Bacterial Growth on Halogenated Aliphatic Hydrocarbons: Genetics and Biochemistry

Janssen, Dick B.; Oppentocht, Jantien E.; Poelarends, Gerrit J.

doi:10.1007/0-306-48011-5_7

Cited by 2 publications

(3 citation statements)

References 61 publications

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“…Some interesting groups of enzymes without specific physiological role are also encoded in the genome of this bacterium: (i) Bacterial dehalogenases are important in the metabolism of diverse halogenated compounds originated from natural and anthropogenic sources [33] , [34] , and some representatives of different kinds of dehalogenases seem to be encoded in the genome of strain JMP134. They include homologs of the hydrolytic (S)-2-haloacid dehalogenase (Reut_A1952 and Reut_B5662) and a reductive dehalogenase belonging to glutathione S-transferase (GST) superfamily (Reut_C5979), probably involved in dechlorination of 2-chloro-5-nitrophenol [19] .…”

Section: Resultsmentioning

confidence: 99%

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

et al. 2010

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Background Cupriavidus necator JMP134 is a Gram-negative β-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.Methodology/Principal FindingsIts genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of “specialized” plasmids.Conclusions/SignificanceThe availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.

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Section: Resultsmentioning

confidence: 99%

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

et al. 2010

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“…In other microorganisms, an enzyme-catalyzed reaction generates an unstable product, which decomposes to release the halide. These dehalogenases and so-called “accidental dehalogenases” display a variety of catalytic strategies ( , ).…”

Section: Discussionmentioning

confidence: 99%

“…CaaD was proposed to be a hydrolytic dehalogenase, which was substantiated by the finding that CaaD catalyzes the hydration of 2-oxo-3-pentynoate ( 6 , Scheme ) to afford acetopyruvate ( 7 ) (). However, a covalent enzyme−substrate intermediate, observed for some haloaliphatic and haloaromatic dehalogenases ( , ), was not favored on the basis of the sequence analysis. Hence, the proposed mechanism for CaaD likely involves the formation of an unstable halohydrin species ( 3 , Scheme ), which collapses to produce malonate semialdehyde ( 5 ) ( , ).…”

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Cloning, Expression, and Characterization of a cis-3-Chloroacrylic Acid Dehalogenase: Insights into the Mechanistic, Structural, and Evolutionary Relationship between Isomer-Specific 3-Chloroacrylic Acid Dehalogenases

Poelarends¹,

Serrano²,

Person³

et al. 2003

Biochemistry

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The gene encoding the cis-3-chloroacrylic acid dehalogenase (cis-CaaD) from coryneform bacterium strain FG41 has been cloned and overexpressed, and the enzyme has been purified to homogeneity and subjected to kinetic and mechanistic characterization. Kinetic studies show that cis-CaaD processes cis-3-haloacrylates, but not trans-3-haloacrylates, with a turnover number of approximately 10 s(-1). The product of the reaction is malonate semialdehyde, which was confirmed by its characteristic 1H NMR spectrum. The enzyme shares low but significant sequence similarity with the previously studied trans-3-chloroacrylic acid dehalogenase (CaaD) and with other members of the 4-oxalocrotonate tautomerase (4-OT) family. While 4-OT and CaaD function as homo- and heterohexamers, respectively, cis-CaaD appears to be a homotrimeric protein as assessed by gel filtration chromatography. On the basis of the known three-dimensional structures and reaction mechanisms of CaaD and 4-OT, a sequence alignment implicated Pro-1, Arg-70, Arg-73, and Glu-114 as important active-site residues in cis-CaaD. Subsequent site-directed mutagenesis experiments confirmed these predictions. The acetylene compounds, 2-oxo-3-pentynoate and 3-bromo- and 3-chloropropiolate, were processed by cis-CaaD to products consistent with an enzyme-catalyzed hydration reaction previously established for CaaD. Hydration of 2-oxo-3-pentynoate afforded acetopyruvate, while the 3-halopropiolates became irreversible inhibitors that modified Pro-1. The results of this work revealed that cis-CaaD and CaaD have different primary and quaternary structures, and display different substrate specificity and catalytic efficiencies, but likely share a highly conserved catalytic mechanism. The mechanism may have evolved independently because sequence analysis indicates that cis-CaaD is not a 4-OT family member, but represents the first characterized member of a new family in the tautomerase superfamily that probably resulted from an independent duplication of a 4-OT-like sequence. The discovery of a fifth family of enzymes within this superfamily further demonstrates the diversity of activities and structures that can be created from 4-OT-like sequences.

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Bacterial Growth on Halogenated Aliphatic Hydrocarbons: Genetics and Biochemistry

Cited by 2 publications

References 61 publications

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Cloning, Expression, and Characterization of a cis-3-Chloroacrylic Acid Dehalogenase: Insights into the Mechanistic, Structural, and Evolutionary Relationship between Isomer-Specific 3-Chloroacrylic Acid Dehalogenases

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