Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases☆

Lupa, Boguslaw; Lyon, Delina Y.; Gibbs, Moreland D.; Reeves, Rosalind A.; Wiegel, Juergen

doi:10.1016/j.ygeno.2005.05.002

Cited by 71 publications

(91 citation statements)

References 47 publications

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“…This reversible hydroxyarylic acid decarboxylase/ phenol carboxylase is encoded by the shdCDB genes, and it is specifically induced in the presence of 4-HBA. Similar shdC (ubiD homolog), shdB (ubiX homolog), and shdD genes have been found in the genomes of other bacteria, and they were suggested to encode a novel enzyme family of reversible, nonoxidative, and cofactor-independent hydroxyarylic acid decarboxylases (230).…”

Section: Vol 73 2009 Anaerobic Biodegradation Of Aromatics 95mentioning

confidence: 63%

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

Carmona

Zamarro

Blázquez

et al. 2009

Microbiol Mol Biol Rev

391

381

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SUMMARY Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.

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Section: Vol 73 2009 Anaerobic Biodegradation Of Aromatics 95mentioning

confidence: 63%

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

Carmona

Zamarro

Blázquez

et al. 2009

Microbiol Mol Biol Rev

391

381

View full text Add to dashboard Cite

show abstract

“…Recent studies indicate that ubiX-like genes in many prokaryotes are located within operons that encode partner proteins (including homologs of ubiD) and both are required to decarboxylate a variety of hydroxyarylic acids [15]. For example, an operon in Streptomyces sp D7 containing the vdcB and vdcC genes show 50% and 29% amino acid sequence identity with E. coli UbiX and UbiD respectively, and both must be present in order to reconstitute the aerobic decarboxylation of vanillate when expressed in Streptomyces lividans [15]. However, when expressed in E. coli, the vdcB gene is no longer needed.…”

Section: Discussionmentioning

confidence: 99%

“…Based on its 50% sequence identity with E. coli UbiX, the authors postulated that Pad1 might function in Q biosynthesis. Other investigators suspect partner proteins may be required for decarboxylation activity [15]. Thus the functional roles of UbiX and Pad1 in E. coli and yeast Q biosynthesis are not known.…”

Section: Introductionmentioning

confidence: 99%

The role of UbiX in Escherichia coli coenzyme Q biosynthesis

Gulmezian¹,

Hyman²,

Marbois³

et al. 2007

Archives of Biochemistry and Biophysics

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The reversible redox chemistry of coenzyme Q serves a crucial function in respiratory electron transport. Biosynthesis of Q in Escherichia coli depends on the ubi genes. However, very little is known about UbiX, an enzyme thought to be involved in the decarboxylation step in Q biosynthesis in E. coli and Salmonella enterica. Here we characterize an E. coli ubiX gene deletion strain, LL1, to further elucidate E. coli ubiX function in Q biosynthesis. LLI produces very low levels of Q, grows slowly on succinate as the sole carbon source, accumulates 4-hydroxy-3-octaprenyl-benzoate, and has reduced UbiG O-methyltransferase activity. Expression of either E. coli ubiX or the Saccharomyces cerevisiae ortholog PAD1, rescues the deficient phenotypes of LL1, identifying PAD1 as an ortholog of ubiX. Our results suggest that both UbiX and UbiD are required for the decarboxylation of 4-hydroxy-3-octaprenyl-benzoate in E. coli coenzyme Q biosynthesis, especially during logarithmic growth.

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“…We first searched for genes with known decarboxylase functions that are responsible for the first decarboxylation step of TA degradation (Supplementary Figure 7). Two gene sets (tadcc27178-79-80 and tadcc16349) from the Pelotomaculum bin were identified to have high sequence similarity and a subunit complement with a known 4-hydroxybenzoate decarboxylase, EC 4.1.1.61, from Sedimentibacter hydroxybenzoicum that consists of three subunits (AAD50377, AAY67850 and AAY67851) and belongs to the UbiD family of proteins (Lupa et al, 2005). Two mechanisms have been described for the subsequent fermentation of benzoate to acetate and CO 2 : the well-known benzoyl-CoA reductase (BCR, EC 1.3.99.15) route used by Thauera aromatica (Boll and Fuchs, 1995) and the less understood BCR-independent mechanism for reductive dearomatization (Wischgoll et al, 2005).…”

Section: Pelotomaculummentioning

confidence: 99%

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

et al. 2010

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Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium inside a hyper-mesophilic (that is, between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified b-oxidation to H 2 /CO 2 and acetate. These intermediates are converted to CH 4 /CO 2 by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to CO 2 /H 2 and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H 2 -producing syntroph-methanogen partnership that may serve to improve community stability. The ISME Journal (2011) 5, 122-130; doi:10.1038/ismej.2010; published online 5 August 2010Subject Category: integrated genomics and post-genomics approaches in microbial ecology Keywords: metagenomics; methanogenesis; syntroph; microbial diversity; carbon cycling Introduction Terephthalate (TA) is used as the raw material for the manufacture of numerous plastic products (for example, polyethylene TA bottles and textile fibers). During its production, TA-containing wastewater is discharged in large volumes (as high as 300 million m 3 per year) and high concentration (up to 20 kg COD (chemical oxygen demand) m À3 ) (Razo-Flores et al., 2006). This wastewater is generally treated by anaerobic biological processes under mesophilic conditions (B35 1C). However, anaerobic processes operated at hyper-mesophilic (46-50 1C) and thermophilic (B55 1C) temperatures may be preferable because of the ability to achieve higher loading rate (van Lier et al., 1997;Chen et al., 2004), which reduces the reactor volume. Moreover, TA wastewater is usually generated at 54-60 1C, and does not require additional energy input for maintaining reactor temperature (Chen et al., 2004). The microbial biomass usually occurs in the form of granules or biofilms attaching on the surface of porous media. Under such environments, TA degradation has been hypothesized (Kleerebezem et al., 1999) to be based on a syntrophic microbial relationship whereby fermentative H 2 -producing bacteria (syntrophs) convert TA through benzoate to acetate and H 2 /CO 2 , and acetoclastic and hydrogenotrophic methanogens further convert the intermediates to methane by physically positioning themselves close to the syntrophs to overcome the www.nature.com/ismej thermodynamic barrier (Stams, 1994;Conrad, 1999;Dolfing, 2001).In practice, the complexities of TA-degrading communities are not...

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Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases☆

Cited by 71 publications

References 47 publications

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

The role of UbiX in Escherichia coli coenzyme Q biosynthesis

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

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