Evolution of Genes for the β-Ketoadipate Pathway in Acinetobacter Calcoaceticus

Ornston, L N; Neidle, Ellen L.

doi:10.1007/978-1-4899-3553-3_15

Cited by 29 publications

(25 citation statements)

References 74 publications

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“…1) (17,26). Many compounds are degraded by this route, each converted to either protocatechuate or catechol, both of which serve as the substrates of ring-cleaving dioxygenases.…”

mentioning

confidence: 99%

“…A. calcoaceticus produces two sets of isozymes to metabolize this common intermediate. During growth with compounds that are metabolized to catechol, enzymes encoded by the catDIJF genes are induced by cis,cis-muconate (6,26). Protocatechuate induces the isofunctional enzymes encoded by the pcaDIJF genes needed for the catabolism of compounds converted to protocatechuate (6,26).…”

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confidence: 99%

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Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acinetobacter calcoaceticus

Gaines¹,

Smith²,

Neidle³

1996

J Bacteriol

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Novel nuclear magnetic resonance spectroscopy techniques, designated metabolic observation, were used to study aromatic compound degradation by the soil bacterium Acinetobacter calcoaceticus. Bacteria which had been rendered spectroscopically invisible by growth with deuterated ( 2 H) medium were used to inoculate cultures in which natural-abundance 1 H hydrogen isotopes were provided solely by aromatic carbon sources in an otherwise 2 H medium. Samples taken during the incubation of these cultures were analyzed by proton nuclear magnetic resonance spectroscopy, and proton signals were correlated with the corresponding aromatic compounds or their metabolic descendants. This approach allowed the identification and quantitation of metabolites which accumulated during growth. This in vivo metabolic monitoring facilitated studies of catabolism in the presence of multiple carbon sources, a topic about which relatively little is known. A. calcoaceticus initiates aromatic compound dissimilation by forming catechol or protocatechuate from a variety of substrates. Degradation proceeds via the ␤-ketoadipate pathway, comprising two discrete branches that convert catechol or protocatechuate to tricarboxylic acid cycle intermediates. As shown below, when provided with several carbon sources simultaneously, all degraded via the ␤-ketoadipate pathway, A. calcoaceticus preferentially degraded specific compounds. For example, benzoate, degraded via the catechol branch, was consumed in preference to p-hydroxybenzoate, degraded via the protocatechuate branch, when both compounds were present. To determine if this preference were governed by metabolites unique to catechol degradation, pathway mutants were constructed. Studies of these mutants indicated that the product of catechol ring cleavage, cis,cis-muconate, inhibited the utilization of p-hydroxybenzoate in the presence of benzoate. The accumulation of high levels of cis,cis-muconate also appeared to be toxic to the cells.Despite extensive research on bacterial hydrocarbon metabolism, little is known about how the presence of multiple carbon sources influences the degradation of an individual compound. In these studies, a new nuclear magnetic resonance (NMR) spectroscopy technique was used to monitor the catabolism of aromatic compound mixtures by the soil bacterium Acinetobacter calcoaceticus. This technique, designated metabolic observation NMR (MO-NMR), is based on the principle that NMR spectrometers will not detect deuterated ( 2 H) compounds when tuned to proton ( 1 H) frequencies (11,14,20,32). As described in this report, A. calcoaceticus was grown in fully deuterated medium, thereby rendering the bacterial cultures spectroscopically invisible. Mixtures of 1 H aromatic compounds were added to the deuterated cultures as sources of carbon and energy, and samples were taken at specific times. NMR spectra of the samples were used to monitor the metabolic fates of the 1 H compounds over time; these spectra provided information about the identity and the accumulation of meta...

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“…1) (17,26). Many compounds are degraded by this route, each converted to either protocatechuate or catechol, both of which serve as the substrates of ring-cleaving dioxygenases.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acinetobacter calcoaceticus

Gaines¹,

Smith²,

Neidle³

1996

J Bacteriol

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“…The basis for the selection is unknown. Remarkable enrichment of the exceptional arginyl codons is also found in other xyl genes from the TOL plasmid pWW0 (10,12,13,19,33 (25)(26)(27)(28)(29). According to this view, the genetic basis for the formation and the conservation of the DNA slippage structures is mismatch repair between the hybridizing regions (16,18 Fig.…”

Section: Resultsmentioning

confidence: 94%

“…In contrast, genes for such isofunctional enzymes have diverged substantially, as indicated by differences in G+C content of about 15% (9,20,27). Such differences in G+C content may be attributed in part to directional pressure exerted by mutations within divergent cell lines (32).…”

mentioning

confidence: 99%

“…Such differences in G+C content may be attributed in part to directional pressure exerted by mutations within divergent cell lines (32). In addition, selection for cognate tRNAs characteristic of the host (1,11) appears to have contributed to divergence of the G+C content in DNA because genes from either A. calcoaceticus or P. putida tend to possess a pattern of codon usage that is similar to that of other genes from closely related organisms (27,35).…”

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Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

et al. 1991

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The xylXYZ DNA region is carried on the TOL pWW0 plasmid in Pseudomonas putida and encodes a benzoate dioxygenase with broad substrate specificity. The DNA sequence of the region is presented and compared with benABC, the chromosomal region encoding the benzoate dioxygenase of Acinetobacter calcoaceticus. Corresponding genes from the two biological sources share common ancestry: comparison of aligned XylX-BenA, XylY-BenB, and XylZ-BenC amino acid sequences revealed respective identities of 58.3, 61.3, and 53%. The aligned genes have diverged to assume G+C contents that differ by 14.0 to 14.9%. Usage of the unusual arginine codons AGA and AGG appears to have been selected in the P. putida xylX gene as it diverged from the ancestor it shared with A. calcoaceticus benA. Homologous A. calcoaceticus and P. putida genes exhibit different patterns of DNA sequence repetition, and analysis of one such pattern suggests that mutations creating different DNA slippage structures made a significant contribution to the evolutionary divergence of xylX.

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AcinetobacterandMoraxella

Riley¹

2010

Topley &Amp; Wilson's Microbiology and Microbial Infections

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Evolution of Genes for the β-Ketoadipate Pathway in Acinetobacter Calcoaceticus

Cited by 29 publications

References 74 publications

Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acinetobacter calcoaceticus

Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acinetobacter calcoaceticus

Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

AcinetobacterandMoraxella

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