Properties of ω-cyclohexane fatty acids in membranes

Precursor-Directed Biosynthesis and Biological Testing of omega-Alicyclic- and neo-Branched Tunicamycin N-Acyl Variants

Tunicamycins (TUNs) are Streptomyces-derived natural products, widely used to block protein N-glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the N-acyl chain length and terminal branching pattern. A small molecule screen of fatty acid biosynthetic primers identified several novel alicyclic- and neo-branched TUN N-acyl variants, with primer incorporation at the terminal omega-acyl position. TUNs with unique 5- and 6-carbon ω-cycloalkane and ω-cycloalkene acyl chains are produced under fermentation and in yields comparable with the native TUN. The purification, structural assignments, and the comparable antimicrobial properties of 15 of these compounds are reported, greatly extending the structural diversity of this class of compounds for potential medicinal and agricultural applications.

Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park

Introduction

Alicyclobacillus has been isolated from extreme environments such as hot springs, volcanoes, as well as pasteurized acidic beverages, because it can tolerate extreme temperatures and acidity. In our previous study, Alicyclobacillus was isolated during the enrichment of methane oxidizing bacteria from Yellowstone Hot Spring samples.

Methods

Physiological characterization and genomic exploration of two new Alicyclobacillus isolates, AL01A and AL05G, are the main focus of this study to identify their potential relationships with a thermoacidophilic methanotroph (Methylacidiphilum) isolated from the same hot spring sediments.

Results and discussion

In the present study, both Alicyclobacillus isolates showed optimal growth at pH 3.5 and 55°C, and contain ω-alicyclic fatty acids as a major lipid (ca. 60%) in the bacterial membrane. Genomic analysis of these strains revealed specific genes and pathways that the methanotroph genome does not have in the intermediary carbon metabolism pathway such as serC (phosphoserine aminotransferase), comA (phosphosulfolactate synthase), and DAK (glycerone kinase). Both Alicyclobacillus strains were also found to contain transporter systems for extracellular sulfate (ABC transporter), suggesting that they could play an important role in sulfur metabolism in this extreme environment. Genomic analysis of vitamin metabolism revealed Alicyclobacillus and Methylacidiphilum are able to complement each other's nutritional deficiencies, resulting in a mutually beneficial relationship, especially in vitamin B1(thiamin), B3 (niacin), and B7 (biotin) metabolism. These findings provide insights into the role of Alicyclobacillus isolates in geothermal environments and their unique metabolic adaptations to these environments.

Inactivation efficacy and mechanisms of atmospheric cold plasma on Alicyclobacillus acidoterrestris: Insight into the influence of growth temperature on survival

The bactericidal effect of dielectric barrier discharge-atmospheric cold plasma (DBD-ACP, 20, and 30 kV) against Alicyclobacillus acidoterrestris on the saline solution and apple juice was investigated. Results show that DBD-ACP is effective for the inactivation of A. acidoterrestris by causing significant changes in cell membrane permeability and bacterial morphology. The effect of culture temperatures on the resistance of A. acidoterrestris to DBD-ACP was also studied. A. acidoterrestris cells grown at 25°C had the lowest resistance but it was gradually increased as the culture temperature was increased (25–45°C) (p < 0.05). Moreover, results from Fourier transform infrared spectroscopy (FT-IR) and Gas Chromatography-Mass Spectrometer (GC-MS) analysis showed that the increase in the culture temperature can gradually cause the decreased level of cyclohexaneundecanoic acid in the cell membrane of A. acidoterrestris (p < 0.05). In contrast, cyclopentaneundecanoic acid, palmitic acid, and stearic acid showed an increasing trend in which the fluidity of the bacterial cell membrane decreased. This study shows a specific correlation between the resistance of A. acidoterrestris and the fatty acid composition of the cell membrane to DBD-ACP.

Preparation of species-specific monoclonal antibody and development of fluorescence immunoassay based on fluorescence resonance energy transfer of carbon dots for accurate and sensitive detection of Alicyclobacillus acidoterrestris in apple juice

The growth and metabolism of Alicyclobacillus acidoterrestris can lead to the spoilage of commercial fruit juice. Existing methods have some drawbacks such as complex sample pretreatment, skilled technician requirement, reduced sensitivity and specificity. Herein, a novel fluorescence immunoassay was developed using a monoclonal antibody (mAb) against A. acidoterrestris as the sensing element and carbon dots (CDs) as the signal response unit. The CDs can be quenched via fluorescence resonance energy transfer (FRET) by the oxidization product of p-phenylenediamine (PPD), a chromogenic substrate of horseradish peroxidase (HRP). This approach showed enhanced accuracy and sensitivity with relatively low limit of detection (LOD) of 6.16 × 10² CFU mL^-1. Moreover, apple juice contaminated with 1 CFU mL^-1 of A. acidoterrestris can be identified after 24 h enrichment. This fluorescence immunoassay could serve as a powerful tool for laboratory identification and on-site inspection of A. acidoterrestris, reducing the adverse effect on the quality of fruit juice.

Heat resistance and genomics of spoilage Alicyclobacillus spp. Isolated from fruit juice and fruit-based beverages

Alicyclobacillus acidoterrestris is a spore-forming bacterium of importance to the fruit juice industry due to its remarkable heat resistance and production of guaiacol taint. Whole genome sequencing analysis reveals species demarcation corresponds to the two major genotypic groups to which A. acidoterrestris isolates belong. Heat resistance was significantly different between genotypic groups 1 and 2 with D₉₀ values of 15.5 and 9.3 min, respectively (p < 0.01). Comparison of squalene-hopene cyclase (shc) encoding sequences reveals non-synonymous changes and the alteration of glutamine residues. Glutamine absence may link to the stability reinforcement of the enzyme structure against thermal denaturation. Genomic islands harbouring heavy metal resistance genes are found in the majority of genotypic group 1 genomes (63%) but occurs in only one genome (5%) of genotypic group 2. Distribution of the genomic islands in the genotypic groups 1 and 2 is also consistent with phylogenetic trees and ANI and dDDH values. Subsequently, we propose genotypic group 1 as a new species closely related to A. acidoterrestris that possesses enhanced heat resistance.

Effect of Ring Size in ω-Alicyclic Fatty Acids on the Structural and Dynamical Properties Associated with Fluidity in Lipid Bilayers

Fatty acids containing a terminal cyclic group such as cyclohexyl and cycloheptyl are commonly found in prokaryotic membranes, especially in those of thermo-acidophilic bacteria. These so-called ω-alicyclic fatty acids have been proposed to stabilize the membranes of bacteria by reducing the fluidity in membranes and increasing lipid packing and lipid chain order. In this article, molecular dynamics simulations are used to examine the effect of 3- to 7-membered cycloalkyl saturated and unsaturated (cyclopent-2-enyl and phenyl) rings in ω-alicyclic fatty acyl chains on the structure (lipid packing, lipid chain order, and fraction of gauche defects in the chains) and dynamics (lateral lipid diffusion) of a model lipid bilayer. It was found that ω-alicyclic chains in which the ring was saturated reduced lipid condensation and lowered chain order which would be associated with enhanced fluidity. However, this effect was limited. The lateral diffusion of the lipids diminished as the ring size increased. In particular, ω-cyclohexyl and ω-cycloheptyl acyl tails led to a decrease in lipid diffusion. In contrast, ω-alicyclic acyl chains that contain an unsaturated ring promoted membrane fluidity both in terms of changes in membrane structure and lipid diffusion. This may indicate that saturated and unsaturated terminal rings in ω-alicyclic fatty acids fulfill alternative functions within membranes. Overall, the simulations suggest that ω-alicyclic fatty acids in which the terminal ring is saturated might protect the membrane of thermo-acidophilic bacteria from high-temperature and low-pH conditions through a "dynamical barrier" that would limit lipid diffusion and transmembrane diffusion of undesired ions and molecules.

Alicyclobacillus spp.: New Insights on Ecology and Preserving Food Quality through New Approaches

Alicyclobacillus spp. includes spore-forming and thermo-acidophilic microorganisms, usually recovered from soil, acidic drinks, orchards and equipment from juice producers. The description of the genus is generally based on the presence of ω-fatty acids in the membrane, although some newly described species do not possess them. The genus includes different species and sub-species, but A. acidoterrestris is generally regarded as the most important spoiler for acidic drinks and juices. The main goal of this review is a focus on the ecology of the genus, mainly on the species A. acidoterrestris, with a special emphasis on the different phenotypic properties and genetic traits, along with the correlation among them and with the primary source of isolation. Finally, the last section of the review reports on some alternative approaches to heat treatments (natural compounds and other chemical treatments) to control and/or reduce the contamination of food by Alicyclobacillus.

Pivalic acid acts as a starter unit in a fatty acid and antibiotic biosynthetic pathway in Alicyclobacillus, Rhodococcus and Streptomyces

A biosynthetic pathway using pivalic acid as a starter unit was found in three bacterial species, Alicyclobacillus acidoterrestris, Rhodococcus erythropolis and Streptomyces avermitilis. When deuterium-labelled pivalic acid was added to A. acidoterrestris and R. erythropolis nutrient media it was incorporated into fatty acids to give rise to tert-butyl fatty acids (t-FAs). In addition, in R. erythropolis, pivalic acid was transformed into two starter units, i.e. isobutyric and 2-methylbutyric acid, which served as precursors of corresponding iso-even FAs and anteiso-FAs. In S. avermitilis the biosynthesis also yielded all three branched FAs; apart from this pathway, both pivalic and 2-methylbutyric acids were incorporated into the antibiotic avermectin.

Alicyclobacillusspp. in the Fruit Juice Industry: History, Characteristics, and Current Isolation/Detection Procedures

The first Alicyclobacillus spp. was isolated in 1982, and was originally thought to be strictly limited to thermophilic and acidic environments. Two years later, another Alicyclobacillus sp., A. acidoterrestris, was identified as the causative agent in spoilage of commercially pasteurized apple juice. Subsequent studies soon found that Alicyclobacillus spp. are soilborne bacteria, and do not strictly require thermophilic and acidic environments. Alicyclobacillus spp. posess several distinct characteristics; the major one is their ability to survive commercial pasteurization processes and produce off-flavors in fruit juices. The fruit juice industry has acknowledged Alicyclobacillus spp. as a major quality control target microorganism. Guaiacol and halophenols were identified as the offensive smelling agent in many Alicyclobacillus spp. related spoilage. Though the exact formation pathway of these off-flavors by Alicyclobacillus spp. are not yet identified, studies report that the presence of Alicyclobacillus spp. in the medium may be a major contributor to the formation of these off-flavors. Many identification methods and isolation media were developed in the last two decades. However, most of these methods were developed specifically for A. acidoterrestris, which was the first identified off-flavor producing Alicyclobacillus. However, recent studies indicate that other species of Alicyclobacillus may also produce guaiacol or the halophenols. In this respect, all Alicyclobacillus spp. should be monitored as potential spoilage bacteria in fruit juices. This article includes an overall review of the history of Alicyclobacillus spp., characteristics, suggested off-flavor production pathways, and commonly used identification methods for the currently identified Alicyclobacillus spp.

Combined treatment of high pressure and heat on killing spores of Alicyclobacillus acidoterrestris in apple juice concentrate

Alicyclobacillus acidoterrestris, a thermoacidophilic and spore-forming bacterium, has been isolated from spoiled acidic juices and is considered to be one of the important target microorganisms in quality control of acidic canned foods. Combined high pressure and heat treatment showed an effectiveness to control A. acidoterrestris spores. However, the effectiveness of the combined treatment may change upon the apple juice concentration. Therefore, the objective of this study was to evaluate different levels of apple juice concentrate for reduction of Alicyclobacillus spores by high pressure and heat. Spores of A. acidoterrestris were inoculated into three different concentrations of apple juice (17.5, 35, and 70 degrees Brix), and subjected to three high-pressure treatments (207, 414, and 621 MPa) at four different temperatures (22, 45, 71, and 90 degrees C). High-pressure treatment (207, 414, and 621 MPa) at 22degrees C did not reduce the level of spores regardless of the apple juice concentration (P > 0.05). In diluted apple juice (17.5 degrees Brix), the combined treatment of high pressure and heat resulted in spore reductions of about 2 log at 45 degrees C, and more than 5 log at higher temperatures (71 and 90 degrees C) in a high-pressure and temperature-dependent manner. For apple juice with a higher concentration (30 degrees Brix), high-pressure treatment showed no effect at 45 degrees C but resulted in about 2 and 4 log reduction at 71 and 90 degrees C, respectively. However, for apple juice concentrate (70 degrees Brix), treatment with heat or high pressure alone, or their combinations showed no inactivation against spores of A. acidoterrestris. It is likely that differences in the water availability explain the greater resistance of spores to high-pressure inactivation in the juice concentrates than in diluted juices. Our results demonstrate that the effect of high pressure combined with heat against spores of A. acidoterrestris was highly dependent on the apple juice concentration.

Origin, occurrence, and biodegradation of long-side-chain alkyl compounds in the environment: a review

Long-side-chain alkyl compounds, such as those present in oil and oil products, either of natural or of anthropogenic origin or released by industrial activities, are a ubiquitous group of chemicals in the environment. Among them, long-side-chain alkylmonocycloalkanes, alkylbenzenes, and alkyl organic sulfur compounds are largely found in fossil fuels while long-side-chain alkylbenzene sulfonates and alkylphenols are released into the environment primarily due to domestic activities. The present article briefly summarizes the advances that have occurred in this field in terms of the identity, abundance, possible origin and significance of these long-side-chain alkyl compounds found in the environment. In addition, the susceptibility to biodegradation and the fate of these chemicals in the environment are discussed.

Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess omega-alicyclic fatty acids, and emended description of the genus Alicyclobacillus

A thermo-acidophilic endospore-forming bacterium was isolated from a mixed fruit juice. The organism, strain 3A(T), was rod-shaped, grew aerobically at 30-60 degrees C (optimum 45-50 degrees C), pH 3.0-6.0 (optimum pH 4.0-4.5) and produced acid from various sugars. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the DNA was 53.1 mol%. The predominant cellular fatty acids of the strain were iso-C(15 : 0), anteiso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0), but omega-alicyclic fatty acids, which are characteristic of the genus Alicyclobacillus, were not found in the strain. Phylogenetic analyses based on both 16S rRNA and gyrB (DNA gyrase B subunit gene) gene sequences showed that strain 3A(T) falls into the Alicyclobacillus cluster, validated by significant bootstrap values. However, strain 3A(T) did not show a close relationship to the other species of the cluster. The level of 16S rDNA similarity between strain 3A(T) and other strains of the cluster was between 92.5 and 95.5 %. The level of gyrB sequence similarity between strain 3A(T) and other strains of the cluster was between 68.5 and 74.4 %. DNA-DNA hybridization values between strain 3A(T) and phylogenetically related strains of the genera Alicyclobacillus, Bacillus and Sulfobacillus were under 13 %, indicating that strain 3A(T) represents a distinct species. On the basis of these results, strain 3A(T) should be classified as a novel Alicyclobacillus species. The name Alicyclobacillus pomorum is proposed for this organism. The type strain of Alicyclobacillus pomorum is strain 3A(T) (=DSM 14955(T)=IAM 14988(T)).

Properties of unusual phospholipids: I. Synthesis, monolayer investigations and calorimetry of diacylglycerophosphocholines containing monoacetylenic acyl chains

Isomeric diacylglycerophosphocholines containing various octadecynoic acids (4-, 6-, 9-, 12-, 14- and 17-octadecynoic acid) were synthesized and purified to homogeneity. Their behaviour in monolayers, when studied by the Langmuir-Blodgett film balance technique, revealed systematic relationships between structure and packing properties. The thermotropic phase behaviour of these novel phospholipids, as measured by differential scanning calorimetry, depended in a systematic fashion on the position of the triple bond: the gel-to-liquid-crystalline phase transition temperature (Tm) passed through a minimum of -3.4 degrees C for a triple bond in position 9.

The effect of hydrostatic pressure on the bilayer structure of phosphatidylcholines containing omega-cyclohexyl fatty acyl chains

The barotropic behavior of aqueous dispersions of two representative omega-cyclohexyl phosphatidylcholines was investigated by pressure-tuning Fourier transform infrared spectroscopy. In the even-numbered homologue, 1,2-di-14-cyclohexyltetradecanoyl-sn-glycero-3-phosphocholine (14cyPC), the lipid molecules are orientationally disordered until the applied pressure reaches 2.1 kbar. This pressure marks the onset of correlation field splitting of the scissoring and rocking modes of the linear chain methylenes, as well as that of the cyclohexyl ring methylenes. It indicates immobilization of the entire acyl chains, whereby the zig-zag planes of the neighboring straight chain all-trans methylenes are oriented mainly perpendicular to each other. As judged from the magnitude of the correlation field splittings, the interchain interaction is weaker in 14cyPC than that in linear lipids (e.g., DMPC or DPPC). Upon an increase in pressure, up to 20 kbar, the zig-zag methylene planes in 14cyPC undergo a gradual transformation to a parallel orientation. In the odd-numbered homologue, 1,2-di-13-cyclohexyltridecanoyl-sn-glycero-3-phosphocholine (13cyPC), there is no correlation field splitting originating from the straight chain methylenes (up to 21 kbar). The linear, nonbranched segments of the omega-cyclohexyl chains in 13cyPC are closely packed with the all-trans methylene zig-zag planes oriented parallel to each other. There is, however, correlation field splitting of the ring methylenes, indicating interring interactions between the bulky cyclohexyl rings in opposing bilayer leaflets. There are major structural differences between the even- and odd-numbered homologues in the interfacial region, which remain even at high pressures. The ester carbonyl C = O stretching band in 14cyPC is a composite of two discrete bands which do not change considerably in intensity or frequency in the pressure range 2-20 kbar. In contrast, 13cyPC possesses an additional, low-frequency C = O stretching component at low pressures. As the pressure increases, the three component bands coalesce into a single C = O stretching band. Our results suggest equally oriented, fully hydrogen-bonded carbonyl groups in 13cyPC at pressures above approx. 10 kbar.

An infrared spectroscopic study of the thermotropic phase behavior of phosphatidylcholines containing omega-cyclohexyl fatty acyl chains

The thermotropic phase behavior of an odd- and an even-numbered member of the homologous series of 1,2-di-omega-cyclohexylphosphatidylcholines was studied using Fourier transform infrared spectroscopy. The results obtained indicate that the pronounced discontinuities in the behavior of the odd- and even-numbered homologues observed by differential scanning calorimetry can be attributed to differences in the organization of their respective gel states. The single phase transition exhibited by the odd-numbered compounds upon heating is shown by infrared spectroscopy to be a direct transition from a condensed, subgel-like phase (Lc phase) to the liquid-crystalline state (L alpha phase). In contrast, the multiple transitions exhibited by the even-numbered homologues are shown to be due to the initial conversion of an L beta-like phase to a more loosely packed gel phase, followed by the acyl chain-melting transition. Moreover, the major changes in the interaction between the acyl chains, and in the organization of the interfacial region of the bilayers formed by the even-numbered homologue, occur at temperatures below that of the onset of the chain-melting phase transition. The infrared spectroscopic changes observed also suggest that above the chain-melting transition, the odd- and even-numbered homologues form similar liquid-crystalline phases that are more 'ordered' than those of normal saturated straight-chain phosphatidylcholines. Most likely this is because the large size and the intrinsic rigidity of the omega-cyclohexyl group reduces the conformational disorder of the liquid-crystalline state by 'dampening' all acyl chain motions. The formation of a relatively ordered liquid-crystalline state may be the critical property exploited by the thermoacidophylic organisms in which omega-cyclohexyl fatty acids naturally occur.

Thermotropic phase behavior of model membranes composed of phosphatidylcholines containing omega-cyclohexyl fatty acids. Differential scanning calorimetric and 31P NMR spectroscopic studies

The thermotropic phase behavior of aqueous dispersions of 10 phosphatidylcholines containing omega-cyclohexyl-substituted acyl chains was studied by differential scanning calorimetry and 31P nuclear magnetic resonance spectroscopy. The presence of the omega-cyclohexyl group has a profound effect on the thermotropic phase behavior of these compounds in a manner dependent on whether the fatty acyl chains have odd- or even-numbered linear carbon segments. The thermotropic phase behavior of the odd-numbered phosphatidylcholines is characterized by a single heating endotherm that was shown to be a superposition of at least two structural events by calorimetric cooling experiments. 31P NMR spectroscopy also showed that the single endotherm of the odd-chain compounds is the structural equivalent of a concomitant gel-gel and gel to liquid-crystalline phase transition. The calorimetric behavior of the even-numbered phosphatidylcholines is characterized by a complex array of gel-state phenomena, in addition to the chain-melting transition, in both the heating and cooling modes. The gel states of these even-numbered compounds are characterized by a relatively greater mobility of the phosphate head group as seen by 31P NMR spectroscopy. The differences between the odd-numbered and even-numbered compounds are reflected in a pronounced odd-even alternation in the characteristic transition temperatures and enthalpies and in differences in their responses to changes in the composition of the bulk aqueous phase. Moreover, both the odd-numbered and even-numbered omega-cyclohexylphosphatidylcholines exhibit significantly lower chain-melting transition temperatures and enthalpies than do linear saturated phosphatidylcholines of comparable chain length.(ABSTRACT TRUNCATED AT 250 WORDS)