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Feng X, Yan W, Wang A, Ma R, Chen X, Lin TH, Chen YL, Wei S, Jin T, Jiao N, Zhang R. A Novel Broad Host Range Phage Infecting Alteromonas. Viruses 2021; 13:v13060987. [PMID: 34073246 PMCID: PMC8228385 DOI: 10.3390/v13060987] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.
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Affiliation(s)
- Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Wei Yan
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China
| | - Anan Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Tao Jin
- Guangzhou Magigene Biotechnology Co., Ltd., Guangzhou 510000, China;
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Correspondence: (N.J.); (R.Z.)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
- Correspondence: (N.J.); (R.Z.)
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Abstract
High-quality crystals are essential to ensure high-resolution structural information. Protein crystals are controlled by many factors, such as pH, temperature, and the ion concentration of crystalline solutions. We previously reported the development of a device dedicated to protein crystallization. In the current study, we have further modified and improved our device. Exposure to external magnetic field leads to alignment of the crystal toward a preferred direction depending on the magnetization energy. Each material has different magnetic susceptibilities depending on the individual direction of their unit crystal cells. One of the strategies to acquire a large crystal entails controlling the nucleation rate. Furthermore, exposure of a crystal to a magnetic field may lead to new morphologies by affecting the crystal volume, shape, and quality.
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Park SH, Park J, Lee SJ, Yang WS, Park S, Kim K, Park ZY, Song HK. A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser. Sci Rep 2019; 9:16316. [PMID: 31705139 PMCID: PMC6841964 DOI: 10.1038/s41598-019-52825-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 10/22/2019] [Indexed: 01/21/2023] Open
Abstract
The hydroxymethylation of cytosine bases plays a vital role in the phage DNA protection system inside the host Escherichia coli. This modification is known to be catalyzed by the dCMP hydroxymethylase from bacteriophage T4 (T4dCH); structural information on the complexes with the substrate, dCMP and the co-factor, tetrahydrofolate is currently available. However, the detailed mechanism has not been understood clearly owing to a lack of structure in the complex with a reaction intermediate. We have applied the X-ray free electron laser (XFEL) technique to determine a high-resolution structure of a T4dCH D179N active site mutant. The XFEL structure was determined at room temperature and exhibited several unique features in comparison with previously determined structures. Unexpectedly, we observed a bulky electron density at the active site of the mutant that originated from the physiological host (i.e., E. coli). Mass-spectrometric analysis and a cautious interpretation of an electron density map indicated that it was a dTMP molecule. The bound dTMP mimicked the methylene intermediate from dCMP to 5′-hydroxymethy-dCMP, and a critical water molecule for the final hydroxylation was convincingly identified. Therefore, this study provides information that contributes to the understanding of hydroxymethylation.
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Affiliation(s)
- Si Hoon Park
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Jaehyun Park
- PAL-XFEL, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, South Korea
| | - Sang Jae Lee
- PAL-XFEL, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, South Korea
| | - Woo Seok Yang
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Sehan Park
- PAL-XFEL, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, South Korea
| | - Kyungdo Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea.
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