赤红球菌SD3全基因组测序及其热休克蛋白DnaK的表达分析

红球菌属微生物因其自身较强的有机物耐受性和较宽的降解谱,能够适应多种生境而被广泛应用于生物脱硫、石油污染修复、有毒有机化合物降解、污水处理等领域。本研究利用单分子PacBio测序技术,对一株耐有机溶剂的赤红球菌SD3(Rhodococcus ruber SD3)全基因组进行测序并进行生物信息学分析。该菌株的全基因组长度大约为5.37 Mb,GC含量为70.63%,GenBank序列登录号为CP029146。使用Barrnap0.4.2和tRNAscan-SEv1.3.1软件对基因组中包含的rRNA基因和tRNA基因进行预测,发现有12个rRNA基因和53个tRNA基因。利用Glimmer3.02软件对该基因组进行基因预测,共得到5120个编码蛋白的基因。将预测的蛋白序列同时与KEGG、STRING和GO三类数据库进行Blastp比对,共计2836个蛋白基因获得COG功能注释,并且注释得到3130条GO功能条目和2190条KEGG通路条目。此外,基于荧光定量PCR的分析表明在甲苯和苯酚胁迫下,赤红球菌SD3中热休克蛋白DnaK的表达分别上调了29.87倍和3.93倍。这些研究结果为赤红球菌的遗传改造和揭示赤红球菌的有机溶剂耐受性机制提供了理论依据。

Whole-Genome Sequencing and Expression Analysis of Heat Shocking Protein DnaK from Rhodococcus ruber SD3

Microbes belonging to Rhodococcus genus is widely used in all kinds of fields including biological desulfurization,bioremediation of petroleum pollution,degradation of toxic compounds and sewage treatment owing to its strong organic compounds tolerance,wide degradation spectrum and adaption to various habitat.In the present study,single-molecule PacBio sequencing technology was applied to conduct de novo sequencing and bioinformatics analysis of the whole genome of Rhodococcus ruber SD3 with organic solvent-tolerance.The size of whole assembled genome of the strain was approximately 5.37 Mb,with GC content of 70.63%.The BioProject accession number in GenBank is CP029146.Twelve rRNA genes and fifty-three tRNA genes were found in the genome using Barrnap 0.4.2 and tRNAscan-SE v1.3.1 software.The genome was genetically predicted using Glimmer 3.02 software,and a total of 5120 genes encoding protein were obtained.The predicted protein sequences were blastp-aligned with the SREING database,KEGG database and GO database,respectively.COG annotation of 2836 protein genes,3130 GO entries and 2190 KEGG pathways was successfully obtained.Furthermore,analysis based on fluorescence quantitative PCR showed that toluene and phenol stress gave rise to an increase of 29.87 folds and 3.93 folds for the expression of heat shocking protein DnaK,respectively.The results provides a theoretical basis for the genetic modification of R.ruber and unveiling its organic solvents tolerance mechanism.