Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis

The genome of the methanotrophic bacterium Methylohalobius crimeensis strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the M. crimeensis genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in M. crimeensis was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in M. crimeensis. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The etnE gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to M. crimeensis, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph M. crimeensis, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.

Insights into the unique carboxylation reactions in the metabolism of propylene and acetone

Alkenes and ketones are two classes of ubiquitous, toxic organic compounds in natural environments produced in several biological and anthropogenic processes. In spite of their toxicity, these compounds are utilized as primary carbon and energy sources or are generated as intermediate metabolites in the metabolism of other compounds by many diverse bacteria. The aerobic metabolism of some of the smallest and most volatile of these compounds (propylene, acetone, isopropanol) involves novel carboxylation reactions resulting in a common product acetoacetate. Propylene is metabolized in a four-step pathway involving five enzymes where the penultimate step is a carboxylation reaction catalyzed by a unique disulfide oxidoreductase that couples reductive cleavage of a thioether linkage with carboxylation to produce acetoacetate. The carboxylation of isopropanol begins with conversion to acetone via an alcohol dehydrogenase. Acetone is converted to acetoacetate in a single step by an acetone carboxylase which couples the hydrolysis of MgATP to the activation of both acetone and bicarbonate, generating highly reactive intermediates that are condensed into acetoacetate at a Mn2+ containing the active site. Acetoacetate is then utilized in central metabolism where it is readily converted to acetyl-coenzyme A and subsequently converted into biomass or utilized in energy metabolism via the tricarboxylic acid cycle. This review summarizes recent structural and biochemical findings that have contributed significant insights into the mechanism of these two unique carboxylating enzymes.

Kinetics and effects of trace elements and electron complexes on 2-keto-4-methylthiobutyric acid-dependent biosynthesis of ethylene in soil

AIMS

2-Keto-4-methylthiobutyric acid (KMBA) is an established intermediate in microbial biosynthesis of ethylene from methionine. This study demonstrates the kinetics and effects of trace elements and electron complexes on substrate (KMBA)-derived C2H4 biosynthesis in soil.

METHODS AND RESULTS

We have previously reported KMBA-dependent C2H4 production in soil. We studied the kinetics and effects of various trace elements and electron complexes on KMBA-derived C2H4 biosynthesis in soil by gas chromatography. Kinetic analysis revealed that ethylene forming enzyme (EFE) reaction was linear (R2 = 0.9448) when velocity of reaction (V) was plotted against substrate [S] over the range from 2.5 to 10 mmol l(-1) and thus followed a first order reaction. Application of three linear transformations of the Michaelis-Menten equation indicated high affinity of EFE for the substrate because Km values ranged between 5.4 and 6.67 mmol l(-1) and Vmax of reaction was between 22.4 and 35.7 nmol kg(-1) soil 120 cm(-1). Most of the trace elements exhibited positive effects on KMBA-dependent C2H4 production in soil. Maximum stimulatory effect on C2H4 biosynthesis was observed in response to Co(II) application, while Fe(III) inhibited the biotransformation of KMBA into C2H4. Contrarily, most of the tested electron complexes inhibited KMBA-derived C2H4 biosynthesis in the soil. However, lower concentrations (1.0 mmol l(-1)) of mannitol and hydroquinone were stimulatory to C2H4 production in soil compared with controls (substrate only).

CONCLUSIONS

The results revealed that both kind and concentration of trace elements and electron complexes affected the substrate-dependent production of C2H4 in soil with different degrees of efficacy.

SIGNIFICANCE AND IMPACT OF THE STUDY

The C2H4 in the root environment could be physiologically active even at low concentrations, so knowledge regarding various factors which regulate C2H4 biosynthesis in soil could be of significance for plant growth and development.

Microbial species associated with different sections of broccoli harvested from three regions in Australia

The microbial populations associated with the different sections of broccoli harvested from three locations in Australia were studied during storage at 5, 15 and 20 degrees C. Bacterial and yeast populations associated with the outer florets and cut surfaces of the stem were generally 10-fold or more higher than those associated with inner florets or non-cut stems, respectively. The predominating bacterial species varied with the origin of the broccoli. Pseudomonas fluorescens, Ps. corrugata and Ps. viridiflava predominated at populations of 10(5)-10(7) cfu/g on broccoli harvested from Victoria, Ps. fluorescens, Ps. mendocina and Ps. fragii and Arthrobacter spp. (10(-3) 10(6) cfu/g) were prevalent on broccoli harvested from Queensland. Broccoli harvested from New South Wales exhibited a predominance of Ps. fluorescens, Arthrobacter spp. and Enterobacteragglomerans (10(3)-10(5) cfu/g). Most species grew on broccoli during storage. Similar species were found at the different sections of broccoli, although, for some species there was evidence of strain variation at the different locations and for different temperature of storage.

Influence of Ethylene Produced by Soil Microorganisms on Etiolated Pea Seedlings

There is indirect evidence that soil microorganisms producing ethylene (C 2 H 4 ) can influence plant growth and development, but unequivocal proof is lacking in the literature. A laboratory study was conducted to demonstrate the validity of this speculation. Four experiments were carried out to observe the characteristic “triple” response of etiolated pea seedlings to C 2 H 4 microbially derived from l -methionine as a substrate in the presence or absence of Ag(I), a potent inhibitor of C 2 H 4 action. In two experiments, the combination of l -methionine and Acremonium falciforme (as an inoculum) was used, while in another study the indigenous soil microflora was responsible for C 2 H 4 production. A standardized experiment was conducted with C 2 H 4 gas to compare the contribution of the microflora to plant growth. In all cases, etiolated pea seedlings exhibited the classical triple response, which includes reduction in elongation, swelling of the hypocotyl, and a change in the direction of growth (horizontal). The presence of Ag(I) afforded protection to the pea seedlings against the microbially derived C 2 H 4 . This study demonstrates that microbially produced C 2 H 4 in soil can influence plant growth.

Oxidation of Gaseous and Volatile Hydrocarbons by Selected Alkene-Utilizing Bacteria

Eleven strains of alkene-utilizing bacteria belonging to the genera Mycobacterium, Nocardia, and Xanthobacter were tested for their ability to grow with C 1 to C 6 alkanes, C 2 to C 6 alkenes, alkadienes, and monoterpenes furnished individually as sole sources of carbon and energy in a mineral salts medium. A limited number of alkenes and alkanes supported growth of the bacteria; some bacteria were unable to grow on any of the saturated hydrocarbons tested. Monoterpenes were frequently used as carbon and energy sources by alkene-utilizing bacteria belonging to the genera Mycobacterium and Nocardia. Washed cell suspensions of alkene-grown bacteria attacked the whole range of alkenes tested, whereas only three strains were able to oxidize alkanes as well. The alkenes tested were oxidized either to water and carbon dioxide or to epoxyalkanes. Few epoxides accumulated in stoichiometric amounts from the corresponding alkenes, because most epoxides formed were further converted to other compounds like alkanediols.

Ethylene formation by cell-free extracts of Escherichia coli

The pathway leading to the formation of ethylene as a secondary metabolite from methionine by Escherichia coli strain B SPAO has been investigated. Methionine was converted to 2-oxo-4-methylthiobutyric acid (KMBA) by a soluble transaminase enzyme. 2-Hydroxy-4-methylthiobutyric acid (HMBA) was also a product, but is probably not an intermediate in the ethylene-forming pathway. KMBA was converted to ethylene, methanethiol and probably carbon dioxide by a soluble enzyme system requiring the presence of NAD(P)H, Fe3+ chelated to EDTA, and oxygen. In the absence of added NAD(P)H, ethylene formation by cell-free extracts from KMBA was stimulated by glucose. The transaminase enzyme may allow the amino group to be salvaged from methionine as a source of nitrogen for growth. As in the plant system, ethylene produced by E. coli was derived from the C-3 and C-4 atoms of methionine, but the pathway of formation was different. It seems possible that ethylene production by bacteria might generally occur via the route seen in E. coli.

Ethylene formation by cultures of Escherichia coli

Growth of Escherichia coli strain B SPAO on a medium containing glucose, NH4Cl and methionine resulted in production of ethylene into the culture headspace. When methionine was excluded from the medium there was little formation of ethylene. Ethylene formation in methionine-containing medium occurred for a brief period at the end of exponential growth. Ethylene formation was stimulated by increasing the medium concentration of Fe3+ when it was chelated to EDTA. Lowering the medium phosphate concentration also appeared to stimulate ethylene formation. Ethylene formation was inhibited in cultures where NH4Cl remained in the stationary phase. Synthesis of the ethylene-forming enzyme system was determined by harvesting bacteria at various stages of growth and assaying the capacity of the bacteria to form ethylene from methionine. Ethylene forming capacity was greatest in cultures harvested immediately before and during the period of optimal ethylene formation. It is concluded that ethylene production by E. coli exhibits the typical properties of secondary metabolism.