Genome sequence of Streptomyces sp. strain Tü6071

Streptomyces sp. Tü6071 is a soil-dwelling bacterium which has a highly active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anticancer agents, e.g., landomycin. Streptomyces sp. Tü6071 produces the industrially important terpene glycosides phenalinolactones, which have antibacterial activity against several Gram-positive bacteria. The availability of the genome sequence of Streptomyces sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.     

Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005T

“Burkholderia sprentiae” strain WSM5005^T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N₂-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of “Burkholderia sprentiae” strain WSM5005^T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.     

Metabolism of 18β-glycyrrhetinic acid in Sphingomonas paucimobilis strain G5

Seven strains capable of utilizing 18-glycyrrhetinic acid (18-GRA) as a sole carbon and energy source were isolated from soil samples by enrichment culture technique. One of these strains, named strain G5, was identified as Sphingomonas paucimobilis. When this strain grew on 18-GRA, several metabolites were detected in the culture broth. A major metabolite, tentatively named M-A, was isolated and its chemical structure was determined by nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS).     

Microbial transformation of 18β-glycyrrhetinic acid by Sphingomonas paucimobilis strain G5

The effects of the oxygenase inhibitors, 1-aminobenzotriazole (ABT), ketoconazole, metyrapone and proadifen, on the metabolism of 18-glycyrrhetinic acid (18-GRA) in Sphingomonas paucimobilis strain G5 were investigated. Strain G5 transformed 18-GRA into a major new metabolite (M-D) in the presence of 1 mM ABT or metyrapone. M-D was purified and identified as 3-hydroxy-11-oxo-olean-12-en-24,30-dioic acid by NMR and MS. Based on the structure of M-D, we propose the metabolic pathway of 18-GRA in strain G5.     

Physiological–biochemical properties and the ability to synthesize polyhydroxyalkanoates of the glucose-utilizing strain of the hydrogen bacterium Ralstonia eutropha B8562

Physiological–biochemical, genetic, and cultural properties of the glucose-utilizing mutant strain Ralstonia eutropha B8562 have been compared with those of its parent strain R. eutropha B5786. It has been shown that growth characteristics of the strain cultured on glucose as the sole carbon and energy source are comparable with those of the parent strain. Strain B8562 is characterized by high polyhydroxyalkanoate (PHA) yields on different carbon sources (CO₂, fructose, and glucose). PHA accumulation in the strain batch cultured on glucose under nitrogen deficiency reaches 90 %. The major monomer in the PHA is β-hydroxybutyric acid (more than 99 mol %); the identified minor components are β-hydroxyvaleric acid (0.25–0.72 mol %) and β-hydroxyhexanoic acid (0.08–1.5 mol %). The strain is a promising PHA producer on available sugar-containing media with glucose.     

Genome Sequence of the Methanotrophic Poly-β-Hydroxybutyrate Producer Methylocystis parvus OBBP

Methylocystis parvus OBBP is an obligate methylotroph considered the type species of the genus Methylocystis. Two pmoCAB particulate methane monooxygenase operons and one additional singleton pmoC paralog were identified in the sequence. No evidence of genes encoding soluble methane monooxygenase was found. Comparison of M. parvus OBBP and Methylocystis sp. strain Rockwell (ATCC 49242) suggests that both species should be taxonomically classified in different genera.     

Genome sequence of Frateuria aurantia type strain (Kond? 67T), a xanthomonade isolated from Lilium auratium Lindl.

Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67^T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67^T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67^T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

β-carotene from the abscisic acid producing strain of Cercospora rosicola

-carotene was isolated from an extract of Cercospora rosicola mycelia and identified on the basis of chromatographic properties and UV-visible spectroscopic evidence. The accumulation of -carotene was inhibited 71 and 52% by 10 M amounts of decylimidazole and fluridone, resepectively. Abscisic acid accumulation was inhibited 63% by decylimidazole and enhanced about 10% by fluridone. Several other inhibitors of carotenoid synthesis failed to inhibit ABA biosynthesis.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3′-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3′-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5

Background

Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.

Results

In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.

Conclusions

Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1252-7) contains supplementary material, which is available to authorized users.     

Conversion of the BASE prion strain into the BSE strain: the origin of BSE?

Atypical neuropathological and molecular phenotypes of bovine spongiform encephalopathy (BSE) have recently been identified in different countries. One of these phenotypes, named bovine "amyloidotic" spongiform encephalopathy (BASE), differs from classical BSE for the occurrence of a distinct type of the disease-associated prion protein (PrP), termed PrP(Sc), and the presence of PrP amyloid plaques. Here, we show that the agents responsible for BSE and BASE possess different biological properties upon transmission to transgenic mice expressing bovine PrP and inbred lines of nontransgenic mice. Strikingly, serial passages of the BASE strain to nontransgenic mice induced a neuropathological and molecular disease phenotype indistinguishable from that of BSE-infected mice. The existence of more than one agent associated with prion disease in cattle and the ability of the BASE strain to convert into the BSE strain may have important implications with respect to the origin of BSE and spongiform encephalopathies in other species, including humans.     

Nucleotide sequence of the LacN gene encoding thermostable β-galactosidase of a thermophilic anaerobe,strain NA10

The nucleotide sequences of the lacN gene encoding thermostable β-galactosidase of a thermophilic anaerobe, strain NA10, and its flanking regions were determined. The lacN gene was composed of 2031 base pairs coding for a polypeptide of 676 amino acids (molecular weight=79,286). Possible promoter and Shine-Dalgarno sequences were found upstream of the initiation codon, which were highly homologous to the consensus sequences in Escherichia coli.     

Photoaffmity cross-linking of F1ATPase from the thermophilic bacterium PS 3 by 3'-arylazido-β-alanyl-8-azido ATP

To study the localization of the nucleotide binding sites of coupling factor 1 (TF₁) from the thermophilic bacterium PS3 we used the bifunctional (cross-linking) 3'-arylazido-β-alanyl-8-azido ATP (DiN₃ATP) for photoaffinity labeling. DiN₃ATP is hydrolyzed by TF₁ in the absence of ultraviolet light. Irradiation (UV light) of TF₁ in the presence of DiN₃ATP results in a nucleotide-specific reduction of ATPase activity and in a nucleotide-specific formation of different cross-linked proteins (dimers, trimers, oligomers) formed by the major subunits α and/or β. The results suggest that nucleotide binding sites (one, two, possibly all) are located at the interfaces between these subunits.     

Does S-metolachlor affect the performance of Pseudomonas sp. strain ADP as bioaugmentation bacterium for atrazine-contaminated soils?

Atrazine (ATZ) and S-metolachlor (S-MET) are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 μg g(-1) of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD)), the presence of pure S-MET significantly affected neither bacteria survival (~10(7) initial viable cells g(-1) of soil) nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50 × RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days) and extensively (>96%) removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil.     

Conversion of 17α-methyltestosterone to methandrostenolone by the bacterium pimelobacter simplex VKPM Ac-1632 with the presence of cyclodextrins

Conditions of conversion of 17α-methyltestosterone to methandrostenolone with the presence of modified β-cyclodextrins (methylcyclodextrin, hydroxypropylcyclodextrin, and hydroxyethylcyclodextrin) in the steroid: cyclodextrin ratio 1: 1 were studied. The experimental solutions of modified β-cyclodextrins were prepared in deionized water with 5–7% methanol. Under the conditions found to be optimal, 1,2–dehydrogenation of 17α-methyltestosterone was carried out with 2–4 g/l Pimelobacter simplex VKPM Ac-1632 biomass. At the substrate concentration 5–20 g/l, the reaction occurred for 1–15 h without any by-products. The maximum rate of methandrostenolone accumulation was observed with hydroxypropylcyclodextrin. The methylcyclodextrin solution can be reused for complete 17α-methyltestosterone conversion at the concentration 5 g/l.     

Structural–Functional Domains of the Eukaryotic Genome

It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains. The question of what exactly these domains constitute has been re-examined multiple times as our knowledge of principles of chromatin folding has changed. In this review, we discuss structural and functional genomic domains in light of the current model of interphase chromosome organization based on the results of analysis of spatial proximity between remote genomic elements.     

Molecular cloning,nucleotide sequence and expression in Escherichia coli of the β-cyclodextrin glycosyltransferase gene from Bacillus circulans strain no. 8

Summary The -cyclodextrin glycosyltransferase (-CGTase) gene was isolated from a -library prepared from Bacillus circulans strain no. 8. It was subcloned into plasmid pTZ and expressed by its endogenous regulatory sequences in Escherichia coli JM 103. The structural gene was sequenced and showed an open reading frame for a polypeptide of 718 amino acid residues. The recombinant -CGTase had the same enzymatic properties as the extracellular CGTase (684 amino acid residues, corresponding to a mol. wt. of 74416) produced by B. circulans strain no. 8. The amino acid sequence showed the highest homology (74.6% identical amino acids) with the CGTase of B. circulans strain F-2, which had been erroneously described as an amylase. The homology with the enzyme from the alkalophilic Bacillus sp. strain no. 1011 was 71.4%. The amino acid sequence derived will be used for elucidating the three-dimensional structure of the enzyme. Offprint requests to: H. Bender     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3'-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3'-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

Nucleotide sequence of the 17S–25S spacer region from rice rDNA

Summary The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194–195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163–164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5′ terminal region of 25S rDNA.     

Synthesis and characterization of the anomeric pair of 17β-glucuronides of ethynylestradiol

The α- and β-anomers of the 17β-d-glucuronide conjugate of ethynylestradiol were synthesized by the SnCl₄-promoted reaction between β-acetoxy GAM and the t-17β-hydroxyl group of EE₂-3-acetate. The conjugates were resolved by crystallization and HPLC. Positive identification was established by u.v. spectrophotometry, i.r. and mass spectrometry and ¹H- and ¹³⁴C-n.m.r. The structure of the β-anomer was confirmed by X-ray crystallographic analysis. In addition, the α-anomer was refractory to hydrolysis by bovine β-glucuronidase, establishing a biochemical difference between the conjugate pair.