Physiological, numerical and molecular characterization of alkyl ether‐utilizing rhodococci

Abstract

Twenty-seven Gram-positive strains were characterized physiologically and numerically and classified them into four groups according to their specific activities for utilization of linear alkyl ethers (AEs), cyclic AEs, monoalkoxybenzenes and 1,4-diethoxybenzene. The comparative analysis of the 16S ribosomal RNA gene and 16S-23S intergenic spacer region showed that they belonged to the genera Rhodococcus and Gordonia. Alkyl ether-utilizing rhodococci appeared to involve various and diverse cytochromes P450 of the families CYP116 (25 positive strains from 27), CYP153 (5/27), CYP249 (1/27) and a new family P450RR1 (27/27). The presence of P450RR1 was strongly related to the specific activity for utilization of 2-methoxyphenol and 2-ethoxyphenol. In addition, 26 of 27 strains contained multiple alkB genes coding for probable non-haem iron containing alkane monooxygenases and hydroxylases. Similar DNA fragments coding for a tetrahydrofuran monooxygenase A subunit (ThmA) were found in all cyclic AE-utilizing strains and nearly identical DNA fragments coding for likely orthologues of a propane monooxygenase A subunit (PrmA) in all linear AE-utilizing strains. The substrate availability in the degradation of aryl AEs, cyclic AEs and linear AEs agreed with the molecular probing of the respective genes encoding cytochrome P450RR1, ThmA and PrmA.

Constitutive Expression of the Cytochrome P450 EthABCD Monooxygenase System Enables Degradation of Synthetic Dialkyl Ethers in Aquincola tertiaricarbonis L108

“…This regulation may also explain the results obtained with Rhodococcus sp. strain PEG604, which tested negative on MTBE but likely possesses a CYP249A1 monooxygenase system, as the ethB gene with Ͼ99% identity to the sequence found in strain IFP 2001 has been detected in this strain (34). Obviously, the lack of a suitable inducer resulted in insufficient expression of the monooxygenase and, consequently, insignificant degradation of MTBE in strain PEG604.…”

“…Gordonia (7,34). However, all these bacteria do not possess the tert-alcohol degradation pathways needed for complete mineralization of the fuel oxygenate ethers.…”

Linking Low-Level Stable Isotope Fractionation to Expression of the Cytochrome P450 Monooxygenase-Encoding ethB Gene for Elucidation of Methyl tert -Butyl Ether Biodegradation in Aerated Treatment Pond Systems

“…After sequencing of the obtained PCR products, the closest matches found in the National Center for Biotechnology Information (NCBI) database were, in all cases, ethB genes previously obtained from the genus Rhodococcus, such as the ethB sequence of R. ruber IFP 2001, which was also detected in other ETBE degraders, such as R. ruber IFP 2007 (a constitutive strain derived from strain IFP 2001 [16]), Rhodococcus zopfii IFP 2005 (5, 29), and Rhodococcus sp. strain PEG604 (21). However, a high identity (99 to 100%) was also obtained when comparing directly to the A. tertiaricarbonis L108 ethB sequence (98% identical to that of R. ruber IFP 2001).…”

Biodegradation of Tetrahydrofuran and 1,4-Dioxane by Soluble Diiron Monooxygenase in <b><i>Pseudonocardia</i></b> sp. Strain ENV478

“…These THFutilizing strains can also oxidize 1,4-dioxane via metabolic or cometabolic processes. Interestingly, sequence analysis of thm revealed wide distribution of thm -type genes in THF utilizing strains [Kim et al, 2007], including CB1190 [Sales et al, 2011], suggesting that thm enzyme is responsible for the initial step of the degradation in this group of bacteria. Because the genome sequence of CB1190 showed the presence of multiple homologs of oxygenases that have been shown to oxidize 1,4-dioxane in other bacteria [Mahendra and Alvarez-Cohen, 2006], a possibility that 1,4-dioxane is degraded via separate enzymes in CB1190 cannot be ruled out.…”

“…1,4-Dioxane is an important groundwater contaminant throughout the United States and elsewhere, and has been proposed to have carcinogenic properties showing high similarity to soluble methane monooxygenase, propane monooxygenase, and alkene monooxygenase [Thiemer et al, 2003]. Homologs of the thm genes are also found in other THF-oxidizing bacteria [Kim et al, 2007]. Based on gene expression analysis, the thmencoded monooxygenase was proposed to catalyze the initial step of the THF degradation pathway, but so far there have been no genetic studies to confirm its involvement.…”