聚球藻XM24中发现疑似为硅酸转运子的基因

韩雅波; 孙军

doi:10.3799/dqkx.2024.146

Volume 50 Issue 6

Jun. 2025

Turn off MathJax

Article Contents

Article Navigation > Earth Science > 2025 > 50(6): 2444-2451

Han Yabo, Sun Jun, 2025. A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24. Earth Science, 50(6): 2444-2451. doi: 10.3799/dqkx.2024.146

Citation:

Han Yabo, Sun Jun, 2025. A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24. Earth Science, 50(6): 2444-2451. doi: 10.3799/dqkx.2024.146

Han Yabo, Sun Jun, 2025. A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24. Earth Science, 50(6): 2444-2451. doi: 10.3799/dqkx.2024.146

Citation:

Han Yabo, Sun Jun, 2025. A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24. Earth Science, 50(6): 2444-2451. doi: 10.3799/dqkx.2024.146

PDF( 1593 KB)

A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24

doi: 10.3799/dqkx.2024.146

Han Yabo^{1
,
,},
Sun Jun^{1, 2
,
,
,}

1.
Research Centre for Indian Ocean Ecosystem, Tianjin University of Science & Technology, Tianjin 300457, China
2.
State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430078, China

Received Date: 2024-10-07
Available Online: 2025-07-11
Publish Date: 2025-06-25

Abstract

Abstract

Silicate serves as a crucial nutrient for diatoms, which are capable of absorbing dissolved silicon from their surroundings through Silicon Transporter (SIT), thus playing a significant role in the global ocean's silicon cycle. Recent studies have indicated that marine single-celled Synechococcus also has the ability to accumulate silicon. Given that the evolution of Synechococcus predates that of diatoms, it is postulated that Synechococcus may utilize transporters such as SIT found in diatoms, to absorb dissolved silicon in the ocean. This research delves into the silicon accumulation in Synechococcus sp. XM24, particularly focusing on two key aspects. Firstly, the study investigates the potential presence of SIT in Synechococcus sp. XM24 under the condition of Depleted-Repleted silicate. Subsequently, two gene sequences suspected to encode SIT, were identified, and their protein sequences and functions were successfully predicted, shedding light on their involvement in membrane transport processes. Finally, AutoDock4 software was used to predict the active site of the protein.
- SIT gene,
- Synechococcus,
- macrotranscriptome,
- protein prediction,
- molecular docking simulation,
- marine biology

FullText(HTML)

References(48)

References

Alverson, A. J., 2007. Strong Purifying Selection in the Silicon Transporters of Marine and Freshwater Diatoms. Limnology and Oceanography, 52(4): 1420-1429. https://doi.org/10.4319/lo.2007.52.4.1420

Amo, Y. D., Brzezinski, M. A., 1999. The Chemical Form of Dissolved Si Taken up by Marine Diatoms. Journal of Phycology, 35(6): 1162-1170. https://doi.org/10.1046/j.1529⁃8817.1999.3561162.x

Armbrust, E. V., Berges, J. A., Bowler, C., et al., 2004. The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science, 306(5693): 79-86. https://doi.org/10.1126/science.1101156

Azam, F., Hemmingsen, B. B., Volcani, B. E., 1974. Role of Silicon in Diatom Metabolism: V. Silicic Acid Transport and Metabolism in the Heterotrophic Diatom Nitzschia Alba. Archives of Microbiology, 97(1): 103-114. https://doi.org/10.1007/bf00403050

Bai, Y. L., Wang, J. L., Sun, H. T., et al., 2019. Determination of Silicon in Beryllium⁃Aluminium Alloy with High Content of Beryllium by Silicon Molybdenum Blue Spectrophotometry. Metallurgical Analysis, 39(9): 81-85 (in Chinese with English abstract).

Baines, S. B., Twining, B. S., Brzezinski, M. A., et al., 2012. Significant Silicon Accumulation by Marine Picocyanobacteria. Nature Geoscience, 5(12): 886-891. https://doi.org/10.1038/ngeo1641

Bäuerlein, E., 2000. Silicic Acid Transport and Its Control during Cell Wall Silicification in Diatoms. In: Hildebrand, M., ed., Biomineralization: From Biology to Biotechnology and Medical Application. Wiley‐VCH Verlag GmbH & Co. KGaA, New Jersey, 159-173.

Bhattacharyya, P., Volcani, B. E., 1980. Sodium⁃Dependent Silicate Transport in the Apochlorotic Marine Diatom Nitzschia Alba. Proceedings of the National Academy of Sciences of the United States of America, 77(11): 6386-6390. https://doi.org/10.1073/pnas.77.11.6386

Binder, B. J., Chisholm, S. W., Olson, R. J., et al., 1996. Dynamics of Picophytoplankton, Ultraphytoplankton and Bacteria in the Central Equatorial Pacific. Deep Sea Research Part Ⅱ: Topical Studies in Oceanography, 43(4-6): 907-931. https://doi.org/10.1016/0967-0645(96)00023⁃9

Brasier, M. D., Green, O. R., Jephcoat, A. P., et al., 2002. Questioning the Evidence for Earth's Oldest Fossils. Nature, 416(6876): 76-81. https://doi.org/10.1038/416076a

Brzezinski, M. A., Krause, J. W., Baines, S. B., et al., 2017. Patterns and Regulation of Silicon Accumulation in Synechococcus Spp. Journal of Phycology, 53(4): 746-761. https://doi.org/10.1111/jpy.12545

Buick, R., 1992. The Antiquity of Oxygenic Photosynthesis: Evidence from Stromatolites in Sulphate⁃Deficient Archaean Lakes. Science, 255(5040): 74-77. https://doi.org/10.1126/science.11536492

Chen, C. J., Wu, Y., Li, J. W., et al., 2023. TBtools⁃Ⅱ: A "One for All, All for One" Bioinformatics Platform for Biological Big⁃Data Mining. Molecular Plant, 16(11): 1733-1742. https://doi.org/10.1016/j.molp.2023.09.010

Conley, D. J., Frings, P. J., Fontorbe, G., et al., 2017. Biosilicification Drives a Decline of Dissolved Si in the Oceans through Geologic Time. Frontiers in Marine Science, 4: 397. https://doi.org/10.3389/fmars.2017.00397

Curnow, P., Senior, L., Knight, M. J., et al., 2012. Expression, Purification, and Reconstitution of a Diatom Silicon Transporter. Biochemistry, 51(18): 3776-3785. https://doi.org/10.1021/bi3000484

Deng, W., Monks, L., Neuer, S., 2015. Effects of Clay Minerals on the Aggregation and Subsequent Settling of Marine Synechococcus. Limnology and Oceanography, 60(3): 805-816. https://doi.org/10.1002/lno.10059

Guidi, L., Chaffron, S., Bittner, L., et al., 2016. Plankton Networks Driving Carbon Export in the Oligotrophic Ocean. Nature, 532: 465-470. https://doi.org/10.1038/nature16942

Hildebrand, M., Dahlin, K., Volcani, B. E., 1998. Characterization of a Silicon Transporter Gene Family in Cylindrotheca Fusiformis: Sequences, Expression Analysis, and Identification of Homologs in Other Diatoms. Molecular and General Genetics MGG, 260(5): 480-486. https://doi.org/10.1007/s004380050920

Hildebrand, M., Volcani, B. E., Gassmann, W., et al., 1997. A Gene Family of Silicon Transporters. Nature, 385: 688-689. https://doi.org/10.1038/385688b0

Johnson, P. W., Sieburth, J. M., 1979. Chroococcoid Cyanobacteria in the Sea: A Ubiquitous and Diverse Phototrophic Biomass. Limnology and Oceanography, 24(5): 928-935. https://doi.org/10.4319/lo.1979.24.5.0928

Kang, L., Feng, C. C., Chang, J., et al., 2015. Diversity and Expression of Diatom Silicon Transporter Genes during a Flood Event in the East China Sea. Marine Biology, 162(7): 1511-1522. https://doi.org/10.1007/s00227⁃015⁃2687⁃8

Krause, J. W., Brzezinski, M. A., Baines, S. B., et al., 2017. Picoplankton Contribution to Biogenic Silica Stocks and Production Rates in the Sargasso Sea. Global Biogeochemical Cycles, 31(5): 762-774. https://doi.org/10.1002/2017gb005619

Krauskopf, K. B., 1956. Dissolution and Precipitation of Silica at Low Temperatures. Geochimica et Cosmochimica Acta, 10(1-2): 1-26. https://doi.org/10.1016/0016⁃7037(56)90009⁃6

Leblanc, K., Hutchins, D. A., 2005. New Applications of a Biogenic Silica Deposition Fluorophore in the Study of Oceanic Diatoms. Limnology and Oceanography: Methods, 3(10): 462-476. https://doi.org/10.4319/lom.2005.3.462

Lomas, M. W., Moran, S. B., 2011. Evidence for Aggregation and Export of Cyanobacteria and Nano⁃Eukaryotes from the Sargasso Sea Euphotic Zone. Biogeosciences, 8(1): 203-216. https://doi.org/10.5194/bg-8-203-201110.5194/bgd⁃7⁃7173⁃2010

Lupas, A., Van Dyke, M., Stock, J., 1991. Predicting Coiled Coils from Protein Sequences. Science, 252(5009): 1162-1164. https://doi.org/10.1126/science.252.5009.1162

Mann, D. G., 1999. The Species Concept in Diatoms. Phycologia, 38(6): 437-495. https://doi.org/10.2216/i0031⁃8884⁃38⁃6⁃437.1

Marchenkov, A. M., Bondar, A. A., Petrova, D. P., et al., 2016. Unique Configuration of Genes of Silicon Transporter in the Freshwater Pennate Diatom Synedra Acus Subsp. Radians. Doklady Biochemistry and Biophysics, 471(1): 407-409. https://doi.org/10.1134/S1607672916060089

Marchenkov, A. M., Petrova, D. P., Morozov, A. A., et al., 2018. A Family of Silicon Transporter Structural Genes in a Pennate Diatom Synedra Ulna Subsp. Danica (KÜTZ. ) Skabitsch. PLoS One, 13(8): e0203161. https://doi.org/10.1371/journal.pone.0203161

Milligan, A. J., Morel, F. M. M., 2002. A Proton Buffering Role for Silica in Diatoms. Science, 297(5588): 1848-1850. https://doi.org/10.1126/science.1074958

Morris, G. M., Huey, R., Lindstrom, W., et al., 2009. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. Journal of Computational Chemistry, 30(16): 2785-2791. https://doi.org/10.1002/jcc.21256

Ohnemus, D. C., Rauschenberg, S., Krause, J. W., et al., 2016. Silicon Content of Individual Cells of Synechococcus from the North Atlantic Ocean. Marine Chemistry, 187: 16-24. https://doi.org/10.1016/j.marchem.2016.10.003

Richardson, T. L., Jackson, G. A., 2007. Small Phytoplankton and Carbon Export from the Surface Ocean. Science, 315(5813): 838-840. https://doi.org/10.1126/science.1133471

Sapriel, G., Quinet, M., Heijde, M., et al., 2009. Genome⁃Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum Tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters. PLoS One, 4(10): e7458. https://doi.org/10.1371/journal.pone.0007458

Shen, W., Le, S., Li, Y., et al., 2016. SeqKit: A Cross⁃Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One, 11(10): e0163962. https://doi.org/10.1371/journal.pone.0163962

Struyf, E., Smis, A., Van Damme, S., et al., 2009. The Global Biogeochemical Silicon Cycle. Silicon, 1(4): 207-213. https://doi.org/10.1007/s12633⁃010⁃9035⁃x

Sun, J., Li, X. Q., Chen, J. F., et al., 2016. Progress in Oceanic Biological Pump. Haiyang Xuebao, 38(4): 1-21 (in Chinese with English abstract).

Sun, J., Wei, Y. Q., 2018. Preliminary Thoughts on Silicon Accumulation in Synechococcus. Acta Ecologica Sinica, 38(14): 5234-5243 (in Chinese with English abstract).

Tang, T. T., Kisslinger, K., Lee, C., 2014. Silicate Deposition during Decomposition of Cyanobacteria may Promote Export of Picophytoplankton to the Deep Ocean. Nature Communications, 5: 4143. https://doi.org/10.1038/ncomms5143

Thamatrakoln, K., Alverson, A. J., Hildebrand, M., 2006. Comparative Sequence Analysis of Diatom Silicon Transporters: Toward a Mechanistic Model of Silicon Transport. Journal of Phycology, 42(4): 822-834. https://doi.org/10.1111/j.1529⁃8817.2006.00233.x

Wang, G. X., Fang, X. M., Wu, Z. H., et al., 2022. HelixFold: An Efficient Implementation of AlphaFold2 Using PaddlePaddle. ArXiv. https://doi.org/10.48550/arXiv.2207.05477

Waterbury, J. B., Watson, S. W., Guillard, R. R. L., et al., 1979. Widespread Occurrence of a Unicellular, Marine, Planktonic, Cyanobacterium. Nature, 277: 293-294. https://doi.org/10.1038/277293a0

Wei, Y. Q., Sun, J., Li, L. Y., et al., 2022. Synechococcus Silicon Accumulation in Oligotrophic Oceans. Limnology and Oceanography, 67(3): 552-566. https://doi.org/10.1002/lno.12015

Werner, D., 1977. The Biology of Diatoms. In: Werner, D., ed., Silicate Metabolism, University of California Press, Berkeley, 498.

Zheng, Q., Wang, Y., Xie, R., et al., 2018. Dynamics of Heterotrophic Bacterial Assemblages within Synechococcus Cultures. Applied and Environmental Microbiology, 84(3): e01517-17. https://doi.org/10.1128/aem.01517⁃17

白英丽, 王佳丽, 孙洪涛, 等, 2019. 硅钼蓝分光光度法测定高铍铍铝合金中硅. 冶金分析, 39(9): 81-85.

孙军, 李晓倩, 陈建芳, 等, 2016. 海洋生物泵研究进展. 海洋学报, 38(4): 1-21.

孙军, 魏玉秋, 2018. 聚球藻硅质化作用初探. 生态学报, 38(14), 5234-5243.

Relative Articles

Supplements(0)

Cited By

Proportional views