bands as specific markers to identify homologous proteins within these isolates by cloning, sequencing, and characterizing these markers. Six out of twelve DNA bands ranged between 600 and 1350 bp previously obtained by RAPD-PCR analysis were purified out of the RAPD gels, and then cloned into pGEM-T Easy vector system. Success of the cloning process was confirmed by digesting purified plasmids with EcoRI. The clones namely No. 54, 55, 20, 56, 57, and 58 were sequenced using the DNA BigDye Terminator Sequencing System utilizing the M13 primer. Results indicated that the size of the inserted sequences is 599, 566, 522, 870, 857, and 254 bp, in clones No. 54. 55, 20, 56, 57, and 58, respectively. Homologous proteins of the six cloned sequences generated by DNA blast software indicated that the highest score of protein homology was scored for clone No. 54 with 87 % homology to putative secreted pectate lyase [Streptomyces coelicolor A3(2)]. The other clones showed less homology with 77 % homology for the clones No. 55 and 56, 73 % homology for the clone No. 20, and 55 % homology for the clones No. 57 and 58. The association of homologous proteins to the reported RAPD pattern is confirmed here for the first time, and the resulting DNA cloned fragments deserve further molecular analysis.
Collapse
Affiliation(s)
- Ismail Saadoun
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Amjad Mahasneh
- Department of Biology, Chemistry & Environmental Sciences, American University of Sharjah, Sharjah, United Arab Emirates
| | - Jazi D. Odat
- Applied Technology High School, Al Ain, Abu Dhabi, United Arab Emirates
| | - Ban Al-Joubori
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Elsiddig Elsheikh
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| |
Collapse
|
48
|
Gillon A, Abdelrahman O, Abou‐Mansour E, L'Haridon F, Falquet L, Allard P, Weisskopf L. Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity. Microbiologyopen 2023; 12:e1389. [PMID: 38129981 PMCID: PMC10616362 DOI: 10.1002/mbo3.1389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/13/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023] Open
Abstract
The Streptomyces genus is known to produce many specialized metabolites of value for medicine, but the potential of these metabolites in agronomy remains largely unexplored. In this study, we investigated three phylogenetically closely related Streptomyces strains (B5, B91, and B135) isolated from three distinct soil samples in Sudan. Despite belonging to the same species, these strains exhibited different ranges of Phytophthora infestans inhibition. The objective of this work was to identify the active compound(s) responsible for the inhibition of P. infestans and of other plant pathogens by comparing the genomes and metabolomes of the three strains which showed distinct activity patterns: B5 was the strongest inhibitor of oomycetes, B5 and B91 both inhibited most fungi and B135 was the only strain showing antibacterial activity. Our comparative genomic and metabolomic analysis identified borrelidin as the bioactive compound underlying B5's strong anti-oomycete activity and highlighted a few other metabolites as putative candidates underlying the strains' antifungal and antibacterial activities. This study illustrates the power of comparative genomics and metabolomics on phylogenetically closely related strains of differing activities to highlight bioactive compounds that could contribute to new sustainable crop protection strategies.
Collapse
Affiliation(s)
- Alisson Gillon
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Ola Abdelrahman
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Department of BotanyUniversity of KhartoumKhartoumSudan
| | | | | | - Laurent Falquet
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Genes and genomesSwiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Laure Weisskopf
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| |
Collapse
|
49
|
Kanchanabanca C, Hosaka T, Kojima M. High-intensity green light potentially activates the actinorhodin biosynthetic pathway in Streptomyces coelicolor A3(2). Arch Microbiol 2023; 206:8. [PMID: 38038757 DOI: 10.1007/s00203-023-03730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
The development of practices that enhance the potential of actinomycetes as major antibiotic producers is a challenge in discovering new secondary metabolites. Light, an essential external stimulus for most microorganisms, could be exploited to manipulate their physiological processes. However, the effects of monochromatic green light on the production of secondary metabolites in actinomycetes have not yet been reported. In this paper, we report a novel and simple method that uses high-intensity monochromatic green light to potentially induce the production of cryptic secondary metabolites in the model actinomycete Streptomyces coelicolor A3(2). Using actinorhodin (ACT), a blue-pigmented antibiotic, and undecylprodigiosin (RED), a red-pigmented antibiotic, as indicators, we found that irradiation with high-intensity monochromatic green light-emitting diodes promoted sporulation, significantly decreased RED production, and increased ACT production. Semi-quantitative reverse transcription-polymerase chain reaction and western blot analyses revealed, for the first time, that stimulation with green light accelerated the expression of ActII-ORF4, a pathway-specific regulator of ACT biosynthesis in S. coelicolor A3(2). This approach of stimulating secondary metabolite biosynthesis pathways in actinomycetes by irradiation with high-intensity monochromatic green light is expected to facilitate the discovery of cryptic antibiotics that are not typically produced under conventional dark culture conditions. However, the effective intensity and duration of irradiation with green light that are required to activate these metabolite pathways may vary markedly among actinomycetes.
Collapse
Affiliation(s)
- Chompoonik Kanchanabanca
- Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Takeshi Hosaka
- Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Masanobu Kojima
- Faculty of Agriculture, Shinshu University, Nagano, 399-4598, Japan.
| |
Collapse
|
50
|
Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
Collapse
Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
| | | | | |
Collapse
|