Sha'arani Shazwana, Hara Hirofumi, Araie Hiroya, Suzuki Iwane, Mohd Noor Megat Johari Megat, Akhir Fazrena Nadia Md, Othman Nor'azizi, Zakaria Zuriati
Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia.
Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi.
J Gen Appl Microbiol. 2019 Sep 14;65(4):173-179. doi: 10.2323/jgam.2018.08.003. Epub 2019 Jan 28.
This study gives the first picture of whole RNA-Sequencing analysis of a PCB-degrading microbe, Rhodococcus jostii RHA1. Genes that were highly expressed in biphenyl-grown cells, compared with pyruvate-grown cells, were chosen based on the Reads Per Kilobase Million (RPKM) value and were summarized based on the criteria of RPKM ≥100 and fold change ≥2.0. Consequently, 266 total genes were identified as genes expressed particularly for the degradation of biphenyl. After comparison with previous microarray data that identified highly-expressed genes, based on a fold change ≥2.0 and p-value ≤0.05, 62 highly-expressed genes from biphenyl-grown cells were determined from both analytical platforms. As these 62 genes involve known PCB degradation genes, such as bph, etb, and ebd, the genes identified in this study can be considered as essential genes for PCB/biphenyl degradation. In the 62 genes, eleven genes encoding hypothetical proteins were highly expressed in the biphenyl-grown cells. Meanwhile, we identified several highly-expressed unannotated DNA regions on the opposite strand. In order to verify the encoded proteins, two regions were cloned into an expression vector. A protein was successfully obtained from one region at approximately 25 kDa from the unannotated strand. Thus, the genome sequence with transcriptomic analysis gives new insight, considering re-annotation of the genome of R. jostii RHA1, and provides a clearer picture of PCB/biphenyl degradation in this strain.
本研究首次展示了对多氯联苯降解微生物约氏红球菌RHA1的全RNA测序分析情况。根据每百万碱基读取数（RPKM）值，选取了与丙酮酸培养细胞相比在联苯培养细胞中高表达的基因，并基于RPKM≥100和倍数变化≥2.0的标准进行汇总。结果，共鉴定出266个基因作为特别用于联苯降解的表达基因。在与先前基于倍数变化≥2.0和p值≤0.05鉴定高表达基因的微阵列数据进行比较后，从两个分析平台确定了来自联苯培养细胞的62个高表达基因。由于这62个基因涉及已知的多氯联苯降解基因，如bph、etb和ebd，本研究中鉴定出的基因可被视为多氯联苯/联苯降解的必需基因。在这62个基因中，有11个编码假定蛋白的基因在联苯培养细胞中高表达。同时，我们在反义链上鉴定出几个高表达的未注释DNA区域。为了验证编码的蛋白质，将两个区域克隆到表达载体中。从一个区域成功获得了一条来自未注释链的约25 kDa的蛋白质。因此，结合转录组分析的基因组序列为约氏红球菌RHA1基因组的重新注释提供了新的见解，并更清晰地展现了该菌株中多氯联苯/联苯的降解情况。
