Biphenyl/PCB Degrading <i>bph</i> Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs)

• Main Authors: Jun Hirose, Hidehiko Fujihara, Takahito Watanabe, Nobutada Kimura, Hikaru Suenaga, Taiki Futagami, Masatoshi Goto, Akiko Suyama, Kensuke Furukawa
• Format: Article
• Language: English
• Published: MDPI AG 2019-05-01
• Series: Genes
• Subjects: biphenyl; <i>bph</i> gene; integrative conjugative element; genome sequence
• Online Access: https://www.mdpi.com/2073-4425/10/5/404

We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to &#946;- and &#947;-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic <i>bph</i> gene cluster as integrative conjugative elements (ICEs), and they were classified into four groups based on the structural features of the <i>bph</i> genes. Group I (five strains) possessed <i>bph</i> genes that were very similar to the ones in <i>Pseudomonas</i> <i>furukawaii</i> KF707 (formerly <i>Pseudomonas pseudoalcaligenes</i> KF707), which is one of the best characterized biphenyl-utilizing strains. This group of strains carried salicylate catabolic <i>sal</i> genes that were approximately 6-kb downstream of the <i>bph</i> genes. Group II (two strains) possessed <i>bph</i> and <i>sal</i> genes similar to the ones in KF707, but these strains lacked the <i>bphX</i> region between <i>bphC</i> and <i>bphD</i>, which is involved in the downstream catabolism of biphenyl. These <i>bph-sal</i> clusters in groups I and II were located on an integrative conjugative element that was larger than 110 kb, and they were named ICE<i>_bph-sal</i>. Our previous study demonstrated that the ICE<i>_bph-sal</i> of <i>Pseudomonas putida</i> KF715 in group II existed both in an integrated form in the chromosome (referred to as ICE<i>_bph-sal</i>KF715 (integrated)) and in a extrachromosomal circular form (referred to as ICE<i>_bph-sal</i> (circular)) (previously called pKF715A, 483 kb) in the stationary culture. The ICE<i>_bph-sal</i> was transferred from KF715 into <i>P. putida</i> AC30 and <i>P. putida</i> KT2440 with high frequency, and it was maintained stably as an extrachromosomal circular form. The ICE<i>_bph-sal</i>KF715 (circular) in these transconjugants was further transferred to <i>P</i>. <i>putida</i> F39/D and then integrated into the chromosome in one or two copies. Meanwhile, group III (one strain) possessed <i>bph</i> genes, but not <i>sal</i> genes. The nucleotide sequences of the <i>bph</i> genes in this group were less conserved compared to the genes of the strains belonging to groups I and II. Currently, there is no evidence to indicate that the <i>bph</i> genes in group III are carried by a mobile element. Group IV (two strains) carried <i>bph</i> genes as ICEs (59&#8722;61 kb) that were similar to the genes found in Tn<i>4371</i> from <i>Cupriavidus oxalacticus</i> A5 and ICE_KKS102<i>4677</i> from the <i>Acidovorax</i> sp. strain KKS102. Our study found that <i>bph</i> gene islands have integrative functions, are transferred among soil bacteria, and are diversified through modification.