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Whole gene transcriptomic analysis of PCB/biphenyl degrading <i>Rhodococcus jostii</i> RHA1

  • Sha'arani Shazwana
    Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
  • Hara Hirofumi
    Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi
  • Araie Hiroya
    Graduate School of Life and Environmental Science, University of Tsukuba
  • Suzuki Iwane
    Graduate School of Life and Environmental Science, University of Tsukuba
  • Mohd Noor Megat Johari Megat
    Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
  • Akhir Fazrena Nadia MD
    Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
  • Othman Nor'azizi
    Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
  • Zakaria Zuriati
    Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia

Abstract

<p>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.</p>

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