Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry
<i>Emiliania huxleyi</i> is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of <i>Emiliania huxleyi</i> have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) sy...
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MDPI AG
2020-07-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/13/3028 |
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| author | Goyeun Yun Jong-Moon Park Van-An Duong Jeong-Hun Mok Jongho Jeon Onyou Nam Joonwon Lee EonSeon Jin Hookeun Lee |
| author_facet | Goyeun Yun Jong-Moon Park Van-An Duong Jeong-Hun Mok Jongho Jeon Onyou Nam Joonwon Lee EonSeon Jin Hookeun Lee |
| author_sort | Goyeun Yun |
| collection | DOAJ |
| description | <i>Emiliania huxleyi</i> is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of <i>Emiliania huxleyi</i> have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of <i>Emiliania huxleyi</i>. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with <i>p</i>-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO<sub>2</sub> fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on <i>Emiliania huxleyi</i> to reveal changes in its protein level and related mechanism. |
| first_indexed | 2024-03-10T18:43:22Z |
| format | Article |
| id | doaj.art-34463b37865a4c41be1b7c3efc8cceb9 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T18:43:22Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-34463b37865a4c41be1b7c3efc8cceb92023-11-20T05:41:01ZengMDPI AGMolecules1420-30492020-07-012513302810.3390/molecules25133028Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass SpectrometryGoyeun Yun0Jong-Moon Park1Van-An Duong2Jeong-Hun Mok3Jongho Jeon4Onyou Nam5Joonwon Lee6EonSeon Jin7Hookeun Lee8College of Pharmacy, Gachon University, Incheon 21936, KoreaCollege of Pharmacy, Gachon University, Incheon 21936, KoreaCollege of Pharmacy, Gachon University, Incheon 21936, KoreaCollege of Pharmacy, Gachon University, Incheon 21936, KoreaCollege of Pharmacy, Gachon University, Incheon 21936, KoreaDepartment of Life Science, Hanyang University, Seoul 04763, KoreaCollege of Letters and Science, University of California Los Angeles, Los Angeles, CA 90095, USADepartment of Life Science, Hanyang University, Seoul 04763, KoreaCollege of Pharmacy, Gachon University, Incheon 21936, Korea<i>Emiliania huxleyi</i> is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of <i>Emiliania huxleyi</i> have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of <i>Emiliania huxleyi</i>. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with <i>p</i>-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO<sub>2</sub> fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on <i>Emiliania huxleyi</i> to reveal changes in its protein level and related mechanism.https://www.mdpi.com/1420-3049/25/13/3028<i>Emiliania huxleyi</i>three-dimensional (3D-LC) separationproteomic profilinggene ontologyphotosynthesis |
| spellingShingle | Goyeun Yun Jong-Moon Park Van-An Duong Jeong-Hun Mok Jongho Jeon Onyou Nam Joonwon Lee EonSeon Jin Hookeun Lee Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry Molecules <i>Emiliania huxleyi</i> three-dimensional (3D-LC) separation proteomic profiling gene ontology photosynthesis |
| title | Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry |
| title_full | Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry |
| title_fullStr | Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry |
| title_full_unstemmed | Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry |
| title_short | Proteomic Profiling of <i>Emiliania huxleyi</i> Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry |
| title_sort | proteomic profiling of i emiliania huxleyi i using a three dimensional separation method combined with tandem mass spectrometry |
| topic | <i>Emiliania huxleyi</i> three-dimensional (3D-LC) separation proteomic profiling gene ontology photosynthesis |
| url | https://www.mdpi.com/1420-3049/25/13/3028 |
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