摘要
为探讨嗜酸硫杆菌(Acidithiobacillus)抗砷基因多样性特征,利用生物信息学方法挖掘出嗜酸氧化亚铁硫杆菌(A.ferrooxidans)、喜温嗜酸硫杆菌(A.caldus)和耐冷嗜酸硫杆菌(A.ferrivorans)共49个抗砷基因,主要包括构成ars操纵子模式的arsA、arsB、arsC、arsD、arsH和arsR基因,为嗜酸硫杆菌重要的抗砷遗传因子。研究了49个抗砷基因的聚类与进化关系、理化性质、二级结构、跨膜区、亚细胞定位、砷结合位点等特征。结果表明:这些抗砷基因聚类为11个组,第2组抗砷基因(arsB)为嗜酸硫杆菌所共有,编码泵砷内膜蛋白(ArsB),该基因可能为嗜酸硫杆菌抗砷机制所必需;聚类和进化分析表明其中5个抗砷基因可能源于基因水平迁移;脂溶指数分析显示25个抗砷蛋白脂溶指数大于100,为亲水性蛋白,其余24个抗砷蛋白脂溶指数均小于100,为疏水性蛋白;从不稳定指数分析结果可知,大部分抗砷转录调控因子ArsR是不稳定的,49个抗砷基因蛋白二级结构均由α-螺旋、无规则卷曲和扩展链结构3种形式组成。亚细胞定位分析发现抗砷蛋白在细菌内膜、细菌外膜和细胞周质空间均有出现,ArsB具有10-11个跨膜区;所有抗砷蛋白均无信号肽。对嗜酸硫杆菌的ArsC、ArsD和ArsH抗砷功能蛋白与砷结合位点进行预测和建模,发现活性位点均存在Cys残基;与其他抗砷蛋白结合位点(含Cys残基)不同的是,Acife1530(ArsA)2个甲硫氨酸(Met)与As(III)直接结合,暗示着Met残基中存在与Cys残基功能相同的巯基,由此可见,Cys残基或Met残基的巯基对于构成嗜酸硫杆菌抗砷功能蛋白与砷结合的活性位点是必不可少的。
To explore the diversity of arsenic resistance genes in Acidithiobacillus genus, 49 arsenic resistance genes were mined by bioinformatics method from species of A. ferrooxidans, A. caldus, and A. ferrivorans. These 49 genes are ars-related includingarsA, arsB, arsC, arsD, arsH and arsR, which form the arsenic-resistance operon. The characteristic of arsenic resistance genes were analyzed on basis of their clustering and evolution, physicochemical properties, secondary structure, transmembrane regions, subcellular localization, and arsenic binding sites. Results showed that all 49 arsenic resistance genes were clustered into 11 groups, of which the arsB gene belonging to the second group was common with Acidithiobacillus genus. The arsB gene, coding for the arsenical pump membrane protein （ArsB） may be essential to the arsenic resistance of Acidithiobacillus strains. The clustering and evolution analyses showed that five arsenic resistance genes may originate from the horizontal gene transformation. Aliphatic index analysis showed that 25 arsenic resistance proteins were hydrophilic and the other 24 were hydrophobic. The instability indices revealed that most of ArsRs were unstable. The secondary structures of corresponding 49 arsenic resistance proteins were comprised ofα-helix, random coil, and extended chain. Subcellular localization analysis implied that arsenic resistance proteins might exist in inner and outer membrane, periplasmic space, and cytoplasm. ArsB proteins contained 10-11 transmembrane regions, and no signal peptide was found in all arsenic resistance proteins. Based on the arsenic binding site prediction and modeling results, we found that the Cys residues occurred in all active sites of ArsC, ArsD and ArsH proteins. Compared with other arsenic resistance proteins, the active sites of protein Acife1530 （i.e. ArsA） possessed two Met residues binding As （III）, implying that the thiol probably existed in Met and played a same role in binding As （III） directly as that in Cys residue. Therefore, the thiol in Cys or Met residue is vital for the arsenic binding site of arsenic resistant proteins in Acidithiobacillus microorganisms.
出处
《生态环境学报》
CSCD
北大核心
2013年第7期1141-1147,共7页
Ecology and Environmental Sciences
基金
国家自然科学基金项目(51064007)
江西省科技厅对外科技合作计划项目(20111bdh80032)
江西省科技厅科技支撑计划项目(20123bbf60170
20121BBG70004)
江西省教育厅科学技术研究项目(GJJ13397)
关键词
嗜酸硫杆菌
抗砷基因
聚类分析
多样性分析
生物信息学
Acidithiobacillus
arsenic resistance gene
ortholog analysis
diversity analysis
bioinformatics
