Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol

Yadid, Itamar; Rudolph, Johannes; Hlouchová, Klára; Copley, Shelley D.

doi:10.1073/pnas.1214052110

Cited by 44 publications

(42 citation statements)

References 55 publications

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“…The lag times reported for PutA enzymes thus far range from no apparent lag to 23 s for E. coli PutA (8,9,11). The longer lag time of the TtPRODH- (50). Thus, our kinetics data provide strong evidence that the TtPRODH-TtP5CDH reaction employs a channeling mechanism and imply a protein-protein complex.…”

Section: Discussionmentioning

confidence: 56%

First Evidence for Substrate Channeling between Proline Catabolic Enzymes

Sanyal

Arentson

Luo

et al. 2015

Journal of Biological Chemistry

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Background: PRODH and P5CDH from Thermus thermophilus are monofunctional enzymes in proline catabolism. Results: Steady-state kinetics and intermediate trapping data show the PRODH and P5CDH reactions are coupled by a channeling step. Conclusion: Substrate channeling in monofunctional enzymes is achieved via weak interactions. Significance: Evidence for substrate channeling between monofunctional proline catabolic enzymes is shown and confirms the Rosetta Stone hypothesis.

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Section: Discussionmentioning

confidence: 56%

First Evidence for Substrate Channeling between Proline Catabolic Enzymes

Sanyal

Arentson

Luo

et al. 2015

Journal of Biological Chemistry

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“…Furthermore, the evidence obtained with these experiments is not sufficient to determine the source of DMBQ. For instance, a benzoquinone has been described as a toxic intermediate in the degradation pathway of pentachlorophenol by Sphingobium chlorophenolicum (39). The decrease in DMBQ concentration observed in experiments with 4-HBA and succinate could be a result of either DMBQ being slowly degraded, or reacting with cellular components as described for tetrachlorobenzoquinone in S. chlorophenolicum (39).…”

Section: Resultsmentioning

confidence: 99%

Anaerobic degradation of syringic acid by an adapted strain ofRhodopseudomonas palustris

Oshlag

Morse

et al. 2019

Preprint

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18While lignin represents a major fraction of the carbon in plant biomass, biological strategies to 19 convert the components of this heterogenous polymer into products of industrial and 20 biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a 21 byproduct of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin 22 streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known 23 degrader of phenolic compounds under photoheterotrophic conditions, via the benzoyl-CoA 24 degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to 25 metabolize meta-methoxylated phenolics such as syringic acid. We isolated a strain of R. palustris 26 (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under 27 photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. 28 An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow 29 on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the 30 BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement 31 of products of the vanARB operon (rpa3619-rpa3621), which has been described as catalyzing 32 aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In 33 addition, experiments with a vanARB deletion mutant demonstrated the involvement of the 34 vanARB operon in anaerobic syringic acid degradation. These observations provide new insights 35 into the anaerobic degradation of meta-methoxylated and other aromatics by R. palustris. 36 IMPORTANCE 37Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually 38 substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological 39 applications. Engineering microorganisms for production of aromatic-based biochemicals requires 40 3 detailed knowledge of metabolic pathways for the degradation of aromatics that are present in 41 lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid 42 degradation reveals a previously unknown metabolic route for aromatic degradation in R. palustris. 43 This study highlights several key features of this pathway and sets the stage for a more complete 44 understanding of the microbial metabolic repertoire to metabolize aromatic compounds from lignin 45 and other renewable sources. 46 48 renewable source of carbon for the bio-based production of compounds that are currently derived 49 from petroleum. Unfortunately, the ability to derive chemicals of commercial, chemical, or 50 medicinal value from lignin is limited by information needed to improve the biological conversion 51 of the aromatics in lignin into valuable products. We are interested in improving our understanding 52 of how bacteria metabolize the aromatic building blocks in lignin and using this information to 53 devel...

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“…81 Pentachlorophenol is a halogenated aromatic pollutant found in several pesticides and disinfectants. 82 Pentachlorophenol hydroxylase (PcpB) is a flavin monooxygenase that catalyzes the first step in pentachlorophenol bioremediation.…”

Section: Evidence Of Natural Enzyme Recruitmentmentioning

confidence: 99%

Enzyme Recruitment and Its Role in Metabolic Expansion

Schulenburg

Miller

2014

Biochemistry

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Although more than 109 years have passed since the existence of the last universal common ancestor, proteins have yet to reach the limits of divergence. As a result, metabolic complexity is ever expanding. Identifying and understanding the mechanisms that drive and limit the divergence of protein sequence space impact not only evolutionary biologists investigating molecular evolution but also synthetic biologists seeking to design useful catalysts and engineer novel metabolic pathways. Investigations over the past 50 years indicate that the recruitment of enzymes for new functions is a key event in the acquisition of new metabolic capacity. In this review, we outline the genetic mechanisms that enable recruitment and summarize the present state of knowledge regarding the functional characteristics of extant catalysts that facilitate recruitment. We also highlight recent examples of enzyme recruitment, both from the historical record provided by phylogenetics and from enzyme evolution experiments. We conclude with a look to the future, which promises fruitful consequences from the convergence of molecular evolutionary theory, laboratory-directed evolution, and synthetic biology.

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Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol

Cited by 44 publications

References 55 publications

First Evidence for Substrate Channeling between Proline Catabolic Enzymes

First Evidence for Substrate Channeling between Proline Catabolic Enzymes

Anaerobic degradation of syringic acid by an adapted strain ofRhodopseudomonas palustris

Enzyme Recruitment and Its Role in Metabolic Expansion

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