Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins

Background

The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions.

Results

In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B₁₂- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone.

Conclusions

We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.     

7a-O-methyldeguelol, a modified rotenoid with an open ring-C, from the roots of Derris trifoliata

From the acetone extract of the roots of Derris trifoliata an isoflavonoid derivative, named 7a-O-methyldeguelol, a modified rotenoid with an open ring-C, representing a new sub-class of isoflavonoids (the sub-class is here named as rotenoloid), was isolated and characterised. In addition, the known rotenoids, rotenone, deguelin and alpha-toxicarol, were identified. The structures were determined on the basis of spectroscopic evidence. Rotenone and deguelin were identified as the larvicidal principles of the acetone extract of the roots of Derris trifoliata.     

Analysis of bacterial polyhydroxybutyrate production by multimodal nanoimaging

In this paper, we will employ two microscopy techniques, transmission electron microscopy and infrared nanospectromicroscopy, to study the production of polyhydroxybutyrate in Rhodobacter capsulatus and to evaluate the influence of glucose and acetone on the production yield. The results overlap which leads us to a consistent conclusion, highlighting that each technique brings specific and complementary information. By using electron microscopy and infrared nanospectromicroscopy we have proved that both glucose and acetone had a positive effect on the biopolymer production, although the first study done by Fourier transform infrared spectroscopy only identified the effect of acetone. In conclusion, we have now established a method to be able to perform fast diagnostic for PHB production.     

Antifeedant neo-clerodanes from Teucrium tomentosum Heyne. (Labiatae)

From the acetone extract of Teucrium tomentosum, a new antifeedant neo-clerodane diterpenoid teuctosin (1) was isolated along with teuflin (2), teucrin-H(2) (3), 6beta-hydroxyteuscordin (4), 6beta-acetylteuscordin (5) and montanin-D (6). The structure of the new compound was elucidated comprehensively using 1D and 2D NMR methods and confirmed by X-ray crystallography. All the compounds showed effective antifeedancy against Plutella xylostella and Spodoptera litura at 10 mug/cm(2) of leaf area.     

Acetophenone C-glucosides and stilbene O-glucosides in Upuna borneensis

Three acetophenone C-glycosides; 2,4,6-trihydroxyacetophenone 3-C-beta-(2'-O-p-hydroxybenzoyl)-glucopyranoside, 2,4,6-trihydroxyacetophenone 3-C-beta-(2'-O-E-coumaroyl)-glucopyranoside, 2,4,6-trihydroxyacetophenone 3-C-beta-(2'-O-E-cinnamoyl)-glucopyranoside, and two resveratrol O-glycosides; piceid 2'-O-p-hydroxybenzoate and, piceid 2'-O-E-ferulate, together with three known compounds were isolated from the acetone soluble part of stem of Upuna borneensis (Dipterocarpaceae). The structures of isolates were determined by spectral analysis including extensive 2D-NMR spectral analyses.     

Preparation and characterization of mucilage polysaccharide for biomedical applications

In the present investigation, the polysaccharide/mucilage from waste of Abelmoscus esculentus by modification in hot extraction using two different solvents (Acetone, Methanol) were extracted, characterized and further compared with seaweed polysaccharide for their potential applications. The percentage yield, emulsifying capacity and swelling index of this mucilage were determined. The macro algae and okra waste, gave high % yield (22.2% and 8.6% respectively) and good emulsifying capacity (EC% = 52.38% and 54.76% respectively) with acetone, compared to methanol (11.3% and 0.28%; EC% = 50%) (PH = 7) while swelling index was greater with methanol than acetone extracts respectively. The infrared (I.R.) spectrum of the samples was recorded to investigate the chemical structure of mucilage. Thermal analysis of the mucilage was done with TGA (Thermal Gravimetric Analyzer) and DSC (Differential Scanning Calorimeter) which showed both okra and algal polysaccharide were thermostable hydrogels.     

neo-Clerodane diterpenoids from Baccharis flabellata

Three diterpenoid derivatives were isolated from the acetone extract of Baccharis flabellata. Their structures were elucidated as 2,19;15,16-diepoxy-neo-clerodan-3,13(16),14-trien-18-oic acid, 15,16-epoxy-5,10-seco-clerodan-1(10),2,4,13(16),14-pentaen-18,19-olide and 15,16-epoxy-neo-clerodan-1,3,13(16),14-tetraen-18,19-olide through spectroscopic analyses.     

Aryltetralone lignans and 7,8-seco-lignans from Holostylis reniformis

Aryltetralone lignans and two 7,8-seco-lignans were isolated from the acetone and hexane extracts of the roots of Holostylis reniformis, together with (-)-galbacin. Their structures were determined by spectroscopic methods.     

Xanthones and benzophenones from Garcinia griffithii and Garcinia mangostana

A new polyisoprenylated benzophenone, guttiferone I, together with the known compounds cambogin, 1,7-dihydroxyxanthone, 1,3,6,7-tetrahydroxyxanthone and 1,3,5,6-tetrahydroxyxanthone were isolated from the stem bark of Garcinia griffithii. The acetone extract of the heartwood of Garcinia mangostana contained one new diprenylated xanthone (mangoxanthone) and a new benzophenone (3',6-dihydroxy-2,4,4'-trimethoxybenzophenone) as well as the known xanthones dulxanthone D, 1,3,7-trihydroxy-2-methoxyxanthone, 1,3,5-trihydroxy-13,13-dimethyl-2H-pyran[7,6-b]xanthen-9-one. Their structures were established on the basis of spectroscopic studies and chemical correlation.     

Stilbenoids from the stem of Gnetum latifolium (Gnetaceae)

An acetone extract of the stem of Gnetum latifolium Blume afforded the stilbene trimer (latifolol) together with five known stilbenoids (gnetin E, gnetin D, gnetin C, (-)epsilon -viniferin and resveratrol). Their structures were elucidated on the basis of spectral evidence, in particular by using 2D NMR methods.     

A simple method for the extraction and quantification of photopigments from Symbiodinium spp.

We have developed a simple, mild extraction procedure using methanol which, when coupled with HPLC analysis and diode array detection (DAD), can be used to quantify the major photopigments found in cultured Symbiodinium spp. Extracts were prepared by suspending, fresh or frozen (− 70 °C), wet cell pellets in methanol and sonicating or not sonicating the cell suspensions before soaking the cells for 2 h in an ice bath. To assist the soaking process, cell suspensions were vortex mixed at 30 min intervals. After soaking, 0.5 M ammonium acetate buffer was added (1 part buffer to 9 parts methanol) before suspensions were stored over night at − 20 °C. Greater than 92% the recoverable pigment was obtained in the initial extraction of the four major photopigments, chlorophyll c, peridinin, diadinoxanthin, and chlorophyll a. Neither sonication nor freezing substantially increased the recovery of photopigments extracted with methanol. Extraction by other commonly used solvents such as acetone or acetone:water with or without freezing and sonication were less effective.     

Free radical scavenging activity,total phenolic content,total antioxidant status,and total oxidant status of endemic Thermopsis turcica

Thermopsis turcica, endemic to Turkey, is in danger of extinction. Studies on this species are very few due to the fact that it was only discovered in 1983 and grows in a small circumscribed area in Turkey. In this study, free radical scavenging activity, total phenolic content, total oxidant status (TOS), and total antioxidant status (TAS) of methanol (TTM) and acetone (TTA) extracts of T. turcica were measured spectroscopically. Free radical scavenging activity was determined according to the elimination of DPPH radicals and total phenol content was determined by the Folin–Ciocalteu reaction. Total oxidant status (TOS) and total antioxidant status (TAS) were measured with commercially available kits. Methanol and acetone extracts of T. turcica were found to have a specific radical scavenging effect. This effect was found to be related to the total phenolic content of the extracts. Since the TTA had a higher phenolic content than the methanol extract, it had a stronger radical scavenging effect. In addition, the total antioxidant capacity of the methanol extract was observed to be higher than that of its acetone counterpart. As a result, due to its antioxidative properties, T. turcica is thought to be a natural source of antioxidants.     

A Nematicide Seed Treatment to Control Ditylenchus dipsaci on Seedling Alfalfa

Three nematicides were evaluated as seed treatments to control the alfalfa stem nematode (Ditylenchus dipsaci) on seedling alfalfa. Alfalfa seeds were soaked for 10 hours in a 0.5% (formulated by weight) concentration of either carbofuran, phenamiphos or oxamyl in acetone with no adverse effect on seed germination. All three treatments decreased nematode damage and increased survival of ''Ranger'' (susceptible) and ''Lahontan'' (resistant) alfalfa plants, when seeds were planted in soil infested with D. dipsaci. Mean live plant counts after 6 weeks in the untreated control, acetone alone, carbofuran, phenamiphos, and oxamyl treatments, respectively, were 4.3, 6.3, 19.0, 19.8, and 19.0 for Lahontan and 4.5, 1.5, 18.5, 19.3, and 18.0 for Ranger from 20 seeds/pot. Nematicide seed treatments resulted in significantly healthier Ranger alfalfa plants 4 months after planting. The combination of seed treatment and host resistance may provide a means of establishing alfalfa in an alfalfa monocropped system where soil populations of D. dipsaci are high.     

New 4-methylated and 19-oxygenated steroids from the Formosan soft coral Nephthea erecta

Two new 4-methylated steroids, erectasteroids A and B (1 and 2), six new 19-oxygenated steroids, erectasteroids C-H (3-8) and two known 19-oxygenated steroids (9 and 10) were isolated from the acetone solubles of the Formosan soft coral Nephthea erecta. The structures were elucidated by extensive NMR spectroscopic analysis and their cytotoxicity against selected cancer cells was measured in vitro.     

Typhaphthalide and typharin,two phenolic compounds from Typha capensis

Two new phenolics, named typhaphthalide (a benzylphthalide) and typharin (an isocoumarin) plus sitosterol were isolated and identified from the hexane extract of the rhizomes of Typha capensis. The acetone extract yielded afzelechin, epiafzelechin, and catechin.     

Insect-antifeedant and antibacterial activity of diterpenoids from species of Plectranthus

Bio-assay guided fractionation of an acetone extract of leaf material from Plectranthus saccatus Benth. resulted in the isolation of a beyerane diterpenoid. This compound, characterised by spectroscopic methods as ent-3beta-(3-methyl-2-butenoyl)oxy-15-beyeren-19-oic acid, showed insect antifeedant activity against Spodoptera littoralis. Known quinonoid abietane diterpenoids obtained from new sources included a mixture of the (4R,19R) and (4R,19S) diastereoisomers of coleon A from P. aff. puberulentus J.K. Morton, coleon A lactone from P. puberulentus J.K. Morton, and coleon U and coleon U quinone from P. forsteri 'Marginatus' Benth. These compounds, and the crude acetone extracts from the leaf surfaces of 11 species of Plectranthus, were tested for antifeedant activity against S. littoralis, antibacterial activity against Bacillus subtilis and Pseudomonas syringae and antifungal activity against Cladosporium herbarum. The coleon A mixture showed potent antifeedant activity against S. littoralis, whereas coleon U showed the greatest antimicrobial activity.     

Two labdane diterpenoids and a seco-tetranortriterpenoid from Turreanthus africanus

Examination of the methylene chloride soluble portion of the acetone extract of the seeds of Turreanthus africanus yielded two labdane diterpenoids 12,15-epoxylabda-8(17),12,14-trien-16-al (1) and 16-acetoxy-12(R),15-epoxy-15beta-hydroxylabda-8(17),13(16)-diene (2) and a limonoid, 17-epi 12-dehydroxyheudebolin (3). Structures elucidation was based on the analysis of spectroscopic data.     

Stilbene derivatives from Gnetum gnemon Linn

Four stilbene derivatives, gnemonols K and L (resveratrol trimers), M (isorhapontigenin dimer), and gnemonoside K (glucoside of resveratrol trimer) together with eleven known stilbenoids and a lignan were isolated from the acetone, methanol and 70% methanol soluble parts of the root of Gnetum gnemon (Gnetaceae). The structures of the isolates were determined by spectral analysis. The antioxidant activity of the stilbenoids on lipid peroxide inhibition and super oxide scavenging activity were also investigated.     

Tetrahydroisoquinoline alkaloids and 2-deoxyribonolactones from Aristolochia arcuata

2-Deoxyribonolactones and four tetrahydroisoquinoline alkaloids were isolated from the acetone extract of the leaves of Aristolochia arcuata Mast., together with pinitol, sequoyitol, glycerol, fructose, sucrose, eupomatenoid-7, salsolinol, and 6,7-dihydroxy-1,1-dimethyl-1,2,3,4-tetrahydroisoquinoline. Their structures were determined on the basis of spectroscopic methods, mainly using 1H, 13C, 15N, and 31P NMR.     

Diterpene esters of aristolochic acids from Aristolochia pubescens

From the acetone and ethanol extracts of the tubercula of Aristolochia pubescens, two diterpene esters of aristolochic acids were isolated, together with 23 known compounds. The structures of the compounds were determined on the basis of spectroscopic analysis.