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Microbial Monoterpene Transformations—A Review

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Microbial Monoterpene Transformations—A Review REVIEW ARTICLE published: 15 July 2014 doi: 10.3389/fmicb.2014.00346 Microbial monoterpene transformations—a review Robert Marmulla and Jens Harder* Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany Edited by: Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Colin Murrell, University of East Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These Anglia, UK natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, Reviewed by: abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms Terry John McGenity, University of Essex, UK encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and Andrew Crombie, University of East on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds Anglia, UK can serve as carbon and energy source for aerobic and anaerobic microorganisms. *Correspondence: Besides these catabolic reactions, transformations may occur as part of detoxification Jens Harder, Max Planck Institute processes. Initial transformations of monoterpenes involve the introduction of functional for Marine Microbiology, Celsiusstr. 1, Bremen 28359, Germany groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. e-mail: [email protected] Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge. Keywords: isoprenoids, acyclic monoterpene utilization, camphor, pinene, limonene, linalool, myrcene, eucalyptol INTRODUCTION citrus plants are the major source of limonene. Flowers, however, Annually about 120 Pg of carbon dioxide are assimilated by produce and emit a variety of oxygenated monoterpenes (e.g. plants. A part is transformed into chemically complex molecules linalool) (Kesselmeier and Staudt, 1999 and references therein, and released into the environment by emission or excretion Sharkey and Yeh, 2001; Bicas et al., 2009). (Ghirardo et al., 2011). Volatile organic compounds (VOCs) In the atmosphere, monoterpenes are transformed in purely comprise a large number of molecules, including various hydro- chemical reactions within hours. Photolysis and reactions with carbons, single carbon compounds (e.g. methane), isoprene and molecular oxygen, ozone, hydroxyl radicals, NOx species, and terpenes (e.g. mono- and sesquiterpenes). The atmosphere is chlorine atoms result in carbonyls, alcohols, esters, halogenated loaded with an estimated VOC emission rate of about 1150 Tg hydrocarbons, and peroxynitrates. These products condense and Cyr−1 (Stotzky and Schenck, 1976; Guenther et al., 1995; lead to the formation of secondary aerosols. Rain or precipita- Atkinson and Arey, 2003). These estimates included only non- tion transports them to soils (Atkinson and Arey, 2003; Fu et al., methane VOCs of biogenic origin (BVOCs); a second source 2009; Ziemann and Atkinson, 2012). Monoterpenes reach the sur- are anthropogenic VOCs. Among the BVOCs, isoprene and face layers of soils by leaf fall and excreted resins. Also roots emit monoterpenes dominate with estimated emission rates of about monoterpenes into the rhizosphere (Wilt et al., 1993; Kainulainen 500 Tg C yr−1 and 127 Tg C yr−1,respectively(Guenther et al., and Holopainen, 2002). Deeper soil layers do contain significant 1995). Monoterpenes (C10H16) consist of two linked isoprene less monoterpenes than the surface soil layer. Emission into the (C5H8) units and include in the strict sense only hydrocarbons. atmosphere and biotransformations in the surface layer mainly by Often the term monoterpene is applied including monoter- microorganisms are the major sinks. An alternative, abiotic pho- penoids which are characterized by oxygen-containing func- toreactions like in the atmosphere, is limited by light availability tional groups. Structural isomers—acyclic, mono-, and bicyclic in soil (Kainulainen and Holopainen, 2002; Insam and Seewald, monoterpenes—, stereoisomers as well as a variety of substi- 2010). tutions result in a large diversity of molecules. Today, more Bacteria encountering monoterpenes have to deal with their than 55,000 different isoprenoids are known (Ajikumar et al., toxic effects (reviewed by Bakkali et al., 2008). In order to pre- 2008). Monoterpenes are not only emitted as cooling substances vent the accumulation of monoterpenes in the cell and cyto- (Sharkey et al., 2008), but can also be stored intracellularly serv- plasmatic membrane, bacteria modify their membrane lipids, ing mainly as deterrent or infochemical (Dudareva et al., 2013). transform monoterpenes and use active transport by efflux Wood plants mainly accumulate pinene and other pure hydro- pumps (Papadopoulos et al., 2008; Martinez et al., 2009). Below carbon monoterpenes as constituents of their resins, whereas toxic concentrations monoterpenes are used by microorganisms www.frontiersin.org July 2014 | Volume 5 | Article 346 | 1 Marmulla and Harder Enzymes and microorganisms transforming monoterpenes as sole carbon and energy source. The mineralization of the pathways were rarely disclosed. More important for the mainte- hydrocarbons requires the introduction of functional groups to nance of our knowledge, only a small portion of the investigated access beta-oxidation like fragmentation reactions yielding cen- strains were deposited in culture collections. Without detailed tral metabolites, e.g. acetyl-CoA. In many aerobic microorgan- knowledge of genes or the availability of strains, the observa- isms molecular oxygen serves as reactive agent to functional- tions of biotransformation experiments are of limited value for ize the monoterpenes (Figure 1). Strains of Pseudomonas and future studies. Therefore, this review on the transformation of Rhodococcus have become model organisms for the elucidation of monoterpenes focusses on enzymes for which the gene and pro- pathways in aerobic bacteria. Nearly 40 years after the first reports tein sequences are available in public databases as well as on on aerobic mineralization (Seubert, 1960; Seubert and Fass, 1964; microorganisms that at least have been deposited in a public Dhavalikar and Bhattacharyya, 1966; Dhavalikar et al., 1966), culture collection and ideally are validly described (Table 1). A the mineralization of monoterpenes in denitrifying bacteria and broad overview on microbial biotransformations is also provided methanogenic communities was discovered (Harder and Probian, byanumberofolderreviewarticles(Trudgill, 1990, 1994; van 1995; Harder and Foss, 1999). Betaproteobacterial strains of the der Werf et al., 1997; Hylemon and Harder, 1998; Duetz et al., genera Castellaniella and Thauera are the study objects for the elu- 2003; Ishida, 2005; Li et al., 2006; Bicas et al., 2009; Li and Lan, cidation of anaerobic pathways. All these bacteria were obtained 2011; Schewe et al., 2011; Tong, 2013). KEGG and MetaCyc, two in single-fed batch enrichments with high substrate concentra- widely used reference datasets of metabolic pathways (reviewed by tions (mmol∗L−1), in contrast to low concentrations in nature Altman et al., 2013), include degradation pathways of limonene, (μmol∗L−1). Consequently, in batch enrichments isolated strains pinene, geraniol, and citronellol. Single reactions of p-cymene exhibit often a solvent tolerance; they grow in the presence of and p-cumate degradation are covered. MetaCyc additionally a pure monoterpene phase. Cultivation was rarely attempted covers the metabolism of myrcene, camphor, eucalyptol, and by physical separation followed by single-fed batch cultivations. carveol. Such dilution-to-extinction series performed in replicates—also known as most-probable-number (MPN) method—revealed a BICYCLIC MONOTERPENES frequent presence of the degradative capacities in natural popu- (+)-Camphor [1, Figure 2](C10H16O) is the substrate of lations: denitrifying communities in sewage sludge and forest soil one of the first and best described monoterpene transform- yielded 106–107 monoterpene-utilizing cells ml−1, representing ingenzymes,aspecificcytochromeP450monooxygenase(cam- 0.7–100% of the total cultivable nitrate-reducing microorganisms ABC, P450cam, EC 1.14.15.1) from Pseudomonas putida (ATCC (Harder et al., 2000). MPN cultivations for aerobic bacteria have 17453). Initially, (+)-camphor is hydroxylated. The resulting not been reported so far, and for both cases the highly abun- 5-exo-hydroxycamphor [2] is oxidized by a NAD-reducing dehy- dant bacteria with the capacity to grow on monoterpenes have drogenase (EC 1.1.1.327) which gene camD is part of the operon not been identified. camDCAB. The diketone is oxidized in a Baeyer–Villiger like Over the last 50 years, many monoterpene transformations oxidation to a lactone, either by a 2,5-diketocamphane 1,2- have been reported for microbial cultures, but the biochemical monooxygenase or a 3,6-diketocamphane 1,6-monooxygenase FIGURE 1 | Selected monoterpene transformations. (A) (+)-camphor
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