Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

Abstract

Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.

Enzymes Involved in a Novel Anaerobic Cyclohexane Carboxylic Acid Degradation Pathway

“…6). We propose that with the exception of R. palustris and probably F. placidus (17), the pathway identified in G. metallireducens is present in all CHCdegrading anaerobic microorganisms. This proposal is based on the finding that except for R. palustris (and F. placidus), all aromatic compound-degrading anaerobes employ the T. aromatica type of benzoyl-CoA degradation pathway, where CHdieneCoA but not CHeneCoA is the intermediate formed by class I or II benzoyl-CoA reductases (37).…”

“…During the degradation of the latter, the central benzoyl-CoA intermediate is dearomatized by a four-electron reduction to CHeneCoA, catalyzed by an ATP-dependent class I benzoyl-CoA reductase (15,16). This so-called R. palustris type of benzoyl-CoA degradation pathway via the characteristic CHeneCoA intermediate has also been suggested to be present in the archaeon Ferroglobus placidus by genomic and transcriptomic analyses (17). However, it differs from the Thauera aromatica type of benzoyl-CoA degradation pathway present in all other known aromatic compound-degrading anaerobic bacteria.…”

An unusual strategy for the anoxic biodegradation of phthalate

“…It explains why the encoding genes are often located adjacent to each other, as it is also the case for the ubiD-like genes coding for putative phthaloyl-CoA decarboxylases identified in this work. UbiD-like enzymes have also been proposed to be involved in the carboxylation of aromatic rings such as benzene or naphthalene in sulfate-reducing or Fe(III)-reducing bacteria and archaea (Abu Laban et al, 2010;Bergmann et al, 2011;Holmes et al, 2012). However, owing to the extremely slow growth of these organisms with non-substituted aromatic hydrocarbons, the limited biomass available largely hampered the biochemical characterization of such enzymatic reactions.…”

“…Deduced proteins of this cluster derive from denitrifying Gram-negative bacteria, Gram-negative and Gram-positive sulfate-reducing bacteria and from a marine metagenome suggesting a wide occurrence of phthaloyl-CoA decarboxylases. More distantly related UbiD-like decarboxylases comprise putative 3-octaprenyl-4-hydroxybenzoate decarboxylases, and experimentally verified or putative carboxylases involved in the degradation of phenol (phenylphosphate carboxylases) (Breinig et al, 2000) as well as other aromatic compounds (Abu Laban et al, 2010;Bergmann et al, 2011;Holmes et al, 2012).…”

Anaerobic Metabolism of Indoleacetate

“…In addition to the betaproteobacterium A. aromaticum, these microbes including the alphaproteobacterium Rhodopseudomonas palustris (only strain BisA3), the deltaproteobacterial strain NaphS2 (13), and the euryarchaeum Ferroglobus placidus (2). Although separated by a wide phylogenetic distance, it is remarkable that all these microorganisms are capable of anaerobic benzoate degradation (2,13,15,26), which is the prerequisite for further metabolizing the intermediate 2-aminobenzoyl-CoA generated from IAA. The fact that IAA is a common substrate derived from a canonical amino acid is in stark contrast to the apparently sparse occurrence of the detected pathway in very few organisms, suggesting that there may be other strategies of anaerobic tryptophan and IAA degradation.…”