1
|
Armstrong DW, Berthod A. Occurrence of D-amino acids in natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:47. [PMID: 37932633 PMCID: PMC10628113 DOI: 10.1007/s13659-023-00412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023]
Abstract
Since the identified standard genetic code contains 61 triplet codons of three bases for the 20 L-proteinogenic amino acids (AAs), no D-AA should be found in natural products. This is not what is observed in the living world. D-AAs are found in numerous natural compounds produced by bacteria, algae, fungi, or marine animals, and even vertebrates. A review of the literature indicated the existence of at least 132 peptide natural compounds in which D-AAs are an essential part of their structure. All compounds are listed, numbered and described herein. The two biosynthetic routes leading to the presence of D-AA in natural products are: non-ribosomal peptide synthesis (NRPS), and ribosomally synthesized and post-translationally modified peptide (RiPP) synthesis which are described. The methods used to identify the AA chirality within naturally occurring peptides are briefly discussed. The biological activity of an all-L synthetic peptide is most often completely different from that of the D-containing natural compounds. Analyzing the selected natural compounds showed that D-Ala, D-Val, D-Leu and D-Ser are the most commonly encountered D-AAs closely followed by the non-proteinogenic D-allo-Thr. D-Lys and D-Met were the least prevalent D-AAs in naturally occurring compounds.
Collapse
Affiliation(s)
- Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019, USA.
| | - Alain Berthod
- Institut des Sciences Analytiques, CNRS, University of Lyon 1, 69100, Villeurbanne, France
| |
Collapse
|
2
|
Duan Y, Zhao L, Jiang W, Chen R, Zhang R, Chen X, Yin C, Mao Z. The Phlorizin-Degrading Bacillus licheniformis XNRB-3 Mediates Soil Microorganisms to Alleviate Apple Replant Disease. Front Microbiol 2022; 13:839484. [PMID: 35308362 PMCID: PMC8927668 DOI: 10.3389/fmicb.2022.839484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Chengmiao Yin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Zhiquan Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| |
Collapse
|
3
|
Wan C, Fan X, Lou Z, Wang H, Olatunde A, Rengasamy KRR. Iturin: cyclic lipopeptide with multifunction biological potential. Crit Rev Food Sci Nutr 2022; 62:7976-7988. [PMID: 33983074 DOI: 10.1080/10408398.2021.1922355] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Iturin, a metabolite produced by Bacillus subtilis, has a broad-spectrum antibacterial effect, and because they are secreted in the rhizosphere of plants, iturins are often mixed with many organic molecules. In recent years, people have improved their separation and purification methods but still cannot achieve simple and effective procedures, making Iturins an ideal biological control agent for insects and bacteria; commercial value still cannot be realized. With the in-depth studies of Iturins, its anti-cancer, hemolysis and other biological activities have gradually been discovered. This article reviews the branches of the Iturin family, structural features of these metabolite, separation and purification methods used for producing it, culture optimization, and various biological activities of the Iturin family, such as insecticidal, antibacterial, hemolytic and anticarcinogenic properties, among others have been summarized. Furthermore, this review revealed some commercial applications of Iturins and their relevance in research works. For example, in food packaging, clean water has good development potential.This can promote the commercial application of Iturins instead of other chemical and biological control agents that are environmentally friendly, pollution-free and have no side effects on humans. Furthermore, work documented anticancer, hemolytic and other biological activities of Iturin.
Collapse
Affiliation(s)
- Chunpeng Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaoyuan Fan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zaixiang Lou
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxin Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ahmed Olatunde
- Department of Biochemistry, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Kannan R R Rengasamy
- Green Biotechnologies Research Centre of Excellence, University of Limpopo, Mankweng, South Africa
| |
Collapse
|
4
|
Zhou L, Song C, Muñoz CY, Kuipers OP. Bacillus cabrialesii BH5 Protects Tomato Plants Against Botrytis cinerea by Production of Specific Antifungal Compounds. Front Microbiol 2021; 12:707609. [PMID: 34539606 PMCID: PMC8441496 DOI: 10.3389/fmicb.2021.707609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/22/2022] Open
Abstract
The gray mold caused by the phytopathogen Botrytis cinerea presents a threat to global food security. For the biological regulation of several plant diseases, Bacillus species have been extensively studied. In this work, we explore the ability of a bacterial strain, Bacillus cabrialesii BH5, that was isolated from tomato rhizosphere soil, to control the fungal pathogen B. cinerea. Strain B. cabrialesii BH5 showed a strong antifungal activity against B. cinerea. A compound was isolated and identified as a cyclic lipopeptide of the fengycin family by high-performance liquid chromatography and tandem mass spectrometry (ESI-MS/MS) that we named fengycin H. The fengycin H-treated hyphae of B. cinerea displayed stronger red fluorescence than the control, which is clearly indicating that fengycin H triggered the hyphal cell membrane defects. Moreover, root inoculation of tomato seedlings with BH5 effectively promoted the growth of tomato plants. Transcription analysis revealed that both BH5 and fengycin H stimulate induced systemic resistance of tomato plants via the jasmonic acid signaling pathway and provide a strong biocontrol effect in vivo. Therefore, the strain BH5 and fengycin H are very promising candidates for biological control of B. cinerea and the associated gray mold.
Collapse
Affiliation(s)
- Lu Zhou
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Chunxu Song
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Claudia Y Muñoz
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| |
Collapse
|
5
|
Kaspar F, Neubauer P, Gimpel M. Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review. JOURNAL OF NATURAL PRODUCTS 2019; 82:2038-2053. [PMID: 31287310 DOI: 10.1021/acs.jnatprod.9b00110] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.
Collapse
Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Peter Neubauer
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| | - Matthias Gimpel
- Institute of Biotechnology , Technical University of Berlin , Ackerstraße 76 , 13355 Berlin , Germany
| |
Collapse
|
6
|
Wu JY, Liao JH, Shieh CJ, Hsieh FC, Liu YC. Kinetic analysis on precursors for iturin A production from Bacillus amyloliquefaciens BPD1. J Biosci Bioeng 2018; 126:630-635. [PMID: 29907529 DOI: 10.1016/j.jbiosc.2018.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 11/25/2022]
Abstract
In this study, the precursor effect for iturin A production was quantitatively analyzed. A strain identified as Bacillus amyloliquefaciens BPD1 (Ba-BPD1) was selected due to its ability to produce iturin A. The enhancement of iturin A production in a submerged culture was tested using various additives, including palmitic acid, oils, and complex amino acids. Among these, complex amino acids triggered the highest yield at 559 mg/L. The respective amino acids that contribute to the structure of iturin A were used as precursors. In fact, it was found that the addition of l-proline, l-glutamine, l-asparagine and l-serine could improve iturin A yield in the defined medium. However, during the kinetic analysis, all the amino acids exhibited a lower saturation level than l-serine, which exhibited a high saturation level at 1.2% resulting in an iturin A yield of 914 mg/L. In contrast, a negative effect was observed following the addition of l-tyrosine. To analyze the kinetic behavior of l-serine, three kinetic models were adopted: the kinetic order equation, the Langmuir kinetic equation, and a modified logistic equation. The regression results showed that the modified logistic model was the best fit for the kinetic behavior of l-serine as the major precursor, which could be further referred to the biosynthesis pathway of iturin A. Among the proposed processes for iturin A production, this study achieved the highest iturin A levels as a result of the addition of precursors.
Collapse
Affiliation(s)
- Jiun-Yan Wu
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Rd., South Dist, Taichung 40227, Taiwan
| | - Jen-Hung Liao
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Rd., South Dist, Taichung 40227, Taiwan; Biopesticides Division, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung 41358, Taiwan
| | - Chwen-Jen Shieh
- Biotechnology Center, National Chung Hsing University, 145 Xingda Rd., South Dist, Taichung 40227, Taiwan
| | - Feng-Chia Hsieh
- Biopesticides Division, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung 41358, Taiwan
| | - Yung-Chuan Liu
- Department of Chemical Engineering, National Chung Hsing University, 145 Xingda Rd., South Dist, Taichung 40227, Taiwan.
| |
Collapse
|
7
|
Qian S, Sun J, Lu H, Lu F, Bie X, Lu Z. L-glutamine efficiently stimulates biosynthesis of bacillomycin D in Bacillus subtilis fmbJ. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
8
|
Identification of 4″-isovaleryl-spiramycin III produced by Bacillus sp. fmbJ. Arch Microbiol 2013; 196:87-95. [PMID: 24356910 DOI: 10.1007/s00203-013-0939-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/11/2013] [Accepted: 11/01/2013] [Indexed: 10/25/2022]
Abstract
The production of secondary metabolites with antibiotic properties is a common characteristic to Bacillus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities with medicinal and agricultural interests such as antibiotic. Bacillus sp. fmbJ has been found to produce lipopeptides fengycin and surfactin in accordance with our previous report. In this study, another antimicrobial substance was separated and purified from the culture supernatant of strain fmbJ using the silica gel column chromatography and preparative reversed-phase high-performance liquid chromatography. By means of electrospray ionization mass spectroscopy, infrared spectroscopy, and nuclear magnetic resonance, the antagonistic compound was determined to be 4″-isovaleryl-spiramycin III with the molecular weight of 982 Da. This report is the first to introduce the finding of spiramycin produced from Bacillus sp. The study provides a novel source for the production of spiramycin in pharmaceutical industries.
Collapse
|
9
|
Analysis of free amino acids during fermentation by Bacillus subtilis using capillary electrophoresis. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0292-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
10
|
Besson F, Tenoux I, Hourdou ML, Michel G. Synthesis of beta-hydroxy fatty acids and beta-amino fatty acids by the strains of Bacillus subtilis producing iturinic antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1123:51-8. [PMID: 1730046 DOI: 10.1016/0005-2760(92)90170-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The iturinic antibiotics, which contain long chain beta-amino acids, are produced by Bacillus subtilis. Screening these strains for the presence of a possible precursor of the iturinic antibiotics, we isolated a lipopeptide containing beta-hydroxy fatty acids. The structure of this compound was studied and it appears to be identical or structurally very similar to surfactin. The carbon chain of its beta-hydroxy fatty acids was n C16, iso C16, iso C15 or anteiso C15. The percentages of each beta-hydroxy fatty acids varied according to the strain producing iturinic antibiotics and were influenced by addition of branched-chain alpha-amino acids to the culture medium. These results demonstrate for the first time that iso C14 beta-hydroxy fatty acid is a constituent present in such a surfactin like lipopeptide. Besides, the presence of radioactive beta-hydroxy fatty acids in the phospholipids when the strains were grown in the presence of sodium [14C]acetate seems also characterize the different strains producing iturinic antibiotics.
Collapse
Affiliation(s)
- F Besson
- Laboratoire de Biochimie Microbienne (C.N.R.S. UMR 24), Université Claude-Bernard, Lyon, France
| | | | | | | |
Collapse
|