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

2005 ◽  
Vol 71 (4) ◽  
pp. 2036-2045 ◽  
Author(s):  
Bongkeun Song ◽  
Bess B. Ward
Keyword(s):  
Chesapeake Bay ◽  
Aromatic Compounds ◽  
Anaerobic Degradation ◽  
Coenzyme A ◽  
Sequence Similarity ◽  
Rhodopseudomonas Palustris ◽  
Estuarine Sediment ◽  
Degenerate Primers ◽  
Sediment Samples ◽  
Coa Reductase

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 benzoyl-CoA reductase genes from Thauera aromatica, Rhodopseudomonas palustris, and Azoarcus evansii. PCR amplification detected benzoyl-CoA reductase genes in the denitrifying isolates belonging to α-, β-, or γ-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 degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes

2013 ◽  
Vol 16 (3) ◽  
pp. 612-627 ◽  
Author(s):  
Matthias Boll ◽  
Claudia Löffler ◽  
Brandon E. L. Morris ◽  
Johannes W. Kung
Keyword(s):  
Aromatic Compounds ◽  
Anaerobic Degradation ◽  
Coenzyme A ◽  
Key Enzymes ◽  
Coenzyme A Esters

scholarly journals Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris

2019 ◽  
Author(s):  
J. Zachary Oshlag ◽  
Yanjun Ma ◽  
Kaitlin Morse ◽  
Brian T. Burger ◽  
Rachelle A. Lemke ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Anaerobic Degradation ◽  
Fossil Fuels ◽  
Plant Biomass ◽  
Rhodopseudomonas Palustris ◽  
Reducing Power ◽  
Sole Source ◽  
Syringic Acid ◽  
Detailed Knowledge ◽  
Acid Degradation

ABSTRACTWhile lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogenous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a byproduct of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions, via the benzoyl-CoA degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to metabolize meta-methoxylated phenolics such as syringic acid. We isolated a strain of R. palustris (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of the vanARB operon (rpa3619-rpa3621), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with a vanARB deletion mutant demonstrated the involvement of the vanARB operon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation of meta-methoxylated and other aromatics by R. palustris.IMPORTANCELignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for production of aromatic-based biochemicals requires detailed knowledge of metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveals a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire to metabolize aromatic compounds from lignin and other renewable sources.

scholarly journals Structures of Homologous Composite Transposons Carrying cbaABC Genes from Europe and North America

1998 ◽  
Vol 64 (5) ◽  
pp. 1940-1946 ◽  
Author(s):  
Diana Di Gioia ◽  
Michelle Peel ◽  
Fabio Fava ◽  
R. Campbell Wyndham
Keyword(s):  
Coenzyme A ◽  
Sequence Similarity ◽  
Rhodopseudomonas Palustris ◽  
Direct Repeats ◽  
Catabolic Gene ◽  
Reading Frame ◽  
Niagara Falls ◽  
Sequence Identity ◽  
Coenzyme A Ligase ◽  
The Right

ABSTRACT IS1071 is a class II transposable element carrying atnpA gene related to the transposase genes of the Tn3 family. Copies of IS1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. The sequences of chlorobenzoate catabolic transposons found on pBRC60 (Tn5271) in Niagara Falls, N.Y., and on pCPE3 in Bologna, Italy, show that these transposons were formed from highly homologous IS1071 and cbaABCcomponents (levels of identity, >99.5 and >99.3%, respectively). Nevertheless, the junction sequences between the IS1071Land IS1071R elements and the internal DNA differ by 41 and 927 bp, respectively, suggesting that these transposons were assembled independently on the two plasmids. The formation of the right junction in both transposons truncated an open reading frame for a putative aryl-coenzyme A ligase with sequence similarity to benzoate- andp-hydroxybenzoate-coenzyme A ligases ofRhodopseudomonas palustris.

scholarly journals BadM Is a Transcriptional Repressor and One of Three Regulators That Control Benzoyl Coenzyme A Reductase Gene Expression in Rhodopseudomonas palustris

2006 ◽  
Vol 188 (24) ◽  
pp. 8662-8665 ◽  
Author(s):  
Caroline M. Peres ◽  
Caroline S. Harwood
Keyword(s):  
Gene Expression ◽  
Coenzyme A ◽  
Rhodopseudomonas Palustris ◽  
Transcriptional Repressor ◽  
Benzoate Degradation ◽  
Highly Sensitive ◽  
Reductase Gene ◽  
Unknown Gene ◽  
Coa Reductase ◽  
Rate Limiting

ABSTRACT The rate-limiting enzyme of anaerobic benzoate degradation by Rhodopseudomonas palustris, benzoyl coenzyme A (CoA) reductase, is highly sensitive to oxygen, and its synthesis is tightly regulated. We determined that a previously unknown gene in the benzoate gene cluster, badM, encodes a transcriptional repressor of benzoyl-CoA reductase gene expression. BadM controls gene expression from the benzoyl-CoA reductase promoter in concert with two previously described transcriptional activators.

scholarly journals Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris

2019 ◽  
Vol 86 (3) ◽  
Author(s):  
J. Zachary Oshlag ◽  
Yanjun Ma ◽  
Kaitlin Morse ◽  
Brian T. Burger ◽  
Rachelle A. Lemke ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Anaerobic Degradation ◽  
Fossil Fuels ◽  
Plant Biomass ◽  
Rhodopseudomonas Palustris ◽  
Reducing Power ◽  
Syringic Acid ◽  
Detailed Knowledge ◽  
Content Type ◽  
Acid Degradation

ABSTRACT While lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogeneous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a by-product of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions via the benzoyl coenzyme A (CoA) degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to metabolize meta-methoxylated phenolics, such as syringic acid. We isolated a strain of R. palustris (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of the vanARB operon (rpa3619, rpa3620, rpa3621), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with a vanARB deletion mutant demonstrated the involvement of the vanARB operon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation of meta-methoxylated and other aromatics by R. palustris. IMPORTANCE Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources.

scholarly journals The 5,6,7,8-Tetrahydro-2-Naphthoyl-Coenzyme A Reductase Reaction in the Anaerobic Degradation of Naphthalene and Identification of Downstream Metabolites

2020 ◽  
Vol 86 (15) ◽  
Author(s):  
Philip Weyrauch ◽  
Isabelle Heker ◽  
Andrey V. Zaytsev ◽  
Christian A. von Hagen ◽  
Meike E. Arnold ◽  
...  
Keyword(s):  
Electron Donor ◽  
Anaerobic Degradation ◽  
Coenzyme A ◽  
Degradation Pathway ◽  
Electron Donors ◽  
Ring Cleavage ◽  
Naphthalene Degradation ◽  
Cell Extracts ◽  
Polycyclic Aromatic ◽  
Coa Reductase

ABSTRACT Anaerobic degradation of polycyclic aromatic hydrocarbons has been investigated mostly with naphthalene as a model compound. Naphthalene degradation by sulfate-reducing bacteria proceeds via carboxylation to 2-naphthoic acid, formation of a coenzyme A thioester, and subsequent reduction to 5,6,7,8-tetrahydro-2-naphthoyl-coenzyme A (THNCoA), which is further reduced to hexahydro-2-naphthoyl-CoA (HHNCoA) by tetrahydronaphthoyl-CoA reductase (THNCoA reductase), an enzyme similar to class I benzoyl-CoA reductases. When analyzing THNCoA reductase assays with crude cell extracts and NADH as electron donor via liquid chromatography-mass spectrometry (LC-MS), scanning for putative metabolites, we found that small amounts of the product of an HHNCoA hydratase were formed in the assays, but the downstream conversion by an NAD+-dependent β-hydroxyacyl-CoA dehydrogenase was prevented by the excess of NADH in those assays. Experiments with alternative electron donors indicated that 2-oxoglutarate can serve as an indirect electron donor for the THNCoA-reducing system via a 2-oxoglutarate:ferredoxin oxidoreductase. With 2-oxoglutarate as electron donor, THNCoA was completely converted and further metabolites resulting from subsequent β-oxidation-like reactions and hydrolytic ring cleavage were detected. These metabolites indicate a downstream pathway with water addition to HHNCoA and ring fission via a hydrolase acting on a β’-hydroxy-β-oxo-decahydro-2-naphthoyl-CoA intermediate. Formation of the downstream intermediate cis-2-carboxycyclohexylacetyl-CoA, which is the substrate for the previously described lower degradation pathway leading to the central metabolism, completes the anaerobic degradation pathway of naphthalene. IMPORTANCE Anaerobic degradation of polycyclic aromatic hydrocarbons is poorly investigated despite its significance in anoxic sediments. Using alternative electron donors for the 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase reaction, we observed intermediary metabolites of anaerobic naphthalene degradation via in vitro enzyme assays with cell extracts of anaerobic naphthalene degraders. The identified metabolites provide evidence that ring reduction terminates at the stage of hexahydro-2-naphthoyl-CoA and a sequence of β-oxidation-like degradation reactions starts with a hydratase acting on this intermediate. The final product of this reaction sequence was identified as cis-2-carboxycyclohexylacetyl-CoA, a compound for which a further downstream degradation pathway has recently been published (P. Weyrauch, A. V. Zaytsev, S. Stephan, L. Kocks, et al., Environ Microbiol 19:2819–2830, 2017, https://doi.org/10.1111/1462-2920.13806). Our study reveals the first ring-cleaving reaction in the anaerobic naphthalene degradation pathway. It closes the gap between the reduction of the first ring of 2-naphthoyl-CoA by 2-napthoyl-CoA reductase and the lower degradation pathway starting from cis-2-carboxycyclohexylacetyl-CoA, where the second ring cleavage takes place.

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