Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB

Abstract

Rhodococcus sp. strain TFB is a versatile gram-positive bacterium able to grow on a wide variety of aromatic compounds as carbon and energy sources. Since the strain is refractory to genetic analysis, a proteomic approach was used to study the metabolic pathways involved in the catabolism of such compounds by analyzing differentially induced proteins. The most marked difference was observed when the proteome profiles of phthalate-grown cells were compared with those cultured in the presence of tetralin- or naphthalene, suggesting that different metabolic pathways are involved in the degradation of mono- and polyaromatic compounds. Comparison with the proteome of glucose-grown cells indicated that each pathway was specifically induced by the corresponding aromatic compound. A combination of proteomics and molecular biology led to the identification of 14 proteins (65-80% identical to known Pht proteins) that describe a complete pathway for the catabolism of phthalate to central metabolites via intradiol cleavage of protochatechuic acid. Chaperonins were also induced in phthalate-grown cells, indicating that growth on this compound induces a stress response. Absence of catabolite repression by glucose was observed by both transcriptional and proteome analysis, suggesting that Rhodococcus sp. strain TFB may have advantages over other tightly regulated strains in bioremediation.

Monooxygenases involved in the n-alkanes metabolism by Rhodococcus sp. BCP1: molecular characterization and expression of alkB gene

“…Rhodococcus opacus B4 [292,342] and Rhodococcus erythropolis PR4 [292,293]. Indeed, the literature about rhodococcal functional proteomic studies focused mainly on the study of the metabolic pathways associated with mono-and polyaromatic catabolism in Rhodococcus jostii RHA1 [282,352]. Additionally, most of these studies considered only the soluble protein fraction, because of the limitations imposed by the association of low solubility and high hydrophobicity of membrane proteins with the peculiar recalcitrant characteristics of the Rhodococcus genus members.…”

“…Proteomic studies have been conducted to analyze catabolic pathways for both mono-and polyaromatic compounds in Rhodococcus sp. strain TFB [352] and to investigate the apparent redundancy of degradation pathways for mono-aromatic compounds in Rhodococcus jostii RHA1 [282]. A few other studies combined proteome analysis with molecular biology techniques to identify new enzymes involved in xenobiotic degradation pathways in Rhodococcus strains [353][354][355].…”

Analysis of phthalate degradation operon from Arthrobacter sp. 68b

“…The previous findings that phthalic acid degradation genes in various Actinomycetales (Arthrobacter and Rhodococcus spp.) are plasmid located [35,36,39] raise the question if a catabolic plasmid encoding analogous genes exist in Arthrobacter sp. 68b cells.…”

“…DK17 [35] and Rhodococcus sp. TFB [36] strains. The decarboxylase encoding gene is not presented in pht operon of Mycobacterium vanbaalenii PYR-1, hence, genes are set in phtRAaAbBAcAd order [37].…”

“…The decarboxylase encoding gene is not presented in pht operon of Mycobacterium vanbaalenii PYR-1, hence, genes are set in phtRAaAbBAcAd order [37]. All genes of the operons are transcribed in the same direction, except the regulatory protein gene (phtR), which is located upstream of the operon and is transcribed from the opposite strand in these strains [35][36][37]. Phylogenetic analysis of pht genes encoding proteins shows that Arthrobacter sp.…”