Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis
Deep-sea sediment-derived bacterium may make full use of self-genes to produce more bioactive metabolites to adapt to extreme environment, resulting in the discovery of novel metabolites with unique structures and metabolic mechanisms. In the paper, we systematically investigated the metabolites in...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Marine Drugs |
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| Online Access: | https://www.mdpi.com/1660-3397/20/7/431 |
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| author | Wenping Ding Yanqun Li Xinpeng Tian Min Chen Zhihui Xiao Rouwen Chen Hao Yin Si Zhang |
| author_facet | Wenping Ding Yanqun Li Xinpeng Tian Min Chen Zhihui Xiao Rouwen Chen Hao Yin Si Zhang |
| author_sort | Wenping Ding |
| collection | DOAJ |
| description | Deep-sea sediment-derived bacterium may make full use of self-genes to produce more bioactive metabolites to adapt to extreme environment, resulting in the discovery of novel metabolites with unique structures and metabolic mechanisms. In the paper, we systematically investigated the metabolites in structurally diversity and their biosynthesis from the deep-sea sediment-derived bacterium <i>Agrococcus</i> sp. SCSIO 52902 based on OSMAC strategy, Molecular Networking tool, in combination with bioinformatic analysis. As a result, three new compounds and one new natural product, including 3<i>R</i>-OH-1,6-diene-cyclohexylacetic acid (<b>1</b>), linear tetradepsipeptide (<b>2</b>), <i>N</i><sup>1</sup>,<i>N</i><sup>5</sup>-di-<i>p</i>-(<i>EE</i>)-coumaroyl-<i>N</i><sup>10</sup>-acetylspermidine (<b>3</b>) and furan fatty acid (<b>4</b>), together with nineteen known compounds (<b>5</b>–<b>23</b>) were isolated from the ethyl acetate extract of SCSIO 52902. Their structures were elucidated by comprehensive spectroscopic analysis, single-crystal X-ray diffraction, Marfey’s method and chiral-phase HPLC analysis. Bioinformatic analysis revealed that compounds <b>1</b>, <b>3</b>, <b>9</b> and <b>13</b>–<b>22</b> were closely related to the shikimate pathway, and compound <b>5</b> was putatively produced by the OSB pathway instead of the PKS pathway. In addition, the result of cytotoxicity assay showed that compound <b>5</b> exhibited weak cytotoxic activity against the HL-60 cell line. |
| first_indexed | 2024-03-09T13:29:02Z |
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| id | doaj.art-379970dae13f4655a1947589d6ca1bc9 |
| institution | Directory Open Access Journal |
| issn | 1660-3397 |
| language | English |
| last_indexed | 2024-03-09T13:29:02Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Marine Drugs |
| spelling | doaj.art-379970dae13f4655a1947589d6ca1bc92023-11-30T21:20:10ZengMDPI AGMarine Drugs1660-33972022-06-0120743110.3390/md20070431Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their BiosynthesisWenping Ding0Yanqun Li1Xinpeng Tian2Min Chen3Zhihui Xiao4Rouwen Chen5Hao Yin6Si Zhang7CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaDeep-sea sediment-derived bacterium may make full use of self-genes to produce more bioactive metabolites to adapt to extreme environment, resulting in the discovery of novel metabolites with unique structures and metabolic mechanisms. In the paper, we systematically investigated the metabolites in structurally diversity and their biosynthesis from the deep-sea sediment-derived bacterium <i>Agrococcus</i> sp. SCSIO 52902 based on OSMAC strategy, Molecular Networking tool, in combination with bioinformatic analysis. As a result, three new compounds and one new natural product, including 3<i>R</i>-OH-1,6-diene-cyclohexylacetic acid (<b>1</b>), linear tetradepsipeptide (<b>2</b>), <i>N</i><sup>1</sup>,<i>N</i><sup>5</sup>-di-<i>p</i>-(<i>EE</i>)-coumaroyl-<i>N</i><sup>10</sup>-acetylspermidine (<b>3</b>) and furan fatty acid (<b>4</b>), together with nineteen known compounds (<b>5</b>–<b>23</b>) were isolated from the ethyl acetate extract of SCSIO 52902. Their structures were elucidated by comprehensive spectroscopic analysis, single-crystal X-ray diffraction, Marfey’s method and chiral-phase HPLC analysis. Bioinformatic analysis revealed that compounds <b>1</b>, <b>3</b>, <b>9</b> and <b>13</b>–<b>22</b> were closely related to the shikimate pathway, and compound <b>5</b> was putatively produced by the OSB pathway instead of the PKS pathway. In addition, the result of cytotoxicity assay showed that compound <b>5</b> exhibited weak cytotoxic activity against the HL-60 cell line.https://www.mdpi.com/1660-3397/20/7/431<i>Agrococcus</i> sp. SCSIO 52902metabolitesstructural elucidationbiosynthetic pathway |
| spellingShingle | Wenping Ding Yanqun Li Xinpeng Tian Min Chen Zhihui Xiao Rouwen Chen Hao Yin Si Zhang Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis Marine Drugs <i>Agrococcus</i> sp. SCSIO 52902 metabolites structural elucidation biosynthetic pathway |
| title | Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis |
| title_full | Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis |
| title_fullStr | Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis |
| title_full_unstemmed | Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis |
| title_short | Investigation on Metabolites in Structural Diversity from the Deep-Sea Sediment-Derived Bacterium <i>Agrococcus</i> sp. SCSIO 52902 and Their Biosynthesis |
| title_sort | investigation on metabolites in structural diversity from the deep sea sediment derived bacterium i agrococcus i sp scsio 52902 and their biosynthesis |
| topic | <i>Agrococcus</i> sp. SCSIO 52902 metabolites structural elucidation biosynthetic pathway |
| url | https://www.mdpi.com/1660-3397/20/7/431 |
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