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Janthanom R, Kikuchi Y, Kanto H, Hirose T, Tahara A, Ishii T, Thamchaipenet A, Inahashi Y. A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001. Beilstein J Org Chem 2024; 20:497-503. [PMID: 38440171 PMCID: PMC10910382 DOI: 10.3762/bjoc.20.44] [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: 12/15/2023] [Accepted: 02/14/2024] [Indexed: 03/06/2024] Open
Abstract
Actinomycetes are well-known as the main producers of bioactive compounds such as antibiotics, anticancers, and immunosuppressants. Screening of natural products from actinomycetes has been an essential part of several drug discovery programs. Finding such novel biologically active metabolites is immensely important because of their beneficial health effects. Recently, the discovery of new compounds has diverted attention to rare actinomycetes, since they are rich sources of natural products. In this study, a collection of rare actinomycetes at Kitasato University has been screened for potential novel compound producers. Among the rare actinomycetes, Saccharopolyspora sp. KR21-0001 isolated from soil on Ōha Island, Okinawa, Japan was selected as a potential producer. The strain was cultured in 20 L of production medium in a jar fermenter and the culture broth was extracted. Further purification revealed the presence of a new compound designated KR21-0001A (1). The structure was elucidated by NMR, and the absolute stereochemistry was determined by advanced Marfey's method. The results indicated that 1 is a new analog of dihydroxybenzoic acid. 1 has no antimicrobial activity against bacteria and fungi but showed potent antioxidant activity.
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Affiliation(s)
- Rattiya Janthanom
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan Road, Ladyao, Chatuchak, Bangkok 10900, Thailand
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yuta Kikuchi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroki Kanto
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Arisu Tahara
- Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Takahiro Ishii
- Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan Road, Ladyao, Chatuchak, Bangkok 10900, Thailand
| | - Yuki Inahashi
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4074. [PMID: 38140401 PMCID: PMC10748132 DOI: 10.3390/plants12244074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Ansari M, Devi BM, Sarkar A, Chattopadhyay A, Satnami L, Balu P, Choudhary M, Shahid MA, Jailani AAK. Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation. J Xenobiot 2023; 13:572-603. [PMID: 37873814 PMCID: PMC10594471 DOI: 10.3390/jox13040037] [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: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.
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Affiliation(s)
- Mariya Ansari
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - B. Megala Devi
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
| | - Ankita Sarkar
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - Anirudha Chattopadhyay
- Pulses Research Station, S.D. Agricultural University, Sardarkrushinagar 385506, Gujarat, India;
| | - Lovkush Satnami
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; (M.A.); (A.S.); (L.S.)
| | - Pooraniammal Balu
- Department of Biotechnology, Sastra Deemed University, Thanjavur 613401, Tamil Nadu, India;
| | - Manoj Choudhary
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA;
| | - A. Abdul Kader Jailani
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
- Plant Pathology Department, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
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Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223065. [PMID: 36432794 PMCID: PMC9694258 DOI: 10.3390/plants11223065] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/07/2023]
Abstract
Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
| | - Maria R. Galyamova
- Center for Entrepreneurial Initiatives, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Zhu M, Ye H, Lai M, Ye J, Li R, Zhang W, Liang H, Zhu R, Fan H, Chen S. The gold nanoparticle sensitized pRGO-MWCNTs grid modified carbon fiber microelectrode as an efficient sensor system for simultaneous detection of three dihydroxybenzoic acid isomers. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.134765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Roy EM, Griffith KL. Characterization of a Novel Iron Acquisition Activity That Coordinates the Iron Response with Population Density under Iron-Replete Conditions in Bacillus subtilis. J Bacteriol 2017; 199:e00487-16. [PMID: 27795321 PMCID: PMC5165090 DOI: 10.1128/jb.00487-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/24/2016] [Indexed: 01/10/2023] Open
Abstract
Iron is an essential micronutrient required for the viability of many organisms. Under oxidizing conditions, ferric iron is highly insoluble (∼10-9 to 10-18 M), yet bacteria typically require ∼10-6 M for survival. To overcome this disparity, many bacteria have adopted the use of extracellular iron-chelating siderophores coupled with specific iron-siderophore uptake systems. In the case of Bacillus subtilis, undomesticated strains produce the siderophore bacillibactin. However, many laboratory strains, e.g., JH642, have lost the ability to produce bacillibactin during the process of domestication. In this work, we identified a novel iron acquisition activity from strain JH642 that accumulates in the growth medium and coordinates the iron response with population density. The molecule(s) responsible for this activity was named elemental Fe(II/III) (Efe) acquisition factor because efeUOB (ywbLMN) is required for its activity. Unlike most iron uptake molecules, including siderophores and iron reductases, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur repressor. Restoring bacillibactin production in strain JH642 inhibits the activity of Efe acquisition factor, presumably by sequestering available iron. A similar iron acquisition activity is produced from a mutant of Escherichia coli unable to synthesize the siderophore enterobactin. Given the conservation of efeUOB and its regulation by catecholic siderophores in B. subtilis and E. coli, we speculate that Efe acquisition factor is utilized by many bacteria, serves as an alternative to Fur-mediated iron acquisition systems, and provides cells with biologically available iron that would normally be inaccessible during aerobic growth under iron-replete conditions. IMPORTANCE Iron is an essential micronutrient required for a variety of biological processes, yet ferric iron is highly insoluble during aerobic growth. In this work, we identified a novel iron acquisition activity that coordinates the iron response with population density in laboratory strains of Bacillus subtilis We named the molecule(s) responsible for this activity elemental Fe(II/III) (Efe) acquisition factor after the efeUOB (ywbLMN) operon required for its uptake into cells. Unlike most iron uptake systems, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur, the master regulator of the iron response. We speculate that Efe acquisition factor is highly conserved among bacteria and serves as a backup to Fur-mediated iron acquisition systems.
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Affiliation(s)
- Emily M Roy
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kevin L Griffith
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Fazary AE, Al-Shihri AS, Alfaifi MY, Saleh KA, Alshehri MA, Elbehairi SEI, Ju YH. Microbial production of four biodegradable siderophores under submerged fermentation. Int J Biol Macromol 2016; 88:527-41. [DOI: 10.1016/j.ijbiomac.2016.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 11/29/2022]
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Fazary AE, Ju YH, Al-Shihri AS, Alfaifi MY, Alshehri MA. Biodegradable siderophores: survey on their production, chelating and complexing properties. REV INORG CHEM 2016. [DOI: 10.1515/revic-2016-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.
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Raza W, Wu H, Shah MAA, Shen Q. Retracted: A catechol type siderophore, bacillibactin: biosynthesis, regulation and transport in Bacillus subtilis. J Basic Microbiol 2008; 48. [PMID: 18785660 DOI: 10.1002/jobm.200800097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Retraction: The following article from the Journal of Basic Microbiology, "A catechol type siderophore, bacillibactin: biosynthesis, regulation and transport in Bacillus subtilis" by Waseem Raza, Hongsheng Wu, Muhammad Ali Abdullah Shah and Qirong Shen, published online on 11 September 2008 in Wiley InterScience (www.interscience.wiley.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Erika Kothe, and the publisher Wiley-VCH. The retraction has been agreed due to substantial overlap of the content of this article with previously published articles in other journals.The Journal of Basic Microbiology apologises to our readership.
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Affiliation(s)
- Waseem Raza
- College of Resource and Environmental Sciences, Nanjing Agriculture University, Nanjing, China
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Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol 2006; 188:3664-73. [PMID: 16672620 PMCID: PMC1482855 DOI: 10.1128/jb.188.10.3664-3673.2006] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ferric uptake regulator (Fur) protein mediates the iron-dependent repression of at least 20 operons encoding approximately 40 genes. We investigated the physiological roles of Fur-regulated genes by the construction of null mutations in 14 transcription units known or predicted to function in siderophore biosynthesis or iron uptake. We demonstrate that ywbLMN, encoding an elemental iron uptake system orthologous to the copper oxidase-dependent Fe(III) uptake system of Saccharomyces cerevisiae, is essential for growth in low iron minimal medium lacking citric acid. 2,3-Dihydroxybenzoyl-glycine (Itoic acid), the siderophore precursor produced by laboratory strains of B. subtilis, is of secondary importance. In the presence of citrate, the YfmCDEF ABC transporter is required for optimal growth. B. subtilis is unable to grow in minimal medium containing the iron chelator EDDHA unless the ability to synthesize the intact bacillibactin siderophore is restored (by the introduction of a functional sfp gene) or exogenous siderophores are provided. Utilization of the catecholate siderophores bacillibactin and enterobactin requires the FeuABC importer and the YusV ATPase. Utilization of hydroxamate siderophores requires the FhuBGC ABC transporter together with the FhuD (ferrichrome) or YxeB (ferrioxamine) substrate-binding proteins. Growth with schizokinen or arthrobactin is at least partially dependent on the YfhA YfiYZ importer and the YusV ATPase. We have also investigated the effects of a fur mutation on the proteome and documented the derepression of 11 Fur-regulated proteins, including a newly identified thioredoxin reductase homolog, YcgT.
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Affiliation(s)
- Juliane Ollinger
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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May JJ, Wendrich TM, Marahiel MA. The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin. J Biol Chem 2001; 276:7209-17. [PMID: 11112781 DOI: 10.1074/jbc.m009140200] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus subtilis was reported to produce the catecholic siderophore itoic acid (2,3-dihydroxybenzoate (DHB)-glycine) in response to iron deprivation. However, by inspecting the DNA sequences of the genes dhbE, dhbB, and dhbF as annotated by the B. subtilis genome project to encode the synthetase complex for the siderophore assembly, various sequence errors within the dhbF gene were predicted and confirmed by re-sequencing. According to the corrected sequence, dhbF encodes a dimodular instead of a monomodular nonribosomal peptide synthetase. We have heterologously expressed, purified, and assayed the substrate selectivity of the recombinant proteins DhbB, DhbE, and DhbF. DhbE, a stand-alone adenylation domain of 59.9 kDa, activates, in an ATP-dependent reaction, DHB, which is subsequently transferred to the free thiol group of the cofactor phosphopantetheine of the bifunctional isochorismate lyase/aryl carrier protein DhbB. The third synthetase, DhbF, is a dimodular nonribosomal peptide synthetase of 264 kDa that specifically adenylates threonine and, to a lesser extent, glycine and that covalently loads both amino acids onto their corresponding peptidyl carrier domains. To functionally link the dhb gene cluster to siderophore synthesis, we have disrupted the dhbF gene. Comparative mass spectrometric analysis of culture extracts from both the wild type and the dhbF mutant led to the identification of a mass peak at m/z 881 ([M-H](1-)) that corresponds to a cyclic trimeric ester of DHB-glycine-threonine.
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Affiliation(s)
- J J May
- Department of Chemistry, Philipps-Universität Marburg, D-35032 Marburg, Germany
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