喜温嗜酸硫杆菌SM-1在不同温度下基因组的可塑性

摘要

[Objective] The aim of this study is to gain the acclimated strain ofAcidithiobacillus caldus SM-1 with high activity when growing at the temperatures below the optimum,and elaborate its genomic plasticity and adaptation at different temperatures.[Methods] Strains were incubated at 37 ℃,40 ℃ and 45 ℃.We used 454 genome resequencing technology to find the single nucleotide mutant sites in genome.The genes including mutant sites were studied to understand their relationship with the temperature adaptation.[Results] By long-term breeding,we obtained strains with higher viability than unacclimated strain at temperatures (37 ℃),which is lower than initial optimum growth temperature (45 ℃).Resequencing results showed the genome of SM-1 with high plasticity.In the genome of different strains (incubated at 37 ℃,40 ℃ and 45 ℃),418,384 and 347 single nucleotide mutation sites were accumulated,respectively.Among them,20 mutant sites were commonly occurred in the three strains.The genes they affected are involved in heavy metals and toxic resistance system,DNA methylation and protein acylation,and nucleic acid metabolism.In comparison,the specific mutations of the strains,grown at the 37 ℃ and 40 ℃,were related to energy metabolism,signal transduction and DNA/RNA stability.Three genes contained mutant sites are common in L37 and M40,of which,Atc 1031 and Atc 1623 encode proteins related to transposon insertion,Atc_1130 encodes a hypothetical protein that is similar to the out membrane protein assembly factor B or the disulfide bond formation protein with 23％ and 35％ similarity.In addition,some single nucleotide mutations cause the amino acid changes of the related proteins during the adaption.[Conclusion] The genome of At.caldus SM-1 showed highly plasticity at different temperatures.The study provided a set of genomic data for understanding the temperature adaptability molecular mechanism of microorganisms.The study revealed that At.caldus SM-1 evolved to fit lower temperature through multiple pathways,not only by the general environment adaptation mechanism of microorganism,but also by the specific pathway of the strain.%[目的]驯化得到喜温嗜酸硫杆菌(Acidithiobacillus caldus) SM-1在低于最适生长温度下具有较高生长活力的突变菌株,并认知喜温嗜酸硫杆菌在不同温度下的基因组可塑性.[方法]利用实验室长期进化实验对菌株进行3个温度的驯化:37、40、45℃.运用454测序技术对驯化获得的菌株进行基因组重测序,通过比较基因组分析驯化株基因组单核苷酸位点变化(SNPs),对包含位点变化的基因从功能上进行分类,在此基础上,分析可能与温度适应性相关的基因.[结果]通过不同温度下的长期驯化,得到了在低于最适生长温度下具有较高活力的菌株;重测序结果发现,SM-1基因组具有较好的可塑性,不同温度(37、40、45℃)生长的菌株中,基因组中分别有418、384和347个核苷酸位点发生累计变化,其中3个温度下有20个相同的非同义突变位点,分别分布于编码重金属和毒性抗性系统、DNA甲基化和蛋白乙酰化酶、核酸代谢相关酶类等相关基因上;相比而言,在低于最适生长温度(37、40℃)下生长菌株特有的位点变化涉及能量代谢、信号转导以及DNA/RNA稳定性相关基因;其中,2个低温菌株共同发生位点变化的基因有3个,其中两个编码转座相关的蛋白Atc 1031与Atc_1623,另一个编码假想蛋白Atc 1130,该蛋白分别与外膜蛋白组装因子B和二硫键形成蛋白具有23％和35％的相似性.另外,不同生长温度下相关蛋白中氨基酸的组成也发生变化.[结论]喜温嗜酸硫杆菌SM-1基因组具有较好的可塑性,对于其基因组变化的研究结果为认识微生物温度适应性提供了组学数据.本研究揭示喜温嗜酸硫杆菌(At.caldus) SM-1可能通过多种途径适应向低温过渡生长,既包括微生物通用的环境适应机制,也存在菌株特有的温度适应途径.