Substrate specificity of the paraffin hydroxylase of Pseudomonas aeruginosa

Structure and Function of Alkane Monooxygenase (AlkB)

Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.

Structure and mechanism of the alkane-oxidizing enzyme AlkB

Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms.

Investigation of the prevalence and catalytic activity of rubredoxin-fused alkane monooxygenases (AlkBs)

Interest in understanding the environmental distribution of the alkane monooxygenase (AlkB) enzyme led to the identification of over 100 distinct alkane monooxygenase (AlkB) enzymes containing a covalently bound, or fused, rubredoxin. The rubredoxin-fused AlkB from Dietzia cinnamea was cloned as a full-length protein and as a truncated protein with the rubredoxin domain deleted. A point mutation (V91W) was introduced into the full-length protein, with the goal of assessing how steric bulk in the putative substrate channel might affect selectivity. Based on activity studies with alkane and alkene substrates, the rubredoxin-fused AlkB oxidizes a similar range of alkane substrates relative to its rubredoxin domain-deletion counterpart. Oxidation of terminal alkenes generated both an epoxide and a terminal aldehyde. The products of V91W-mutant-catalyzed oxidation of alkenes had a higher aldehyde-to-epoxide ratio than the products formed in the presence of the wild type protein. These results are consistent with this mutation causing a structural change impacting substrate positioning.

Fungal biotransformation of short-chain n-alkylcycloalkanes

The cycloalkanes, comprising up to 45% of the hydrocarbon fraction, occur in crude oil or refined oil products (e.g., gasoline) mainly as alkylated cyclohexane derivatives and have been increasingly found in environmental samples of soil and water. Furthermore, short-chain alkylated cycloalkanes are components of the so-called volatile organic compounds (VOCs). This study highlights the biotransformation of methyl- and ethylcyclohexane by the alkane-assimilating yeast Candida maltosa and the phenol- and benzoate-utilizing yeast Trichosporon mucoides under laboratory conditions. In the course of this biotransformation, we detected 25 different metabolites, which were analyzed by HPLC and GC-MS. The biotransformation process of methylcyclohexane in both yeasts involve (A) ring hydroxylation at different positions (C2, C3, and C4) and subsequent oxidation to ketones as well as (B) oxidation of the alkyl side chain to hydroxylated and acid products. The yeast T. mucoides additionally performs ring hydroxylation at the C1-position and (C) oxidative decarboxylation and (D) aromatization of cyclohexanecarboxylic acid. Both yeasts also oxidized the saturated ring system and the side chain of ethylcyclohexane. However, the cyclohexylacetic acid, which was formed, seemed not to be substrate for aromatization. This is the first report of several new transformation reactions of alkylated cycloalkanes for eukaryotic microorganisms.

Oxidation of gasoline oxygenates by closely related non-haem-iron alkane hydroxylases in Pseudomonas mendocina KR1 and other n-octane-utilizing Pseudomonas strains

Pseudomonas mendocina KR1 oxidizes the gasoline oxygenate methyl tertiary butyl ether (MTBE) to tertiary butyl alcohol (TBA) during growth on C5 -C8 n-alkanes. We have further explored oxidation of ether oxygenates by this strain to help identify the enzyme that catalyses these reactions. High levels of MTBE-oxidizing activity occurred in resting cells grown on C5 -C8 n-alkanes. Lower activities occurred in cells grown on longer-chain n-alkanes (C9 -C11 ) and 1°-alcohols (C5 -C10 ). N-octane-grown cells also oxidized tertiary amyl methyl ether (TAME) to tertiary amyl alcohol (TAA), but did not oxidize ethyl tertiary butyl ether (ETBE), TBA or TAA. A 39 kDa polypeptide in whole cell extracts of n-octane-grown cells strongly cross-reacted with an anti-AlkB polyclonal antiserum in an SDS-PAGE/immunoblot. This polypeptide was absent or less abundant in cells grown on dextrose, dextrose plus dicyclopropylketone or 1-octanol. N-octane-grown cells of Pseudomonas aeruginosa strains KSLA-473 and ATCC 17423 oxidized MTBE and TAME but not ETBE. N-hexadecane-grown cells of these strains and strain PAO1 did not oxidize any of the oxygenates tested. Our results indicate ether oxygenate-degrading activity in alkane-utilizing pseudomonads is consistently observed with close homologues of the GPo1 non-haem-iron alkane hydroxylases but is otherwise not a consistent catalytic feature of these diverse enzymes.

Mechanisms of membrane toxicity of hydrocarbons

Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.

Genetics of alkane oxidation by Pseudomonas oleovorans

Many Pseudomonads are able to use linear alkanes as sole carbon and energy source. The genetics and enzymology of alkane metabolism have been investigated in depth for Pseudomonas oleovorans, which is able to oxidize C5-C12 n-alkanes by virtue of two gene regions, localized on the OCT-plasmid. The so-called alk-genes have been cloned in pLAFR1, and were subsequent analyzed using minicell expression experiments, DNA sequencing and deletion analysis. This has led to the identification and characterization of of the alkBFGHJKL and alkST genes which encode all proteins necessary to convert alkanes to the corresponding acyl-CoA derivatives. These then enter the beta-oxidation-cycle, and can be utilized as carbon- and energy sources. Medium (C6-C12)- or long-chain (C13-C20) n-alkanes can be utilized by many strains, some of which have been partially characterized. The alkane-oxidizing enzymes used by some of these strains (e.g. two P. aeruginosa strains, a P. denitrificans strain and a marine Pseudomonas sp.) appear to be closely related to those encoded by the OCT-plasmid.

Microbial degradation and assimilation of n-alkyl-substituted cycloparaffins

Studies were conducted on the oxidation and assimilation of n-alkyl-substituted cycloalkane substrates by several hydrocarbon-utilizing microorganisms. These microorganisms utilized heptadecylcyclohexane and dodecylcyclohexane as the sole source of carbon and energy. Neither methylcyclohexane nor ethylcyclohexane was utilized as a growth substrate by any organisms tested. Gas-liquid chromatographic analyses of fatty acids present in cells after growth on dodecylcyclohexane confirm direct incorporation of both alpha- and beta-oxidation products. Growth patterns of these organisms on n-alkyl-substituted cyclohexane fatty acids of varying chain lengths suggest a greater probability of ring cleavage when the side chain contains an odd number of carbons.