A Gene Suspected to be Silicon Transporter was Found in Synechococcus sp. XM24
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摘要: 硅是硅藻所必需的营养物质.硅藻可以通过硅酸转运子（Silicon Transporter，SIT）蛋白吸收环境中的溶解硅，在全球海洋的硅循环中起着重要作用.海洋单细胞聚球藻（Synechococcus）也被发现可以进行硅的累积作用.由于聚球藻进化出现的时间远远早于硅藻，推测也可以像硅藻一样通过SIT这样的转运蛋白来吸收海洋中的溶解硅.本研究在有硅和无硅两种条件下探究聚球藻中SIT存在的可能性，最终找到2条疑似为SIT基因序列，并成功预测得到其蛋白质序列及功能，结果显示均与膜转运过程有关.最终利用AutoDock4软件成功预测到蛋白质的活性位点.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.
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Key words:
- SIT gene /
- Synechococcus /
- macrotranscriptome /
- protein prediction /
- molecular docking simulation /
- marine biology
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图 1 有硅和无硅条件下，细胞中硅累积量的变化
a.表示总生物硅的浓度；b.表示新生生物硅的浓度.*.P < 0.01，代表具有显著差异
Fig. 1. Under Depleted-Repleted conditions, the amount of silicon accumulated in the cell changes
图 2 A07_TRINITY_DN753_c0_g1蛋白质与硅酸分子对接结果
白色为氢原子，红色为氧原子，蓝色为氮原子，黄色为碳原子，棕色为硅原子.SER代表丝氨酸残基，数字代表氨基酸残基在蛋白质中的位置
Fig. 2. The docking result of A07_TRINITY_DN753_c0_g1 protein and orthosilicic acid
图 3 e_TRINITY_DN668_c0_g1蛋白质与硅酸分子对接结果
白色为氢原子，红色为氧原子，蓝色为氮原子，橘黄色为碳原子，棕色为硅原子.LEU、ARG、ASP、GLY、PRO、CYS、PHE、SER分别代表亮氨酸残基、天冬氨酸残基、甘氨酸残基、脯氨酸残基、半胱氨酸残基、苯丙氨酸残基、丝氨酸残基，数字代表氨基酸残基在蛋白质中的位置
Fig. 3. The docking result of e_TRINITY_DN668_c0_g1 protein and orthosilicic acid
表 1 A07_TRINITY_DN753_c0_g1蛋白质功能预测结果
Table 1. A07_TRINITY_DN753_c0_g1 protein function prediction results
Category GO-Term GO-Name Confidence Biological process GO: 0051179 Localization 0.66 Biological process GO: 0051234 Establishment of localization 0.65 Biological process GO: 0006810 Transport 0.65 Cellular component GO: 0031224 Intrinsic component of membrane 0.84 Cellular component GO: 0016021 Integral component of membrane 0.84 Cellular component GO: 0098796 Membrane protein complex 0.71 
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表 2 e_TRINITY_DN668_c0_g1蛋白质功能预测结果
Table 2. e_TRINITY_DN668_c0_g1 protein function prediction results
Category GO-Term GO-Name Confidence Biological process GO: 0051179 Localization 0.55 Biological process GO: 0051234 Establishment of localization 0.54 Biological process GO: 0006810 Transport 0.53 Cellular component GO: 0031224 Intrinsic component of membrane 0.72 Cellular component GO: 0016021 Integral component of membrane 0.72
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