Genetic Diversity of Benzoyl Coenzyme A Reductase Genes Detected in Denitrifying Isolates and Estuarine Sediment Communities

Abstract

Benzoyl coenzyme A (benzoyl-CoA) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-CoA) in the metabolism of many aromatic compounds. The diversity of benzoyl-CoA reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the Arthur Kill in New Jersey and the Chesapeake Bay in Maryland was investigated. Degenerate primers were developed from the known benzoylCoA reductase genes from Thauera aromatica, Rhodopseudomonas palustris, and Azoarcus evansii. PCR amplification detected benzoyl-CoA reductase genes in the denitrifying isolates belonging to ␣-, ␤-, or ␥-Proteobacteria as well as in the sediment samples. Phylogenetic analysis, sequence similarity comparison, and conserved indel determination grouped the new sequences into either the bcr type (found in T. aromatica and R. palustris) or the bzd type (found in A. evansii). All the Thauera strains and the isolates from the genera Acidovorax, Bradyrhizobium, Paracoccus, Ensifer, and Pseudomonas had bcr-type benzoyl-CoA reductases with amino acid sequence similarities of more than 97%. The genes detected from Azarocus strains were assigned to the bzd type. A total of 50 environmental clones were detected from denitrifying consortium and sediment samples, and 28 clones were assigned to either the bcr or the bzd type of benzoyl-CoA reductase genes. Thus, we could determine the genetic capabilities for anaerobic degradation of aromatic compounds in sediment communities of the Chesapeake Bay and the Arthur Kill on the basis of the detection of two types of benzoyl-CoA reductase genes. The detected genes have future applications as genetic markers to monitor aromatic compound degradation in natural and engineered ecosystems.

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

“…Based on amino acid sequence comparison analyses, two types of ATP-dependent BCR enzymes that might share a common ancestor have been proposed, i.e., the bcr-type BCR present in T. aromatica, R. palustris, and Magnetospirillum strains and the bzd-type BCR present in Azoarcus strains (30,343). Despite the possibility that BCR Ta and BCR Rp may have evolved from a common ancestor, these two enzymes might differ in their biochemical properties, which could account for the single and the two successive two-electron reduction steps of benzoyl-CoA, respectively ( Fig.…”

“…The genes encoding BCR, the key enzyme in the anaerobic degradation of many aromatic compounds (see above), have been successfully used as functional markers to determine the distribution and the capability for anaerobic degradation of aromatic compounds in bacterial isolates and in the environment (163,343). Degenerate oligonucleotide primer pairs were developed for the genes encoding the ␣-subunit of BCRs from T. aromatica (bcrA), R. palustris (badF), and A. evansii (bzdQ).…”

New insights into the BzdR-mediated transcriptional regulation of the anaerobic catabolism of benzoate in Azoarcus sp. CIB

“…The biochemistry of the benzoyl-CoA central pathway has been well studied in some facultative anaerobic bacteria such as Rhodopseudomonas palustris, Azoarcus evansii and Thauera aromatica (Boll, 2005;Gibson & Harwood, 2002;Harwood et al, 1999) and to a lesser extent in strict anaerobes such as Desulfococcus multivorans (Peters et al, 2004), Geobacter metallireducens Wischgoll et al, 2005) and Syntrophus aciditrophicus (Elshahed et al, 2001;Peters et al, 2007). Moreover, molecular microbial ecology studies suggest that the ability to degrade aromatic compounds under anaerobic conditions is more widespread among bacteria than previously thought (Jahn et al, 2005;Safinowski et al, 2006;Song & Ward, 2005). In contrast to the current knowledge on the biochemistry of the anaerobic benzoyl-CoA central pathway, few studies have been conducted to unravel the regulatory circuits that control the expression of the cognate genes, being mainly restricted to the regulation of the bad genes in Rhodopseudomonas palustris and the bzd genes in Azoarcus sp.…”

Dynamic Changes in Aromatic Hydrocarbon Associated Catabolic Gene Profiles Linked to Aerobic and Anaerobic Microcosm Studies

“…Total microbial DNA was quantified by UV absorption at 260 nm [15]. Primer pair BZAQ4F/R [16] were used to amplify a 484bp fragment from the, α subunit of the bcr gene. The bcr products generated were used to prepare standards for use in qPCR assays with primer BZAQ4F and PFR1 (5`TCCTGMCCGCCSATGTCSAG`3) [17].…”