Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications

Ma, Qiao; Qu, Yuanyuan; Zhang, Zhaojing; Li, Pengpeng; Tang, Hongzhi

doi:10.1128/genomea.00102-15

Cited by 11 publications

(12 citation statements)

References 12 publications

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“…However, indigoid accumulation is a limitation that prevents the use of such microorganisms to remove the smell of indole in situ. Therefore, bacteria capable of utilizing indole as the sole carbon source [95] would provide a better means of completely mineralizing indole so that they can be used in bioremediation of animal and industrial wastes.…”

Section: Roles Of Indole In Plants Insects and The Soil Environmentmentioning

confidence: 99%

Roles of Indole as an Interspecies and Interkingdom Signaling Molecule

Lee

Wood

2015

Trends in Microbiology

414

298

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Section: Roles Of Indole In Plants Insects and The Soil Environmentmentioning

confidence: 99%

Roles of Indole as an Interspecies and Interkingdom Signaling Molecule

Lee

Wood

2015

Trends in Microbiology

414

298

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“…Several bacteria have acquired the capability to degrade indole in natural environments, yet the molecular mechanisms of the degradation process have not been documented (Arora and Bae, ; Arora et al ., ). Compared to the versatile aromatic degraders Pseudomonas and Comamonas , Cupriavidus strains exhibit relatively higher indole degradation efficiency (Ma et al ., ; Qu et al ., ). The work presented herein is the deepest molecular‐level study on indole biodegradation.…”

Section: Discussionmentioning

confidence: 99%

“…For example, we previously isolated another Cupriavidus sp. strain IDO (Ma et al ., ), which could degrade indole more efficiently than strain SHE. However, the functional genes and molecular mechanisms for indole metabolism in strain IDO remained totally unclear.…”

Section: Discussionmentioning

confidence: 99%

“…S1). Alcaligenes (Claus and Kutzner, ; Kim et al ., ), Pseudomonas (Doukyu and Aono, ; Yin et al ., ) and Cupriavidus (Fukuoka et al ., ; Ma et al ., ) are the most extensively investigated indole‐degrading bacterial genera that can use indole as a sole carbon source. Some species, such as Agrobacterium tumefaciens (Lee et al ., ), Pseudomonas aeruginosa , (Lee et al ., ) and Burkholderia unamae (Kim et al ., ), can also degrade indole in the presence of other carbon sources.…”

Section: Introductionmentioning

confidence: 99%

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Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain

Liu

et al. 2017

Molecular Microbiology

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Indole, an important signaling molecule as well as a typical N-heterocyclic aromatic pollutant, is widespread in nature. However, the biotransformation mechanisms of indole are still poorly studied. Here, we sought to unlock the genetic determinants of indole biotransformation in strain Cupriavidus sp. SHE based on genomics, proteomics and functional studies. A total of 177 proteins were notably altered (118 up- and 59 downregulated) in cells grown in indole mineral salt medium when compared with that in sodium citrate medium. RT-qPCR and gene knockout assays demonstrated that an indole oxygenase gene cluster was responsible for the indole upstream metabolism. A functional indole oxygenase, termed IndA, was identified in the cluster, and its catalytic efficiency was higher than those of previously reported indole oxidation enzymes. Furthermore, the indole downstream metabolism was found to proceed via the atypical CoA-thioester pathway rather than conventional gentisate and salicylate pathways. This unusual pathway was catalyzed by a conserved 2-aminobenzoyl-CoA gene cluster, among which the 2-aminobenzoyl-CoA ligase initiated anthranilate transformation. This study unveils the genetic determinants of indole biotransformation and will provide new insights into our understanding of indole biodegradation in natural environments and its functional studies.

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“…In multispecies communities, many non-indole-producing bacteria can transform indole into downstream metabolites, whereas the indole transformation pathways are poorly concerned. Furthermore, indole also belongs to the typical N-heterocyclic pollutants [4]. It is abundant in coking wastewater influents, which may harm microbes, plants, and animals.…”

Section: Introductionmentioning

confidence: 99%

Indigoids Biosynthesis from Indole by Two Phenol-Degrading Strains, Pseudomonas sp. PI1 and Acinetobacter sp. PI2

Wang

Zhang

Fan

et al. 2015

Appl Biochem Biotechnol

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In this study, two phenol-degrading bacterial strains, designated as PI1 and PI2, were isolated from activated sludge for the production of indigoids from indole. According to the 16S ribosomal RNA (rRNA) gene sequence analysis, strains PI1 and PI2 were identified as Pseudomonas sp. and Acinetobacter sp., respectively. Liquid chromatography/time-of-flight/mass spectrometry (LC/TOF/MS) was applied to analyze the metabolites during the biotransformation of indole by the phenol-degrading strains. The results indicated that both strains could catalyze the formation of four indigoids with the same prominent molecular ion (M-H)(-) peak at m/z 261.067 and molecular formula of C16H10N2O2, including indigo and a purple product, 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one. Isatin and 7-hydroxyindole were detected as the intermediates. Thus, the possible pathways for the production of indigoids from indole were proposed. Subsequently, the optimal conditions for the production of indigo from indole were determined using response surface methodology, and 11.82 ± 0.30 and 17.19 ± 0.49 mg/L indigo were produced by strains PI1 and PI2, respectively. The present study should provide potential candidates for microbial production of indigoids.

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Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications

Cited by 11 publications

References 12 publications

Roles of Indole as an Interspecies and Interkingdom Signaling Molecule

Roles of Indole as an Interspecies and Interkingdom Signaling Molecule

Unveiling the biotransformation mechanism of indole in a Cupriavidus sp. strain

Indigoids Biosynthesis from Indole by Two Phenol-Degrading Strains, Pseudomonas sp. PI1 and Acinetobacter sp. PI2

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