<i>In vitro</i> reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in <i>Rhodococcus jostii</i> RHA1

Yamanashi, Tomoya; Kim, Seung Young; Hara, Hirofumi; Funa, Nobutaka

doi:10.1080/09168451.2014.993915

Cited by 22 publications

(13 citation statements)

References 21 publications

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“…To further interrogate the genomic basis for the ability of BU33N to utilize complex aromatic hydrocarbons, the phenanthrene biodegradation pathway was identified and reconstructed ( Fig 8 ). On the basis of the identified genes, BU33N could be predicted to catabolize phenanthrene via the ortho-cleavage pathway [47, 48] to yield 3-carboxy-cis cis-muconate and subsequently beta-ketoadipate [49] through the β-ketoadipate pathway ( Fig 8 ). Unlike the benzoate degradation pathway described above, the enzymes involved in phenanthrene biodegradation are encoded in different genomic regions and only genes for (EC 1.14.12.10: benzoate 1,2-dioxygenase), (EC 1.3.1.25:1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase), (EC 1.2.1.10: Acetaldehyde dehydrogenase) and (EC 4.1.3.39: 4-hydroxy-2-oxovalerate aldolase) were positioned within the major aromatic compound degradation gene clusters.…”

Section: Resultsmentioning

confidence: 99%

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

Mahjoubi¹,

Aliyu

Cappello

et al. 2019

PLoS ONE

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Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

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Section: Resultsmentioning

confidence: 99%

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

Mahjoubi¹,

Aliyu

Cappello

et al. 2019

PLoS ONE

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“…Catechol is cleaved by catechol 1,2-dioxygenase and protocatechuic acid is cleaved by protocatechuate 3,4-dioxygenase. The two branches converge at the same intermediate, or β-ketoadipate enol-lactone, which acts as feedback inhibitor of dioxygenase activity 13, 39, 11…”

Section: Discussionmentioning

confidence: 99%

Phenol degradation and genotypic analysis of dioxygenase genes in bacteria isolated from sediments

Tian

Zhou

et al. 2017

Brazilian Journal of Microbiology

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The aerobic degradation of aromatic compounds by bacteria is performed by dioxygenases. To show some characteristic patterns of the dioxygenase genotype and its degradation specificities, twenty-nine gram-negative bacterial cultures were obtained from sediment contaminated with phenolic compounds in Wuhan, China. The isolates were phylogenetically diverse and belonged to 10 genera. All 29 gram-negative bacteria were able to utilize phenol, m-dihydroxybenzene and 2-hydroxybenzoic acid as the sole carbon sources, and members of the three primary genera Pseudomonas, Acinetobacter and Alcaligenes were able to grow in the presence of multiple monoaromatic compounds. PCR and DNA sequence analysis were used to detect dioxygenase genes coding for catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and protocatechuate 3,4-dioxygenase. The results showed that there are 4 genotypes; most strains are either PNP (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is positive) or PNN (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is negative). The strains with two dioxygenase genes can usually grow on many more aromatic compounds than strains with one dioxygenase gene. Degradation experiments using a mixed culture representing four bacterial genotypes resulted in the rapid degradation of phenol. Determinations of substrate utilization and phenol degradation revealed their affiliations through dioxygenase genotype data.

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“…As illustrated in Fig. 23 , the degradation of PCA in microbes has been classified into three pathways: 3,4-cleavage [ 224 ], 4,5-cleavage [ 225 ], and 2,3-cleavage [ 226 ]. Although no PCA ring cleavage pathways have been discovered in yeasts, the yeast Arxula adeninivorans converts PCA to catechol via a process catalyzed by Gdc [ 227 ].…”

Section: Pathways For Lignin-based Aromatics Degradation By Yeast Inh...mentioning

confidence: 99%

Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review

Ali

Al-Tohamy

Mohamed

et al. 2022

Biotechnol Biofuels

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Biodiesel is a renewable fuel that can be produced from a range of organic and renewable feedstock including fresh or vegetable oils, animal fats, and oilseed plants. In recent years, the lignin-based aromatic wastes, such as various aromatic waste polymers from agriculture, or organic dye wastewater from textile industry, have attracted much attention in academia, which can be uniquely selected as a potential renewable feedstock for biodiesel product converted by yeast cell factory technology. This current investigation indicated that the highest percentage of lipid accumulation can be achieved as high as 47.25% by an oleaginous yeast strain, Meyerozyma caribbica SSA1654, isolated from a wood-feeding termite gut system, where its synthetic oil conversion ability can reach up to 0.08 (g/l/h) and the fatty acid composition in yeast cells represents over 95% of total fatty acids that are similar to that of vegetable oils. Clearly, the use of oleaginous yeasts, isolated from wood-feeding termites, for synthesizing lipids from aromatics is a clean, efficient, and competitive path to achieve "a sustainable development" towards biodiesel production. However, the lacking of potent oleaginous yeasts to transform lipids from various aromatics, and an unknown metabolic regulation mechanism presented in the natural oleaginous yeast cells are the fundamental challenge we have to face for a potential cell factory development. Under this scope, this review has proposed a novel concept and approach strategy in utilization of oleaginous yeasts as the cell factory to convert aromatic wastes to lipids as the substrate for biodiesel transformation. Therefore, screening robust oleaginous yeast strain(s) from wood-feeding termite gut system with a set of the desirable specific tolerance characteristics is essential. In addition, to reconstruct a desirable metabolic pathway/network to maximize the lipid transformation and accumulation rate from the aromatic wastes with the applications of various “omics” technologies or a synthetic biology approach, where the work agenda will also include to analyze the genome characteristics, to develop a new base mutation gene editing technology, as well as to clarify the influence of the insertion position of aromatic compounds and other biosynthetic pathways in the industrial chassis genome on the expressional level and genome stability. With these unique designs running with a set of the advanced biotech approaches, a novel metabolic pathway using robust oleaginous yeast developed as a cell factory concept can be potentially constructed, integrated and optimized, suggesting that the hypothesis we proposed in utilizing aromatic wastes as a feedstock towards biodiesel product is technically promising and potentially applicable in the near future.

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In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1

Cited by 22 publications

References 21 publications

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

Phenol degradation and genotypic analysis of dioxygenase genes in bacteria isolated from sediments

Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review

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