Anaerobic Degradation of Aromatic Compounds by<i>Magnetospirillum</i>Strains: Isolation and Degradation Genes

Shinoda, Yoshifumi; Akagi, Junya; Uchihashi, Yasumitsu; Hiraishi, Akira; Yukawa, Hideaki; Yurimoto, Hiroya; Sakai, Yasuyoshi; Kato, Nobuo

doi:10.1271/bbb.69.1483

Cited by 82 publications

(89 citation statements)

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“…The pattern in which transposase or integrase coding genes are present with gene clusters for aromatic degradation is widely distributed and occurs, e.g., in A. aromaticum EbN1 (14,49). Respective events of lateral gene transfer also have been interpreted from previous phylogenetic analyses of bssA gene relationships (57,63).…”

Section: Discussionmentioning

confidence: 99%

Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

et al. 2010

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The highly enriched deltaproteobacterial culture N47 anaerobically oxidizes the polycyclic aromatic hydrocarbons naphthalene and 2-methylnaphthalene, with sulfate as the electron acceptor. Combined genome sequencing and liquid chromatography-tandem mass spectrometry-based shotgun proteome analyses were performed to identify genes and proteins involved in anaerobic aromatic catabolism. Proteome analysis of 2-methylnaphthalene-grown N47 cells resulted in the identification of putative enzymes catalyzing the anaerobic conversion of 2-methylnaphthalene to 2-naphthoyl coenzyme A (2-naphthoyl-CoA), as well as the reductive ring cleavage of 2-naphthoyl-CoA, leading to the formation of acetyl-CoA and CO 2 . The glycyl radical-catalyzed fumarate addition to the methyl group of 2-methylnaphthalene is catalyzed by naphthyl-2-methyl-succinate synthase (Nms), composed of ␣-, ␤-, and ␥-subunits that are encoded by the genes nmsABC. Located upstream of nmsABC is nmsD, encoding the Nms-activating enzyme, which harbors the characteristic [Fe 4 S 4 ] cluster sequence motifs of S-adenosylmethionine radical enzymes. The bns gene cluster, coding for enzymes involved in beta-oxidation reactions converting naphthyl-2-methyl-succinate to 2-naphthoyl-CoA, was found four intervening open reading frames further downstream. This cluster consists of eight genes (bnsABCDEFGH) corresponding to 8.1 kb, which are closely related to genes for enzymes involved in anaerobic toluene degradation within the denitrifiers "Aromatoleum aromaticum" EbN1, Azoarcus sp. strain T, and Thauera aromatica. Another contiguous DNA sequence harbors the gene for 2-naphthoyl-CoA reductase (ncr) and 16 additional genes that were found to be expressed in 2-methylnaphthalene-grown cells. These genes code for enzymes that were supposed to catalyze the dearomatization and ring cleavage reactions converting 2-naphthoyl-CoA to acetylCoA and CO 2 . Comparative sequence analysis of the four encoding subunits (ncrABCD) showed the gene product to have the closest similarity to the Azoarcus type of benzoyl-CoA reductase. The present work provides the first insight into the genetic basis of anaerobic 2-methylnaphthalene metabolism and delivers implications for understanding contaminant degradation.Polycyclic aromatic hydrocarbons (PAHs) are constantly released into the environment by anthropogenic activities such as industrial use or by accidental contamination. Due to the low chemical reactivity caused by the resonance energy of the aromatic ring structure and the low bioavailability of PAHs, they are persistent in the environment (15). The understanding of microbial metabolic capabilities in terms of anaerobic PAH degradation is in its infancy. However, natural amelioration of contaminated sites relies on the degradation capacities of microorganisms, and therefore, it is an essential prerequisite to broaden knowledge about the microorganisms involved and their potentials concerning PAH breakdown.Numerous microorganisms that can degrade PAHs under aerobic conditions have alread...

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Section: Discussionmentioning

confidence: 99%

Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

et al. 2010

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“…(betaproteobacteria) (39,142,224), and Magnetospirillum spp. (alphaproteobacteria) (225,335); in the photosynthetic bacterium R. palustris (alphaproteobacteria) (104); and in the strictly anaerobic Fe(III)-reducing (G. metallireducens) and fermentative (S. aciditrophicus) deltaproteobacteria (237,377). In all these bacteria, benzoate degradation involves a one-step peripheral pathway that activates benzoate to benzoyl-CoA by the action of an ATP-dependent benzoate-CoA ligase ( Fig.…”

Section: Benzoate Catabolism: the Benzoyl-coa Degradation Pathwaymentioning

confidence: 99%

“…The badF, badE, badD, and badG genes encode the ␣␤␥␦ BCR Rp heterotetramer, and these gene products, together with the badB-encoded ferredoxin, show a significant amino acid sequence identity (64 to 76%) with the corresponding bcrA, bcrB, bcrC, bcrD, and fdx gene products from T. aromatica and Magnetospirillum strains (Fig. 2B) (31,39,52,104,142,225,335).…”

Section: Benzoate Catabolism: the Benzoyl-coa Degradation Pathwaymentioning

confidence: 99%

“…As a consequence, the enzymes responsible for the Thauera-type pathway show different substrate specificities compared with those acting on the Rhodopseudomonas-type pathway, and these differences also parallel two different types of catabolic genes. Whereas the Rhodopseudomonas-type genes (badK, badH, and badI) are found only in R. palustris CGA009 (and other recently sequenced Rhodopseudomonas strains) (104), orthologs of the Thauera-type genes (dch, had, and oah) (39) are found in other nitrate-reducing bacteria (e.g., Azoarcus and Magnetospirillum strains) (224,225,293,335) and in Fe(III)-reducing bacteria (Geobacter strains) (48) (Fig. 2B).…”

Section: Benzoate Catabolism: the Benzoyl-coa Degradation Pathwaymentioning

confidence: 99%

“…In T. aromatica, a strong downregulation of the synthesis of BCR Ta was found in response to oxygen, since the protein was immunologically detected only in trace amounts in aerobically grown cells (150). The bss genes, encoding the benzylsuccinate synthase involved in toluene degradation in M. magnetotacticum TS-6, were transcribed only in anaerobically toluene-grown cells (335). However, there are some reports showing that genes encoding oxygen-sensitive enzymes such as BCR (bcr genes) from M. magnetotacticum TS-6 (335) and benzylsuccinate synthase (bss genes) from Thauera sp.…”

Section: Overimposed Regulationmentioning

confidence: 99%

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Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

Carmona

Zamarro

Blázquez

et al. 2009

Microbiol Mol Biol Rev

392

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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A comparative study of bacterial and fungal‐bacterial steady‐state stages of a biofilter in gaseous toluene removal: performance and microbial community

Zhai

Shi

Zhu

et al. 2017

J of Chemical Tech & Biotech

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BACKGROUND Traditional biofilters can lack efficiency in removing hydrophobic volatile organic compounds (VOCs) due to their low gas‐to‐liquid phase transfer rates. The aim of this research was to construct a high‐performance biofilter for toluene removal, compare the degradation performance with that of a traditional biofilter and reveal the relationship between the microbial community and operational performance with different operational parameters. RESULTS The results illustrate that compared with conventional biofilters, the removal efficiency (RE) and the maximum elimination capacity (ECmax) of the high‐performance, fungal and bacterial biofilter (F&B‐BF) increased by 19.6% and 18 g toluene m‐3 h‐1, respectively. The bed pressure drop (ΔP/H) decreased by 1.6 cm H2O m‐1 at an empty bed residence time (EBRT) of 45 s at pH 4.0 and using nitrate (NO3‐) as a nitrogen source. CONCLUSION Low pH values could properly inhibit bacterial growth and progressively allow fungi to predominate in the biofilm. The degrading capabilities of fungi and bacteria were coupled to improve the biofilter performance in toluene removal. Using NO3‐ as the nitrogen source could control the biofilms' overgrowth and reduce the ΔP/H value. The experimental data analysis showed that the fungal genus Phialophora and the bacterial genus Alicyclobacillus played key roles in toluene and phenol degradation, respectively. © 2017 Society of Chemical Industry

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Anaerobic Degradation of Aromatic Compounds byMagnetospirillumStrains: Isolation and Degradation Genes

Cited by 82 publications

References 36 publications

Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

A comparative study of bacterial and fungal‐bacterial steady‐state stages of a biofilter in gaseous toluene removal: performance and microbial community

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