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Nguyen LTT, Park AR, Van Le V, Hwang I, Kim JC. Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight. Appl Microbiol Biotechnol 2024; 108:49. [PMID: 38183485 DOI: 10.1007/s00253-023-12874-w] [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: 06/14/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 01/08/2024]
Abstract
Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.
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Affiliation(s)
- Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Inmin Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea.
- JAN153 Biotech Incorporated, Gwangju, 61186, Republic of Korea.
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Bello KE, Irekeola AA, Alshehri AA. Streptomyces isolate SOM013, a potential agent against microbial resistance and gastric ulcers. Saudi Pharm J 2024; 32:102101. [PMID: 38799000 PMCID: PMC11127256 DOI: 10.1016/j.jsps.2024.102101] [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: 02/16/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
The menace of microbial resistance and re-emerging disease is still a problem for healthcare givers globally, and the need for newer sources of potent antibiotics has become paramount. This study investigated the antimicrobial and antiulcer activities of Streptomyces isolate SOM013. Streptomyces isolates were cultivated and purified following standard microbiological protocols. Secondary metabolites were recovered and characterized from Streptomyces isolate SOM013 via broth fermentation and extraction. Varying concentrations (0.5 mg/mL, 0.025 mg/mL and 0.0125 mg/mL) of the SOM013 extract were used for antimicrobial screening against resistant bacteria and medically important fungi (methicillin-resistant Escherichia coli, Oxacillin resistant Helicobacter pylori, Shigella spp, extended broad-spectrum resistant Pseudomonas aeruginosa, Streptococcus spp, Campylobacter spp, Candida albicans, Aspergillus niger, and Aspergillus flavus). The antiulcer activity of the SOM013 was also examined in a methanol-induced gastric ulcer animal model. A total of 23 Streptomyces spp were recovered from the study. Methanolic extract of the SOM013 isolates was more potent across the clinical test microorganisms compared to water extract. The antimicrobial activity was dose dependent, with methanolic extract at 0.05 g/mL displaying the highest zone of inhibition (18.8 ± 0.3 mm) when tested against extended broad-spectrum resistant Pseudomonas aeruginosa. Further, the extract's ulcer index and protection efficacy were significant as the concentration increased (P < 0.01). SOM013 isolate has a moderate antimicrobial and high antiulcer activity worthy of pharmacological exploration.
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Affiliation(s)
- Kizito Eneye Bello
- Department of Microbiology, Faculty of Natural Science, Kogi State (Prince Abubakar Audu) University, Anyigba, PMB 1008, Anyigba, Kogi State, Nigeria
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Kwara, Nigeria
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran, Saudi Arabia
- Health research center, Najran University, P.O. Box 1988, Najran, Saudi Arabia
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Alkorta I, Garbisu C. Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2024-0013. [PMID: 38815132 DOI: 10.1515/reveh-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.
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Affiliation(s)
- Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) , Bilbao, Spain
| | - Carlos Garbisu
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
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Huff R, Mann MB, Castro IMS, Kothe CI, Frazzon J, Frazzon APG. First report on the characterization of the gut microbiota in Heliconius erato phyllis caterpillars (Lepidoptera-Nymphalidae) from southern Brazil. BRAZ J BIOL 2024; 84:e282245. [PMID: 38808791 DOI: 10.1590/1519-6984.282245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/06/2024] [Indexed: 05/30/2024] Open
Affiliation(s)
- R Huff
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Microbiologia, Imunologia e Parasitologia, Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Porto Alegre, RS, Brasil
| | - M B Mann
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Microbiologia, Imunologia e Parasitologia, Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Porto Alegre, RS, Brasil
| | - I M S Castro
- Universidade de São Paulo - USP, Interunidades de Pós-graduação em Bioinformática, São Paulo, SP, Brasil
| | - C I Kothe
- Université Paris-Saclay, Institut National de Recherche pour L'agriculture, L'alimentation et L'environnement - INRAE, L'institut Micalis, Jouy-en-Josas, France
| | - J Frazzon
- Universidade Federal do Rio Grande do Sul - UFRGS, Instituto de Ciência e Tecnologia de Alimentos, Porto Alegre, RS, Brasil
| | - A P Guedes Frazzon
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Microbiologia, Imunologia e Parasitologia, Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Porto Alegre, RS, Brasil
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Calvopina-Chavez DG, Bursey DM, Tseng YJ, Patil LM, Bewley KD, Bennallack PR, McPhie JM, Wagstaff KB, Daley A, Miller SM, Moody JD, Price JC, Griffitts JS. Micrococcin cysteine-to-thiazole conversion through transient interactions between the scaffolding protein TclI and the modification enzymes TclJ and TclN. Appl Environ Microbiol 2024:e0024424. [PMID: 38780510 DOI: 10.1128/aem.00244-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase, and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, demonstrate complex formation between TclI, TclJ, and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core. IMPORTANCE Thiopeptides are a family of antimicrobial peptides characterized for having sulfur-containing heterocycles and for being highly post-translationally modified. Numerous thiopeptides have been identified; almost all of which inhibit protein synthesis in gram-positive bacteria. These intrinsic antimicrobial properties make thiopeptides promising candidates for the development of new antibiotics. The thiopeptide micrococcin is synthesized by the ribosome and undergoes several post-translational modifications to acquire its bioactivity. In this study, we identify key interactions within the enzymatic complex that carries out cysteine to thiazole conversion in the biosynthesis of micrococcin.
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Affiliation(s)
| | - Devan M Bursey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Yi-Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Leena M Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Kathryn D Bewley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - Philip R Bennallack
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Josh M McPhie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Kimberly B Wagstaff
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Anisha Daley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Susan M Miller
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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Nugraha AP, Sibero MT, Farabi K, Surboyo MDC, Ernawati DS, Ahmad Noor TNEBT. Marine Ascomycetes Extract Antifungal Susceptibility against Candida spp. Isolates from Oral Candidiasis HIV/AIDS Patient: An In Vitro Study. Eur J Dent 2024; 18:624-631. [PMID: 38387624 PMCID: PMC11132786 DOI: 10.1055/s-0043-1768466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVE The etiology of oral candidiasis (OC) was Candida albicans, C. krusei, C. dubliniensis, C. tropicalis that are frequently found in human immunodeficiency virus/ acquired immunodeficiency syndrome (HIV/AIDS) patients. Marine ascomycetes (MA) have been widely reported as an important producer of various antibiotic compounds. However, there is limited study of antifungal compounds from MA against Candida species. The aim of this study was to investigate the antifungal susceptibility of MA against Candida spp. isolates from OC HIV/AIDS patient. MATERIALS AND METHODS Trichoderma sp. is a sponge-associated fungus collected from Karimunjawa National Park, Central Java, Indonesia. The validation of C. albicans, C. krusei, C. dubliniensis, C. tropicalis. was done by ChromAgar. This study was true experimental with post-test only control group design; the sample was four replications for each group. Nystatin administration (K +), the golden standard antifungal drug, was used. The minimum fungicidal concentration (MFC), minimum inhibitory concentration (MIC), and diffusion zone methods were done. Analysis of variance difference test, and post-hoc Tukey's honest significant different were done to analyze the significant different between groups (p ≤ 0.05). RESULTS The MFC and MIC of MA against C. albicans, C. krusei, C. dubliniensis, and C. tropicalis were found at 12.5%. In addition, the greatest diffusion zone of MA against C. albicans, C. krusei, C. dubliniensis, and C. tropicalis was found at 12.5%. There is no appreciable difference in antifungal activity between K + and 12.5% of MA extract (p ≥ 0.05). CONCLUSION Concentration of 12.5% MA extract has antifungal susceptibility against Candida spp. isolates from OC HIV/AIDS patient.
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Affiliation(s)
- Alexander Patera Nugraha
- Department of Orthodontic, Faculty of Dental Medicine - Universitas Airlangga, Surabaya, Indonesia
- Immunology Study Programme, Postgraduate School, Universitas Airlangga, Surabaya, Indonesia
| | - Mada Triandala Sibero
- Department of Marine Science, Fac. of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Kindi Farabi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Indonesia
| | | | - Diah Savitri Ernawati
- Department of Oral Medicine, Faculty of Dental Medicine - Universitas Airlangga, Surabaya, Indonesia
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Abdelaziz R, Elsheshtawy HM, El-Houseiny W, Aloufi AS, Alwutayd KM, Mansour AT, Hadad G, Arisha AH, El-Murr AE, M Yassin A. A novel metabolite of Streptomyces coeruleorubidus exhibits antibacterial activity against Streptococcus agalactiae through modulation of physiological performance, inflammatory cytokines, apoptosis, and oxidative stress-correlated gene expressions in Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2024; 148:109496. [PMID: 38461875 DOI: 10.1016/j.fsi.2024.109496] [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: 12/21/2023] [Revised: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Using the unique structures found in natural materials to produce new antibacterial drugs is crucial. Actinobacteria is well-known for its ability to produce naturally occurring chemicals with a variety of structural features that can be used as weapons against infectious bacteria. In the present study, the Streptomyces coeruleorubidus metabolites were characterized and their efficacy in suppressing Streptococcus agalactiae growth was carried out both in vitro and in vivo. The metabolites of S. coeruleorubidus were purified and identified as octasiloxane-hexadecamethyl (OHM). In vivo antibacterial activity of OHM revealed an inhibitory minimum concentration value of 0.5 μg/ml against S. agalactiae and induced ultrastructural cell changes revealed by scanning electron microscope. The safe concentration of OHM was determined as 0.8 mg/L for Nile tilapia. Four in vivo treatments were treated with 0 and 0.8 mg/L OHM and with or without challenge by S. agalactiae (1 × 107 CFU/mL) named control, OHM, S. agalactiae, and S. agalactiae + OHM groups. The OHM treatment improved the survival of Nile tilapia by 33.33% than S. agalactiae challenge group. Waterborne OHM treatment significantly mitigated the deleterious effects of S. agalactiae on hematological, hepato-renal functions, stress indicators, and antioxidant balance. OHM significantly alleviated nitric oxide levels, complement 3, IgM, and lysozyme activity, downregulation of liver antioxidant genes expression in S. agalactiae group. Furthermore, the addition of OHM to challenged fish with S. agalactiae-significantly reversed dramatic negative regulation of inflammatory, apoptosis, and immune related gene expression (caspase-3, bax, pcna, tnf-α, ifn-γ, il-8 il-1β, il-10, tgf-β, and bcl-2 in the Nile tilapia spleen. Additionally, the damaged hepatic and splenic structure induced by bacterial infection was restored with OHM treatment. Finally, S. coeruleorubidus metabolites (mainly OHM) revealed in vitro and in vivo antibacterial activity and showed alleviated effects on the physiological status of S. agalactiae infected tilapia.
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Affiliation(s)
- Rewan Abdelaziz
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hassnaa Mahmoud Elsheshtawy
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Walaa El-Houseiny
- Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Abdallah Tageldein Mansour
- Animal and Fish Production Department, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa, 31982, Saudi Arabia; Fish and Animal Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Ghada Hadad
- Department of Animal Hygiene and Zoonoses, Faculty of Veterinary Medicine, University of Sadat City, Egypt
| | - Ahmed H Arisha
- Department of Animal Physiology and Biochemistry, Faculty of Veterinary Medicine, Badr University in Cairo (BUC), Badr City, Cairo, Egypt; Department of Physiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44511, Egypt
| | - Abd Elhakeem El-Murr
- Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amany M Yassin
- Laboratories Unit, Microbiology Department, Zagazig Univeristy Hospiltals, Zagazig University, Zagazig, Egypt
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Res 2024:gkae308. [PMID: 38661211 DOI: 10.1093/nar/gkae308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lia M Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [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: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Zheng J, Zhou Y, Zhang D, Ma K, Gong Y, Luo X, Liu J, Cui S. Intestinal melatonin levels and gut microbiota homeostasis are independent of the pineal gland in pigs. Front Microbiol 2024; 15:1352586. [PMID: 38596375 PMCID: PMC11003461 DOI: 10.3389/fmicb.2024.1352586] [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: 12/08/2023] [Accepted: 02/28/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Melatonin (MEL) is a crucial neuroendocrine hormone primarily produced by the pineal gland. Pinealectomy (PINX) has been performed on an endogenous MEL deficiency model to investigate the functions of pineal MEL and its relationship with various diseases. However, the effect of PINX on the gastrointestinal tract (GIT) MEL levels and gut microbiome in pigs has not been previously reported. Methods By using a newly established pig PINX model, we detected the levels of MEL in the GIT by liquid chromatography-tandem mass spectrometry. In addition, we examined the effects of PINX on the expression of MEL synthesis enzymes, intestinal histomorphology, and the intestinal barrier. Furthermore, 16S rRNA sequencing was performed to analyze the colonic microbiome. Results PINX reduced serum MEL levels but did not affect GIT MEL levels. Conversely, MEL supplementation increased MEL levels in the GIT and intestinal contents. Neither PINX nor MEL supplementation had any effect on weight gain, organ coefficient, serum biochemical indexes, or MEL synthetase arylalkylamine N-acetyltransferase (AANAT) expression in the duodenum, ileum, and colon. Furthermore, no significant differences were observed in the intestinal morphology or intestinal mucosal barrier function due to the treatments. Additionally, 16S rRNA sequencing revealed that PINX had no significant impact on the composition of the intestinal microbiota. Nevertheless, MEL supplementation decreased the abundance of Fibrobacterota and increased the abundance of Actinobacteriota, Desulfobacterota, and Chloroflexi. Conclusion We demonstrated that synthesis of MEL in the GIT is independent of the pineal gland. PINX had no influence on intestinal MEL level and microbiota composition in pigs, while exogenous MEL alters the structure of the gut microbiota.
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Affiliation(s)
- Jiaming Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yewen Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Di Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kezhe Ma
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yuneng Gong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xuan Luo
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiali Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sheng Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Institute of Reproduction and Metabolism, Yangzhou University, Yangzhou, China
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11
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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.
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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.
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12
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Hibbert T, Krpetic Z, Latimer J, Leighton H, McHugh R, Pottenger S, Wragg C, James CE. Antimicrobials: An update on new strategies to diversify treatment for bacterial infections. Adv Microb Physiol 2024; 84:135-241. [PMID: 38821632 DOI: 10.1016/bs.ampbs.2023.12.002] [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: 06/02/2024]
Abstract
Ninety-five years after Fleming's discovery of penicillin, a bounty of antibiotic compounds have been discovered, modified, or synthesised. Diversification of target sites, improved stability and altered activity spectra have enabled continued antibiotic efficacy, but overwhelming reliance and misuse has fuelled the global spread of antimicrobial resistance (AMR). An estimated 1.27 million deaths were attributable to antibiotic resistant bacteria in 2019, representing a major threat to modern medicine. Although antibiotics remain at the heart of strategies for treatment and control of bacterial diseases, the threat of AMR has reached catastrophic proportions urgently calling for fresh innovation. The last decade has been peppered with ground-breaking developments in genome sequencing, high throughput screening technologies and machine learning. These advances have opened new doors for bioprospecting for novel antimicrobials. They have also enabled more thorough exploration of complex and polymicrobial infections and interactions with the healthy microbiome. Using models of infection that more closely resemble the infection state in vivo, we are now beginning to measure the impacts of antimicrobial therapy on host/microbiota/pathogen interactions. However new approaches are needed for developing and standardising appropriate methods to measure efficacy of novel antimicrobial combinations in these contexts. A battery of promising new antimicrobials is now in various stages of development including co-administered inhibitors, phages, nanoparticles, immunotherapy, anti-biofilm and anti-virulence agents. These novel therapeutics need multidisciplinary collaboration and new ways of thinking to bring them into large scale clinical use.
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Affiliation(s)
- Tegan Hibbert
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Zeljka Krpetic
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Joe Latimer
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Hollie Leighton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Rebecca McHugh
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Sian Pottenger
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Charlotte Wragg
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Chloë E James
- School of Science, Engineering, and Environment, University of Salford, Salford, UK.
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13
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Murtaza M, Abrol V, Nehra E, Choudhary P, Singh SK, Jaglan S. Biodiversity and Bioactive Potential of Actinomycetes from Unexplored High Altitude Regions of Kargil, India. Indian J Microbiol 2024; 64:110-124. [PMID: 38468743 PMCID: PMC10924818 DOI: 10.1007/s12088-023-01133-1] [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: 08/24/2023] [Accepted: 10/30/2023] [Indexed: 03/13/2024] Open
Abstract
The effectiveness of currently available antimicrobials and anticancer medications is steadily declining due to the emergence of drug resistance. Since actinobacteria are important producers of bioactive substances, we have isolated them from the soil samples of exotic North-Western Himalayan terrains. Out of 128 isolates, 39 strains were prioritized based on their bioactive potential. The diversity analysis revealed higher abundance distribution of actinomycetes in the soil of an open field (68.7%), followed by the mountainside (34.9%), from which most of the bioactive strains were obtained. The extract of the strain S26-11 was found to be highly active against Gram-positive Staphylococcus aureus and Bacillus subtilis with a MIC of 0.5 μg/mL and 1 μg/mL respectively. A cytotoxicity assay (sulforhodamine B) was performed on a series of cancer cell lines (PC-3, MCF-7, A-549, and HCT-116). The extract of the strain S26-11 showed cytotoxic activity against all cancer cell lines with an IC50 of 2 µg/mL against PC-3, 1.9 µg/mL against MCF-7, 0.52 µg/mL against A-549, and 0.83 µg/mL against HCT-116. Moreover, the antioxidant activity was assessed using a DPPH-based assay and the results revealed that the S17-8 isolate showed the highest antioxidant activity with IC50 of 114.136 μg/mL. The Response Surface Methodology (RSM) had helped to optimize the physical parameters for scaling up of the bioactive strain S26-11. The unexplored soil niches of Kargil (UT, Ladakh), India, is rich in actinomycetes which are having potential bioactivities, would be worth to explore for the discovery of bioactive compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01133-1.
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Affiliation(s)
- Mohd Murtaza
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Vidushi Abrol
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
| | - Ekta Nehra
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Poonam Choudhary
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Shashank K. Singh
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sundeep Jaglan
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180016 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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14
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Chen C, Chen L, Mao C, Jin L, Wu S, Zheng Y, Cui Z, Li Z, Zhang Y, Zhu S, Jiang H, Liu X. Natural Extracts for Antibacterial Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306553. [PMID: 37847896 DOI: 10.1002/smll.202306553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/23/2023] [Indexed: 10/19/2023]
Abstract
Bacteria-induced epidemics and infectious diseases are seriously threatening the health of people around the world. In addition, antibiotic therapy has been inducing increasingly more serious bacterial resistance, which makes it urgent to develop new treatment strategies to combat bacteria, including multidrug-resistant bacteria. Natural extracts displaying antibacterial activity and good biocompatibility have attracted much attention due to greater concerns about the safety of synthetic chemicals and emerging drug resistance. These antibacterial components can be isolated and utilized as antimicrobials, as well as transformed, combined, or wrapped with other substances by using modern assistive technologies to fight bacteria synergistically. This review summarizes recent advances in natural extracts from three kinds of sources-plants, animals, and microorganisms-for antibacterial applications. This work discusses the corresponding antibacterial mechanisms and the future development of natural extracts in antibacterial fields.
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Affiliation(s)
- Cuihong Chen
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Lin Chen
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Congyang Mao
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
| | - Liguo Jin
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Shuilin Wu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Yufeng Zheng
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Zhenduo Cui
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Zhaoyang Li
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Yu Zhang
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shengli Zhu
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Hui Jiang
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Xiangmei Liu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
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15
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Chhetri G, Kim MJ, Kim I, Tran DVH, Kim YW, Kim HW, Seo T. Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula. Front Microbiol 2024; 15:1361583. [PMID: 38495511 PMCID: PMC10940327 DOI: 10.3389/fmicb.2024.1361583] [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: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Duc V. H. Tran
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
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16
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580553. [PMID: 38405983 PMCID: PMC10889028 DOI: 10.1101/2024.02.15.580553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A. Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lia M. Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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17
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Rammali S, Rahim A, El Aalaoui M, Bencharki B, Dari K, Habach A, Abdeslam L, Khattabi A. Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco. Sci Rep 2024; 14:3359. [PMID: 38336871 PMCID: PMC10858231 DOI: 10.1038/s41598-024-53801-x] [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: 09/01/2023] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
Research on microorganisms in various biotopes is required to identify new, natural potent molecules. These molecules are essential to control the development of multi-drug resistance (MDR). In the present study, a Streptomyces sp., namely SCJ, was isolated from a soil sample collected from a Moroccan garden. SCJ isolate was identified on the basis of a polyphasic approach, which included cultural, micro-morphological, biochemical, and physiological characteristics. The sequence of the 16S rRNA gene of the SCJ strain showed 99.78% similarity to strains of Streptomyces coeruleofuscus YR-T (KY753282.1). The preliminary screening indicated that the SCJ isolate exhibited activity against Candida albicans ATCC 60,193, Escherichia coli ATCC 25,922, Staphylococcus aureus CECT 976, Staphylococcus aureus ATCC 25,923, Bacillus cereus ATCC 14,579, Pseudomonas aeruginosa ATCC 27,853, as well as various other clinical MDR bacteria and five phytopathogenic fungi. The ethyl acetate extract of the isolated strain demonstrated highly significant (p < 0.05) antimicrobial activity against multi-resistant bacteria and phytopathogenic fungi. The absorption spectral analysis of the ethyl acetate extract of the SCJ isolate obtained showed no absorption peaks characteristic of polyene molecules. Moreover, no hemolytic activity against erythrocytes was observed in this extract. GC-MS analysis of the ethyl acetate extract of the SCJ isolate revealed the presence of 9 volatile compounds including 3,5-Dimethylpyrazole, and pyrrolizidine derivatives (Pyrrolo[1,2-a]pyrazine 1,4-dione, hexahydro-3-(2-methylpropyl)), which could potentially explain the antimicrobial activity demonstrated in this study.
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Affiliation(s)
- Said Rammali
- Laboratory of Agro-Alimentary and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco.
| | - Abdellatif Rahim
- Laboratory of Biochemistry, Neurosciences, Natural Ressources and Environment, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco
| | - Mohamed El Aalaoui
- Regional Center of Agronomic Research of Settat, Tertiary Road 1406, At 5 Km From Settat, 26400, Settat, Morocco
| | - Bouchaib Bencharki
- Laboratory of Agro-Alimentary and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco
| | - Khadija Dari
- Laboratory of Agro-Alimentary and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco
| | - Aicha Habach
- Biotechnology Unit, National Institute of Agronomic Research of Rabat, Av. Annasr, 10000, Rabat, Morocco
| | - Lamiri Abdeslam
- Applied Chemistry & Environment Laboratory, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco
| | - Abdelkrim Khattabi
- Laboratory of Agro-Alimentary and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, B.P. 539, 26000, Settat, Morocco
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18
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Shen Y, Liu N, Wang Z. Recent advances in the culture-independent discovery of natural products using metagenomic approaches. Chin J Nat Med 2024; 22:100-111. [PMID: 38342563 DOI: 10.1016/s1875-5364(24)60585-6] [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: 08/24/2023] [Indexed: 02/13/2024]
Abstract
Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads. However, the cultivation of only about 1% of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria. Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods. This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening, sequence tag-based homology screening, and bioinformatic-assisted chemical synthesis. Through this process, numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories. This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.
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Affiliation(s)
- Yiping Shen
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Nan Liu
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Zongqiang Wang
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China.
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19
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Liu J, Xu Z, Bai Y, Feng J, Xu L, Li F. Streptomyces albireticuli lung infection managed as a pulmonary air cyst: a case report and literature review. Front Cell Infect Microbiol 2024; 13:1296491. [PMID: 38274731 PMCID: PMC10808341 DOI: 10.3389/fcimb.2023.1296491] [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: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Streptomyces, the largest genus in the Streptomycetaceae family and a prolific producer of antibacterial drugs, is a saprophytic soil organism that rarely causes invasive infections. Here we report a case of necrotic pneumonia caused by Streptomyces albireticuli in a 75-year-old man who presented with progressive chest tightness and dyspnea. Streptomyces albireticuli was isolated from his bronchoalveolar lavage fluid and identified through whole-genome sequencing (WGS) and phylogenetic analysis. The patient responded satisfactorily to clarithromycin therapy. The findings of this study may enhance our vigilance in identifying visceral infections caused by Streptomyces.
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Affiliation(s)
- Jiajiao Liu
- Department of Neurosurgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Critical Care Medicine, The General Hospital of Western Theatre Command Chinese People's Liberation Army (PLA), Chengdu, China
| | - Zhaoxia Xu
- Department of Emergency Department, The General Hospital of Western Theatre Command Chinese People's Liberation Army (PLA), Chengdu, China
| | - Yujie Bai
- Department of Critical Care Medicine, The General Hospital of Western Theatre Command Chinese People's Liberation Army (PLA), Chengdu, China
| | - Jian Feng
- Department of Critical Care Medicine, The General Hospital of Western Theatre Command Chinese People's Liberation Army (PLA), Chengdu, China
| | - Lunshan Xu
- Department of Neurosurgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Fuxiang Li
- Department of Critical Care Medicine, The General Hospital of Western Theatre Command Chinese People's Liberation Army (PLA), Chengdu, China
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20
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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.
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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
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21
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Schmidt JJ, Remme DCLE, Eisfeld J, Brandenburg VB, Bille H, Narberhaus F. The LysR-type transcription factor LsrB regulates beta-lactam resistance in Agrobacterium tumefaciens. Mol Microbiol 2024; 121:26-39. [PMID: 37985428 DOI: 10.1111/mmi.15191] [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] [Revised: 10/20/2023] [Accepted: 10/28/2023] [Indexed: 11/22/2023]
Abstract
Agrobacterium tumefaciens is a plant pathogen, broadly known as the causal agent of the crown gall disease. The soil bacterium is naturally resistant to beta-lactam antibiotics by utilizing the inducible beta-lactamase AmpC. Our picture on the condition-dependent regulation of ampC expression is incomplete. A known regulator is AmpR controlling the transcription of ampC in response to unrecycled muropeptides as a signal for cell wall stress. In our study, we uncovered the global transcriptional regulator LsrB as a critical player acting upstream of AmpR. Deletion of lsrB led to severe ampicillin and penicillin sensitivity, which could be restored to wild-type levels by lsrB complementation. By transcriptome profiling via RNA-Seq and qRT-PCR and by electrophoretic mobility shift assays, we show that ampD coding for an anhydroamidase involved in peptidoglycan recycling is under direct negative control by LsrB. Controlling AmpD levels by the LysR-type regulator in turn impacts the cytoplasmic concentration of cell wall degradation products and thereby the AmpR-mediated regulation of ampC. Our results substantially expand the existing model of inducible beta-lactam resistance in A. tumefaciens by establishing LsrB as higher-level transcriptional regulator.
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Affiliation(s)
| | | | - Jessica Eisfeld
- Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | | | - Hannah Bille
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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22
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Pombubpa N, Lakmuang C, Tiwong P, Kanchanabanca C. Streptomyces Diversity Maps Reveal Distinct High-Specificity Biogeographical and Environmental Patterns Compared to the Overall Bacterial Diversity. Life (Basel) 2023; 14:11. [PMID: 38276260 PMCID: PMC10821021 DOI: 10.3390/life14010011] [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: 10/28/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Despite their enormous impact on the environment and humans, the distribution and variety of the biggest natural secondary metabolite producers, the genus Streptomyces, have not been adequately investigated. We developed representative maps from public EMP 16S rRNA amplicon sequences microbiomics data. Streptomyces ASVs were extracted from the EMP overall bacterial community, demonstrating Streptomyces diversity and identifying crucial diversity patterns. Our findings revealed that while the EMP primarily distinguished bacterial communities as host-associated or free-living (EMPO level 1), the Streptomyces community showed no significant difference but exhibited distinctions between categories in EMPO level 2 (animal, plant, non-saline, and saline). Multiple linear regression analysis demonstrated that pH, temperature, and salinity significantly predicted Streptomyces richness, with richness decreasing as these factors increased. However, latitude and longitude do not predict Streptomyces richness. Our Streptomyces maps revealed that additional samplings in Africa and Southeast Asia are needed. Additionally, our findings indicated that a greater number of samples did not always result in greater Streptomyces richness; future surveys may not necessitate extensive sampling from a single location. Broader sampling, rather than local/regional sampling, may be more critical in answering microbial biogeograph questions. Lastly, using 16S rRNA gene sequencing data has some limitations, which should be interpreted cautiously.
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Affiliation(s)
- Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (N.P.); (C.L.); (P.T.)
- Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chayaporn Lakmuang
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (N.P.); (C.L.); (P.T.)
| | - Pornnapat Tiwong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (N.P.); (C.L.); (P.T.)
| | - Chompoonik Kanchanabanca
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (N.P.); (C.L.); (P.T.)
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23
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Jeyachandran S, Vibhute P, Kumar D, Ragavendran C. Random mutagenesis as a tool for industrial strain improvement for enhanced production of antibiotics: a review. Mol Biol Rep 2023; 51:19. [PMID: 38100064 DOI: 10.1007/s11033-023-08975-4] [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: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Secondary metabolites are produced by microbes in minimal quantities in the natural environment out of necessity. However, in the pharmaceutical industry, their overproduction becomes essential. To achieve higher yields, genetic modifications are employed to create strains that surpass the productivity of the initially isolated strains. While rational screening and genetic engineering have emerged as valuable practices in recent years, the cost-effective technique of mutagenesis and selection, known as "random screening," remains a preferred method for efficient short-term strain development. This review aims to comprehensively explore all aspects of strain improvement, focusing on why random mutagenesis continues to be widely adopted.
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Affiliation(s)
- Sivakamavalli Jeyachandran
- Lab in Biotechnology & Bio-signal Transduction, Department of Orthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Chennai, Tamil Nadu, 600077, India.
| | - Prachi Vibhute
- PG & Research Department of Biotechnology & Microbiology, National College (Autonomous), Tiruchirappalli, Tamil Nadu, 620001, India
| | - Dinesh Kumar
- Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR-Central Salt & Marine Chemical Research Institute, Mandapam, Tamil Nadu, 623 519, India
| | - Chinnasamy Ragavendran
- Department of Cariology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospitals, Saveetha University, Chennai, 600 077, India
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24
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Padayachee T, Lamb DC, Nelson DR, Syed K. Structure-Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family. Biomolecules 2023; 13:1733. [PMID: 38136604 PMCID: PMC10741444 DOI: 10.3390/biom13121733] [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: 11/03/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107's catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107's multifunctionality. This study serves as a reference for understanding the structure-function analysis of CYP107 family members precisely and the structure-function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | - David C. Lamb
- Faculty of Medicine, Health and Life Sciences, Swansea University, Swansea SA2 8PP, UK;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
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25
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Zou J, Mao Y, Hou B, Kang Y, Wang R, Wu H, Ye J, Zhang H. DeoR regulates lincomycin production in Streptomyces lincolnensis. World J Microbiol Biotechnol 2023; 39:332. [DOI: doi.org/10.1007/s11274-023-03788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
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26
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Ongenae V, Kempff A, van Neer V, Shomar H, Tesson F, Rozen D, Briegel A, Claessen D. Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus. Sci Rep 2023; 13:20153. [PMID: 37978256 PMCID: PMC10656467 DOI: 10.1038/s41598-023-47634-3] [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: 08/30/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30-45 °C) and pH values (4-10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.
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Affiliation(s)
- Véronique Ongenae
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Annabel Kempff
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Vera van Neer
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Helena Shomar
- MDM Lab, Department Genomes and Genetics, Pasteur Institute, Paris, France
- INSERM, U1284, Université Paris-Cité, Paris, France
| | | | - Daniël Rozen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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27
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Khan S, Srivastava S, Karnwal A, Malik T. Streptomyces as a promising biological control agents for plant pathogens. Front Microbiol 2023; 14:1285543. [PMID: 38033592 PMCID: PMC10682734 DOI: 10.3389/fmicb.2023.1285543] [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: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.
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Affiliation(s)
- Shaista Khan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Srivastava
- School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Arun Karnwal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical sciences, Jimma University, Jimma, Ethiopia
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28
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Ge ZB, Zhai ZQ, Xie WY, Dai J, Huang K, Johnson DR, Zhao FJ, Wang P. Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria. THE ISME JOURNAL 2023; 17:2090-2102. [PMID: 37737252 PMCID: PMC10579247 DOI: 10.1038/s41396-023-01519-5] [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: 06/21/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.
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Affiliation(s)
- Zhan-Biao Ge
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Qiang Zhai
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wan-Ying Xie
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Dai
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Fang-Jie Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
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Pinheiro Alves de Souza Y, Schloter M, Weisser W, Schulz S. Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum. MICROBIAL ECOLOGY 2023; 86:2882-2893. [PMID: 37624441 PMCID: PMC10640511 DOI: 10.1007/s00248-023-02285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
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Affiliation(s)
- Yuri Pinheiro Alves de Souza
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Wolfgang Weisser
- Technische Universität München, TUM School of Life Science, Chair of Terrestrial Ecology, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany.
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30
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Calvopina-Chavez DG, Bursey DM, Tseng YJ, Patil LM, Bewley KD, Bennallack PR, McPhie JM, Wagstaff KB, Daley A, Miller SM, Moody JD, Price JC, Griffitts JS. Micrococcin cysteine-to-thiazole conversion through transient interactions between a scaffolding protein and two modification enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563616. [PMID: 37961320 PMCID: PMC10634744 DOI: 10.1101/2023.10.23.563616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, we demonstrate complex formation between TclI, TclJ and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core.
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Affiliation(s)
| | - Devan M Bursey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Yi-Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Leena M Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Kathryn D Bewley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
- Currently at: Genentech Inc, San Francisco, CA 94080
| | - Philip R Bennallack
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
- Currently at: Werfen North America, Bedford, MA 01730
| | - Josh M McPhie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Kimberly B Wagstaff
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Anisha Daley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Susan M Miller
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
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Chávez-Hernández M, Ortiz-Álvarez J, Morales-Jiménez J, Villa-Tanaca L, Hernández-Rodríguez C. Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria. Microorganisms 2023; 11:2551. [PMID: 37894209 PMCID: PMC10608816 DOI: 10.3390/microorganisms11102551] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.
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Affiliation(s)
- Michelle Chávez-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - Jossue Ortiz-Álvarez
- Programa “Investigadoras e Investigadores por México”. Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT). Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México 03940, Mexico;
| | - Jesús Morales-Jiménez
- Departamento el Hombre y su Ambiente, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Villa Quietud, Coyoacán, Ciudad de México 04960, Mexico;
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
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Zou J, Mao Y, Hou B, Kang Y, Wang R, Wu H, Ye J, Zhang H. DeoR regulates lincomycin production in Streptomyces lincolnensis. World J Microbiol Biotechnol 2023; 39:332. [PMID: 37801155 DOI: 10.1007/s11274-023-03788-w] [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] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Regulators belonging to the DeoR family are widely distributed among the bacteria. Few studies have reported that DeoR family proteins regulate secondary metabolism of Streptomyces. This study explored the function of DeoR (SLINC_8027) in Streptomyces lincolnensis. Deletion of deoR in NRRL 2936 led to an increase in cell growth. The lincomycin production of the deoR deleted strain ΔdeoR was 3.4-fold higher than that of the wild strain. This trait can be recovered to a certain extent in the deoR complemented strain ΔdeoR::pdeoR. According to qRT-PCR analysis, DeoR inhibited the transcription of all detectable genes in the lincomycin biosynthesis cluster and repressed the expression of glnR, bldD, and SLCG_Lrp, which encode regulators outside the cluster. DeoR also inhibited the transcription of itself, as revealed by the XylE reporter. Furthermore, we demonstrated that DeoR bound directly to the promoter region of deoR, lmbA, lmbC-D, lmbJ-K, lmrA, lmrC, glnR, and SLCG_Lrp, by recognizing the 5'-CGATCR-3' motif. This study found that versatile regulatory factor DeoR negatively regulates lincomycin biosynthesis and cellular growth in S. lincolnensis, which expanded the regulatory network of lincomycin biosynthesis.
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Affiliation(s)
- Jingyun Zou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yue Mao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
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Ashy RA. Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum. Saudi J Biol Sci 2023; 30:103789. [PMID: 37680975 PMCID: PMC10480775 DOI: 10.1016/j.sjbs.2023.103789] [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: 08/02/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.
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Affiliation(s)
- Ruba Abdulrahman Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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Devi S, Sharma M, Manhas RK. Purification and biological analysis of antimicrobial compound produced by an endophytic Streptomyces sp. Sci Rep 2023; 13:15248. [PMID: 37709816 PMCID: PMC10502074 DOI: 10.1038/s41598-023-41296-x] [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: 05/16/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023] Open
Abstract
Fungal phytopathogens and drug-resistant bacteria are two significant challenges in agriculture and public health, respectively. As a result, new sources of antimicrobial compounds are urgently needed. Taking into consideration these aspects, the present study was carried out to explore the antimicrobial activity of Streptomyces sp. SP5 against drug-resistant bacteria, especially methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococcus and fungal phytopathogens. MRSA and VRE are both types of antibiotic-resistant bacteria that pose significant challenges to public health. In vitro analysis of the metabolites of Streptomyces sp. SP5 exhibited broad-spectrum antimicrobial activity against drug-resistant bacteria and phytopathogenic fungi. Further chemical investigation of the diethyl ether extract led to the isolation and purification of an antimicrobial compound. The structure of the purified compound was elucidated by performing detailed spectroscopic analysis including MS, IR, and NMR. The compound was identified as plicacetin. Plicacetin is a nucleoside antibiotic that has been reported for antibacterial activity against Gram-positive bacterium Mycobacterium tuberculosis. According to our knowledge, the present study is the first to demonstrate the antimicrobial properties of plicacetin against Fusarium oxysporum, Alternaria brassicicola, Fusarium solani, VRE and Bacillus subtilis. The outcome of the current study endorses that compound produced by Streptomyces sp. SP5 can be used as an antimicrobial agent against fungal phytopathogens and drug-resistant bacteria.
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Affiliation(s)
- Sapna Devi
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Manish Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Rajesh Kumari Manhas
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Mingjie Y, Yair A, Tali G. The RIDD activity of C. elegans IRE1 modifies neuroendocrine signaling in anticipation of environment stress to ensure survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552841. [PMID: 37609168 PMCID: PMC10441387 DOI: 10.1101/2023.08.10.552841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Xbp1 splicing and regulated IRE1-dependent RNA decay (RIDD) are two RNase activities of the ER stress sensor IRE1. While Xbp1 splicing has important roles in stress responses and animal physiology, the physiological role(s) of RIDD remain enigmatic. Genetic evidence in C. elegans connects XBP1-independent IRE1 activity to organismal stress adaptation, but whether this is via RIDD, and what are the targets is yet unknown. We show that cytosolic kinase/RNase domain of C. elegans IRE1 is indeed capable of RIDD in human cells, and that sensory neurons use RIDD to signal environmental stress, by degrading mRNA of TGFβ-like growth factor DAF-7. daf-7 was degraded in human cells by both human and worm IRE1 RNAse activity with same efficiency and specificity as Blos1, confirming daf-7 as RIDD substrate. Surprisingly, daf-7 degradation in vivo was triggered by concentrations of ER stressor tunicamycin too low for xbp-1 splicing. Decrease in DAF-7 normally signals food limitation and harsh environment, triggering adaptive changes to promote population survival. Because C. elegans is a bacteriovore, and tunicamycin, like other common ER stressors, is an antibiotic secreted by Streptomyces spp., we asked whether daf-7 degradation by RIDD could signal pending food deprivation. Indeed, pre-emptive tunicamycin exposure increased survival of C. elegans populations under food limiting/high temperature stress, and this protection was abrogated by overexpression of DAF-7. Thus, C. elegans uses stress-inducing metabolites in its environment as danger signals, and employs IRE1's RIDD activity to modulate the neuroendocrine signaling for survival of upcoming environmental challenge.
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Affiliation(s)
- Ying Mingjie
- Department of Biology, Drexel University, Philadelphia, PA
- Department of Pathology and Lab Medicine, The Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA, USA
| | - Argon Yair
- Department of Pathology and Lab Medicine, The Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA, USA
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Delbari Y, Mohassel Y, Kakaei E, Bahrami Y. Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa. Sci Rep 2023; 13:13145. [PMID: 37573468 PMCID: PMC10423286 DOI: 10.1038/s41598-023-40478-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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.
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Affiliation(s)
- Yaser Delbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yaser Mohassel
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
- Advanced Marine Biomanufacturing Laboratory, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
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Choksket S, Kaur M, Pinnaka AK, Korpole S. An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land. FEMS MICROBES 2023; 4:xtad014. [PMID: 37701422 PMCID: PMC10495126 DOI: 10.1093/femsmc/xtad014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60T was isolated from soil The isolate exhibited 99.3% and 99.0% identity with Streptomyces laurentii ATCC 31255T and S. roseicoloratus TRM 44457T, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with S. roseicoloratus TRM 44457T. Similarly, the dDDH showed 33.7% identity with S. roseicoloratus TRM 44457T. It formed a cluster with S. roseicoloratus TRM 44457T and S. laurentii ATCC 31255T in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C15:0, anteiso-C15:0, and iso-C16:0. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from S. bernensis UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, S. bernensis is not validly reported and thus SKN60T is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60T differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus Streptomyces. Therefore, it is proposed as a novel species with the name Streptomyces terrae sp. nov. strain SKN60T (=MTCC 13163T; = JCM 35768T).
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Mahaldeep Kaur
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Anil Kumar Pinnaka
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
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Ashok GC, Prakash Pradhan S, Kumar Karki K, Khadka A, Bhandari A, Prasad Pandey B. Antioxidant and Enzyme Inhibitory Potential of Streptomyces sp. G-18 Grown in Various Media. Int J Microbiol 2023; 2023:6439466. [PMID: 37583475 PMCID: PMC10425256 DOI: 10.1155/2023/6439466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/14/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023] Open
Abstract
Streptomyces are bacteria well known for producing bioactive secondary metabolites which are commonly found in diverse habitats. The biosynthesis of metabolites from Streptomyces is influenced by various factors such as the growth medium, environmental conditions, and gene regulation. This study aimed to investigate the influence of different growth media on biomass production and the antioxidant and enzyme inhibitory potential of a crude extract obtained from Streptomyces sp. G-18 isolated from high altitudinal soil of Nepal. The highest dry weight growth was observed in R2YE medium (184 mg/L), followed by R5 (144 mg/L), YEME (38 mg/L), and R5M media (30 mg/L). The crude extract showed notable antioxidant activities against free radicals. The highest alpha-amylase inhibition was observed in the R2YE medium, and worthy lipase and tyrosinase inhibition was observed in the YEME medium. However, only the R2YE medium exhibited inhibitory potential against elastase and acetylcholinesterase, while crude extracts from R5, YEME, and R5 modified did not show any such activity. Overall, our findings suggest that the production of bioactive secondary metabolites in Streptomyces sp. G-18 was significantly influenced by the growth medium. This strain may be a promising source of enzyme inhibitors with potential applications in the pharmaceutical and cosmetic industries.
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Affiliation(s)
- G. C. Ashok
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, Nepal
| | | | - Krishna Kumar Karki
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, Nepal
| | - Aakriti Khadka
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, Nepal
| | - Aishwarya Bhandari
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, Nepal
| | - Bishnu Prasad Pandey
- Department of Chemical Science and Engineering, Kathmandu University, Dhulikhel, Nepal
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Tan KS, Azman AS, Hassandarvish P, Amelia-Yap ZH, Tan TK, Low VL. Protein Profiling of Aedes aegypti Treated with Streptomyces sp. KSF103 Ethyl Acetate Extract Reveals Potential Insecticidal Targets and Metabolic Pathways. Int J Mol Sci 2023; 24:12398. [PMID: 37569772 PMCID: PMC10418484 DOI: 10.3390/ijms241512398] [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: 05/27/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 08/13/2023] Open
Abstract
The insecticidal activity of Streptomyces sp. KSF103 ethyl acetate (EA) extract against mosquitoes is known; however, the underlying mechanism behind this activity remains elusive. In this study, liquid chromatography with tandem mass spectrometry (LC-MS/MS) was employed to investigate changes in the protein profile of Aedes aegypti larvae and adults treated with lethal concentrations of 50 (LC50) EA extract. By comparing the treated and untreated mosquitoes, this study aimed to identify proteins or pathways that exhibit alterations, potentially serving as targets for future insecticide development. Treatment with a lethal concentration of EA extract upregulated 15 proteins in larvae, while in adults, 16 proteins were upregulated, and two proteins were downregulated. These proteins were associated with metabolism, protein regulation/degradation, energy production, cellular organization and structure, enzyme activity, and catalysis, as well as calcium ion transport and homeostasis. Notably, ATP synthase, fructose-bisphosphate aldolase (FBA), and ATP citrate synthase were significantly expressed in both groups. Gene ontology analysis indicated a focus on energy metabolic processes. Molecular docking revealed a strong interaction between dodemorph, selagine (compounds from the EA extract), and FBA, suggesting FBA as a potential protein target for insecticide development. Further studies such as Western blot and transcriptomic analyses are warranted to validate the findings.
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Affiliation(s)
- Ker Shien Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (K.S.T.); (P.H.); (Z.H.A.-Y.)
- Institute for Advanced Studies (IAS), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (K.S.T.); (P.H.); (Z.H.A.-Y.)
| | - Zheng Hua Amelia-Yap
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (K.S.T.); (P.H.); (Z.H.A.-Y.)
| | - Tiong Kai Tan
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia; (K.S.T.); (P.H.); (Z.H.A.-Y.)
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40
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Maglangit F, Kyeremeh K, Deng H. Deletion of the accramycin pathway-specific regulatory gene accJ activates the production of unrelated polyketide metabolites. Nat Prod Res 2023; 37:2753-2758. [PMID: 36125461 DOI: 10.1080/14786419.2022.2126466] [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: 01/20/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 10/14/2022]
Abstract
The manipulation of regulatory genes has been employed to awaken cryptic metabolites in Streptomyces. Of particular interest in recent years is the effect of disruption of a pathway-specific gene to other biosynthetic pathways. Herein, we report the inactivation of the accramycin pathway-specific regulatory gene, accJ in Streptomyces sp. MA37 resulted in the production of unrelated polyketide metabolites. Through detailed mass spectrometric and spectroscopic analyses, and comparison with literature data, their structures were deduced as 3-methoxy-2-methyl-4H-pyran-4-one (1), zanthopyranone (2), propioveratrone (3), and TW94a (4). To the best of our knowledge, this is the first report of the isolation of 1-3 from bacteria. Compounds 1, 2, and 4 showed weak to moderate activity against Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium. Propioveratrone (3) displayed better inhibitory activity (MIC = 6.3 μg/mL) than ampicillin against multi-drug resistant E. faecium K60-39 clinical isolate (MIC = 25 μg/mL), suggesting a promising structural template for the drug development targeting Enterococcus isolates.
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Affiliation(s)
- Fleurdeliz Maglangit
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City, Philippines
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, Legon-Accra, Ghana
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, Scotland, UK
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de Lima Júnior AA, de Sousa EC, de Oliveira THB, de Santana RCF, da Silva SKR, Coelho LCBB. Genus Streptomyces: Recent advances for biotechnological purposes. Biotechnol Appl Biochem 2023; 70:1504-1517. [PMID: 36924211 DOI: 10.1002/bab.2455] [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: 10/27/2022] [Revised: 02/06/2023] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
Actinomycetes are a distinct group of filamentous bacteria. The Streptomyces genus within this group has been extensively studied over the years, with substantial contributions to society and science. This genus is known for its antimicrobial production, as well as antitumor, biopesticide, and immunomodulatory properties. Therefore, the extraordinary plasticity of the Streptomyces genus has inspired new research techniques. The newest way of exploring Streptomyces has comprised the discovery of new natural metabolites and the application of emerging tools such as CRISPR technology in drug discovery. In this narrative review, we explore relevant published literature concerning the ongoing novelties of the Streptomyces genus.
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Affiliation(s)
- Apolonio Alves de Lima Júnior
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | - Thales Henrique Barbosa de Oliveira
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
| | | | | | - Luana Cassandra Breitenbach Barroso Coelho
- Departamento de Bioquímica, Centro de Biociências, CB, Universidade Federal de Pernambuco (UFPE), Avenida Professor Moraes Rego, S/N, Cidade Universitária, Recife, Pernambuco, Brazil
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Singh R, Ali M, Dubey AK. Phenyl Pentyl Ketone and m-isobutyl Methoxy Benzoate Produced by Streptomyces Chrestomyceticus ADP4 are Potent Antimicrobial Agents Displaying Broad Spectrum Activities. Indian J Microbiol 2023; 63:181-189. [PMID: 37325023 PMCID: PMC10267095 DOI: 10.1007/s12088-023-01068-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/19/2023] [Indexed: 03/28/2023] Open
Abstract
Isolation and identification of two antimicrobial compounds, a phenyl pentyl ketone (CP1) and m-isobutyl methoxy benzoate (CP2), from Streptomyces chrestomyceticus ADP4 have been reported. Structure of the compounds were elucidated from analyses of spectral data that included LCMS/MS, NMR, FTIR and UV spectroscopies. Both the compounds displayed significant inhibition of albicans and non-albicans species of Candida (NAC) pathogens including C. auris, which is currently a pathogen of global concern. Also, the compounds showed potent antagonistic activity against Staphylococcus aureus, another significant human pathogen. No in-vitro cytotoxicity against HePG2 cells was observed with either of the compounds. Both displayed favourable drug likeness properties as determined by in-silico ADME and toxicological studies. Also, this is the first report on production of these anti-microbial compounds by an actinobacterium. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01068-7.
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Affiliation(s)
- Radha Singh
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078 India
| | - Mohd Ali
- Faculty of Pharmacy, Hamdard University, New Delhi, 110062 India
| | - Ashok K. Dubey
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078 India
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Saini R, Kumari S, Bhatnagar A, Singh A, Mishra A. Discovery of the allosteric inhibitor from actinomyces metabolites to target EGFR CSTMLR mutant protein: molecular modeling and free energy approach. Sci Rep 2023; 13:8885. [PMID: 37264083 DOI: 10.1038/s41598-023-33065-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/06/2023] [Indexed: 06/03/2023] Open
Abstract
EGFR (epidermal growth factor receptor), a surface protein on the cell, belongs to the tyrosine kinase family, responsible for cell growth and proliferation. Overexpression or mutation in the EGFR gene leads to various types of cancer, i.e., non-small cell lung cancer, breast, and pancreatic cancer. Bioactive molecules identified in this genre were also an essential source of encouragement for researchers who accomplished the design and synthesis of novel compounds with anticancer properties. World Health Organization (WHO) report states that antibiotic resistance is one of the most severe risks to global well-being, food safety, and development. The world needs to take steps to lessen this danger, such as developing new antibiotics and regulating their use. In this study, 6524 compounds derived from Streptomyces sp. were subjected to drug-likeness filters, molecular docking, and molecular dynamic simulation for 1000 ns to find new triple mutant EGFRCSTMLR (EGFR-L858R/T790M/C797S) inhibitors. Docking outcomes revealed that five compounds showed better binding affinity (- 9.074 to - 9.3 kcal/mol) than both reference drug CH7233163 (- 6.11 kcal/mol) and co-crystallized ligand Osimertinib (- 8.07 kcal/mol). Further, molecular dynamic simulation confirmed that ligand C_42 exhibited the best interaction at the active site of EGFR protein and comprised a better average radius of gyration (3.87 Å) and average SASA (Solvent Accessible Surface Area) (82.91 Å2) value than co-crystallized ligand (4.49 Å, 222.38 Å2). Additionally, its average RMSD (Root Mean Square Deviation) (3.25 Å) and RMSF (Root Mean Square Fluctuation) (1.54 Å) values were highly similar to co-crystallized ligand (3.07 Å, 1.54 Å). Compared to the reference ligand, it also demonstrated conserved H-bond interactions with the residues MET_793 and GLN_791 with strong interaction probability. In conclusion, we have found a potential drug with no violation of the rule of three, Lipinski's rule of five, and 26 other vital parameters having great potential in medicinal and pharmaceutical industries applications and can overcome synthetic drug issues.
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Affiliation(s)
- Ravi Saini
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, India
| | - Sonali Kumari
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, India
| | - Aditi Bhatnagar
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, India
| | - Amit Singh
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, India.
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Chanama M, Suriyachadkun C, Chanama S. Streptomyces antimicrobicus sp. nov., a novel clay soil-derived actinobacterium producing antimicrobials against drug-resistant bacteria. PLoS One 2023; 18:e0286365. [PMID: 37256855 DOI: 10.1371/journal.pone.0286365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
A novel actinobacterium, designated strain SMC 277T, was isolated from the clay soil in paddy field of Chonburi Province, Thailand, and characterized using polyphasic taxonomy. Strain SMC 277T formed straight chains of nonmotile cylindrical spores with smooth surface developed on aerial mycelia. The typical chemotaxonomic properties of members of the genus Streptomyces were observed in strain SMC 277T, e.g., cell wall peptidoglycan, whole cell sugars, major menaquinones, cellular fatty acids, and polar lipids. Chemotaxonomic data combined with mycelium and spore morphologies supported the assignment of strain SMC 277T to the genus Streptomyces. The results of comparative analysis of the 16S rRNA gene sequences confirmed that strain SMC 277T represented a member of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 277T shared the highest sequence similarity with Streptomyces bambusae NBRC 110903T (98.8%). Genome sequencing revealed a genome size of 6.55 Mbp and a digital G+C content of 73.4 mol%. In addition to the differences in phenotypic characteristics (morphology and physiology), values of ANI (ANIb and ANIm), AAI and dDDH between strain SMC 277T and its closest relative S. bambusae NBRC 110903T were 81.84, 86.77, 76.91 and 26.1%, respectively. Genome annotation and secondary metabolite gene cluster analysis predicted that SMC 277T contained 35 biosynthetic gene clusters encoding diverse bioactive secondary metabolites. It is in agreement with observed antimicrobial activity against drug-resistant bacteria associated with nosocomial infections (methicillin-resistant Staphylococcus aureus, extended-spectrum β-lactamase producing Klebsiella pneumoniae, and multidrug-resistant Acinetobacter baumannii). On the basis of these genotypic and phenotypic characteristics, strain SMC 277T can be characterized to represent a novel species of the genus Streptomyces, for which the name Streptomyces antimicrobicus is proposed. The type strain is SMC 277T (= TBRC 15568T = NBRC 115422T).
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Affiliation(s)
- Manee Chanama
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Suchart Chanama
- Faculty of Science, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Liu HQ, Zhao ZL, Li HJ, Yu SJ, Cong L, Ding LL, Ran C, Wang XF. Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria. FRONTIERS IN PLANT SCIENCE 2023; 14:1129508. [PMID: 37313258 PMCID: PMC10258322 DOI: 10.3389/fpls.2023.1129508] [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: 12/22/2022] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Huanglongbing (HLB), the most prevalent citrus disease worldwide, is responsible for substantial yield and economic losses. Phytobiomes, which have critical effects on plant health, are associated with HLB outcomes. The development of a refined model for predicting HLB outbreaks based on phytobiome markers may facilitate early disease detection, thus enabling growers to minimize damages. Although some investigations have focused on differences in the phytobiomes of HLB-infected citrus plants and healthy ones, individual studies are inappropriate for generating common biomarkers useful for detecting HLB on a global scale. In this study, we therefore obtained bacterial information from several independent datasets representing hundreds of citrus samples from six continents and used these data to construct HLB prediction models based on 10 machine learning algorithms. We detected clear differences in the phyllosphere and rhizosphere microbiomes of HLB-infected and healthy citrus samples. Moreover, phytobiome alpha diversity indices were consistently higher for healthy samples. Furthermore, the contribution of stochastic processes to citrus rhizosphere and phyllosphere microbiome assemblies decreased in response to HLB. Comparison of all constructed models indicated that a random forest model based on 28 bacterial genera in the rhizosphere and a bagging model based on 17 bacterial species in the phyllosphere predicted the health status of citrus plants with almost 100% accuracy. Our results thus demonstrate that machine learning models and phytobiome biomarkers may be applied to evaluate the health status of citrus plants.
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Affiliation(s)
- Hao-Qiang Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Ze-long Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, China
| | - Hong-Jun Li
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Shi-Jiang Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Lin Cong
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Li-Li Ding
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Chun Ran
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
| | - Xue-Feng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, National Engineering Research Center for Citrus, Chongqing, China
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Zanane C, Mitro S, Mazigh D, Lekchiri S, Hakim T, El Louali M, Latrache H, Zahir H. Characterization of Streptomyces Cell Surface by the Microbial Adhesion to Solvents Method. Int J Microbiol 2023; 2023:8841509. [PMID: 37214152 PMCID: PMC10195169 DOI: 10.1155/2023/8841509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
The cell surface physicochemical properties of Streptomyces should influencing the dispersal and adsorption of spores and hyphae in soil and should conditioning there interactions with organic or metal substances in the bioremediation of contaminated environment. These properties are concerning surface hydrophobicity, electron donor/acceptor, and charge surface. To date, only hydrophobicity of Streptomyces was studied by contact angle measurements and microbial adhesion to hydrocarbons (MATH). In this work, we studied the electron donor/acceptor character of the Streptomyces cell surface in two ionic strength 10-3 M and 10-1 M of KNO3. Thus, to facilitate the characterisation of the surfaces of microbial cells, we used a simple, rapid, and quantitative technique, the microbial adhesion method to solvents (MATS), which is based on the comparison of the affinity of microbial cells for a monopolar solvent with a polar solvent. The monopolar solvent can be acid (electron acceptor) or basic (electron donor), but both solvents should have a surface tension similar to that of the Kifshitz van der Waals components. At the significant ionic strength of the biological medium, the electron donor character is well expressed for all 14 Streptomyces strains with very significant differences among them ranging from 0% to 72.92%. When the cells were placed in a solution with a higher ionic strength, we were able to classify the donor character results into three categories. The first category is that the weak donor character of strains A53 and A58 became more expressed at 10-1 M KNO3 concentration. The second category is that three strains A30, A60, and A63 expressed a weaker character in a higher ionic strength. For the other strains, no expression of the donor trait was obtained at higher ionic strength. In a suspension with a concentration of 10-3 KNO3, only two strains expressed an electron acceptor character. This character is very important for strains A49, A57, A58, A60, A63, and A65 at 10-1M KNO3. This work has shown that these properties vary greatly depending on the Streptomyces strain. It is important to consider the change in physicochemical properties of surface cells with ionic strength when using Streptomyces in different bioprocesses.
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Affiliation(s)
- C. Zanane
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - S. Mitro
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - D. Mazigh
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - S. Lekchiri
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - T. Hakim
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - M. El Louali
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - H. Latrache
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - H. Zahir
- Industrial and Surface Engineering, Research Team of Bioprocesses and Biointerfaces, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
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Shin C, Baik I. Bacterial Extracellular Vesicle Composition in Human Urine and the 10-Year Risk of Abdominal Obesity. Metab Syndr Relat Disord 2023. [PMID: 37134220 DOI: 10.1089/met.2022.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Objective: We aimed to evaluate a causal relationship between commensal bacteria and abdominal obesity. Methods: A prospective study, including 2222 adults who provided urine samples at baseline, was performed. These samples were used for assays of genomic DNA from bacterial extracellular vesicles (EVs). During the 10-year period, the incidence rates of obesity (measured as body mass index) and abdominal obesity (measured as waist circumference) were ascertained as outcomes. To evaluate associations of bacterial composition at the phylum and genus levels with the outcomes, the hazard ratio (HR) and its confidence interval (95% CI) were estimated. Results: No significant association was observed for the risk of obesity, whereas the risk of abdominal obesity was inversely associated with the composition of Proteobacteria and positively associated with that of Firmicutes (adjusted P value <0.05). In joint analysis for the combination groups of Proteobacteria and Firmicutes composition tertiles, the group with top tertiles of both Proteobacteria and Firmicutes showed a significant HR of 2.59 (95% CI: 1.33 - 5.01) compared with the reference with lower tertiles (adjusted P value <0.05). Some genera of these phyla were associated with the risk of abdominal obesity. Conclusions: These findings suggest that bacterial composition in urinary EV samples can predict the 10-year risk of abdominal obesity.
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Affiliation(s)
- Chol Shin
- Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Inkyung Baik
- Department of Foods and Nutrition, College of Science and Technology, Kookmin University, Seoul, Republic of Korea
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Ren M, Jiang S, Wang Y, Pan X, Pan F, Wei X. Discovery and excavation of lichen bioactive natural products. Front Microbiol 2023; 14:1177123. [PMID: 37138611 PMCID: PMC10149937 DOI: 10.3389/fmicb.2023.1177123] [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: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.
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Affiliation(s)
- Meirong Ren
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Shuhua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Feng Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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49
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Xu X, Zhang F, Zhou L, Chang Y, Che Q, Zhu T, Li D, Zhang G. Overexpression of Global Regulator SCrp Leads to the Discovery of New Angucyclines in Streptomyces sp. XS-16. Mar Drugs 2023; 21:md21040240. [PMID: 37103379 PMCID: PMC10146017 DOI: 10.3390/md21040240] [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: 02/25/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Six angucyclines including three unreported compounds (1-3) were isolated from Streptomyces sp. XS-16 by overexpressing the native global regulator of SCrp (cyclic AMP receptor). The structures were characterized based on nuclear magnetic resonance (NMR) and spectrometry analysis and assisted by electronic circular dichroism (ECD) calculations. All compounds were tested for their antitumor and antimicrobial activities, and compound 1 showed different inhibitory activities against various tumor cell lines with IC50 values ranging from 0.32 to 5.33 μM.
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Affiliation(s)
- Xiao Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Falei Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Luning Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yimin Chang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Biomedical Research Institute of Qingdao, Qingdao 266101, China
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50
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Alanzi A, Elhawary EA, Ashour ML, Moussa AY. Aspergillus co-cultures: A recent insight into their secondary metabolites and microbial interactions. Arch Pharm Res 2023; 46:273-298. [PMID: 37032397 DOI: 10.1007/s12272-023-01442-5] [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: 08/05/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023]
Abstract
There is an urgent need for novel antibiotics to combat emerging resistant microbial strains. One of the most pressing resources is Aspergillus microbial cocultures. The genome of Aspergillus species comprises a far larger number of novel gene clusters than previously expected, and novel strategies and approaches are essential to exploit this potential source of new drugs and pharmacological agents. This is the first review consulting recent developments and chemical diversity of Aspergillus cocultures and highlighting its untapped richness. The analyzed data revealed that cocultivation of several Aspergillus species with other microorganisms, including bacteria, plants, and fungi, is a source of novel bioactive natural products. Various vital chemical skeleton leads were newly produced or augmented in Aspergillus cocultures, among which were taxol, cytochalasans, notamides, pentapeptides, silibinin, and allianthrones. The possibility of mycotoxin production or complete elimination in cocultivations was detected, which pave the way for better decontamination strategies. Most cocultures revealed a remarkable improvement in their antimicrobial or cytotoxic behavior due to their produced chemical patterns; for instance, weldone and asperterrin whose antitumor and antibacterial activities, respectively, were superior. Microbial cocultivation elicited the upregulation or production of specific metabolites whose importance and significance are yet to be revealed. With more than 155 compounds isolated from Aspergillus cocultures in the last 10 years, showing overproduction, reduction, or complete suppression under the optimized coculture circumstances, this study filled a gap for medicinal chemists searching for new lead sources or bioactive molecules as anticancer agents or antimicrobials.
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Affiliation(s)
- Abdullah Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Esraa A Elhawary
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
| | - Mohamed L Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
- Pharmacy Program, Department of Pharmaceutical Science, Batterjee Medical College, 21442, Jeddah, Saudi Arabia
| | - Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt.
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