Baceridin, a cyclic hexapeptide from an epiphytic bacillus strain, inhibits the proteasome

A new cyclic hexapeptide, baceridin (1), was isolated from the culture medium of a plant-associated Bacillus strain. The structure of 1 was elucidated by HR-HPLC-MS and 1D and 2D NMR experiments and confirmed by ESI MS/MS sequence analysis of the corresponding linear hexapeptide 2. The absolute configurations of the amino acid residues were determined after derivatization by GC-MS and Marfey's method. The cyclopeptide 1 consists partially of nonribosomal-derived D- and allo-D-configured amino acids. The order of the D- and L-leucine residues within the sequence cyclo(-L-Trp-D-Ala-D-allo-Ile-L-Val-D-Leu-L-Leu-) was assigned by total synthesis of the two possible stereoisomers. Baceridin (1) was tested for antimicrobial and cytotoxic activity and displayed moderate cytotoxicity (1-2 μg mL(-1)) as well as weak activity against Staphylococcus aureus. However, it was identified to be a proteasome inhibitor that inhibits cell cycle progression and induces apoptosis in tumor cells by a p53-independent pathway.

Homologous expression of the nrdF gene of Corynebacterium ammoniagenes strain ATCC 6872 generates a manganese-metallocofactor (R2F) and a stable tyrosyl radical (Y˙) involved in ribonucleotide reduction

Ribonucleotide reduction, the unique step in the pathway to DNA synthesis, is catalyzed by enzymes via radical-dependent redox chemistry involving an array of diverse metallocofactors. The nucleotide reduction gene (nrdF) encoding the metallocofactor containing small subunit (R2F) of the Corynebacterium ammoniagenes ribonucleotide reductase was reintroduced into strain C. ammoniagenes ATCC 6872. Efficient homologous expression from plasmid pOCA2 using the tac-promotor enabled purification of R2F to homogeneity. The chromatographic protocol provided native R2F with a high ratio of manganese to iron (30:1), high activity (69 μmol 2'-deoxyribonucleotide·mg⁻¹ ·min⁻¹) and distinct absorption at 408 nm, characteristic of a tyrosyl radical (Y˙), which is sensitive to the radical scavenger hydroxyurea. A novel enzyme assay revealed the direct involvement of Y˙ in ribonucleotide reduction because 0.2 nmol 2'-deoxyribonucleotide was formed, driven by 0.4 nmol Y˙ located on R2F. X-band electron paramagnetic resonance spectroscopy demonstrated a tyrosyl radical at an effective g-value of 2.004. Temperature dependent X/Q-band EPR studies revealed that this radical is coupled to a metallocofactor. Similarities of the native C. ammoniagenes ribonucleotide reductase to the in vitro activated Escherichia coli class Ib enzyme containing a dimanganese(III)-tyrosyl metallocofactor are discussed.

Crystallization and preliminary X-ray analysis of the small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes

Ribonucleotide reduction, the unique step in DNA-precursor biosynthesis, involves radical-dependent redox chemistry and diverse metallo-cofactors. The metallo-cofactor (R2F) encoded by the nrdF (nucleotide reduction) gene in Corynebacterium ammoniagenes ATCC 6872 was isolated after homologous expression and a new crystal form of ribonucleotide reductase R2F was obtained. R2F was crystallized at 277 K using the vapour-diffusion method with PEG as the precipitating agent. A data set was collected to 1.36 A resolution from a single crystal at 100 K using synchrotron radiation. The crystal belonged to space group C2, with unit-cell parameters a = 96.21, b = 87.68, c = 83.25 A, beta = 99.29 degrees. The crystal contained two molecules per asymmetric unit, with a Matthews coefficient (V(M)) of 2.69 A(3) Da(-1); the solvent content was estimated to be 54.3%. X-ray fluorescence spectroscopy and MAD diffraction data indicated the presence of manganese in the molecule and the absence of iron.

Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium

Strains L10T, L108 and CIP I-2052 were originally obtained from methyl tert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow on tert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Poly β-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69–70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1 cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in the Rubrivivax–Roseateles–Leptothrix–Ideonella–Aquabacterium branch of the Betaproteobacteria with 97 % similarity to 16S rRNA genes of the type strains of Rubrivivax gelatinosus, Leptothrix mobilis and Ideonella dechloratans. However, physiological properties, DNA–DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10T, L108 and CIP I-2052 represent a new genus and novel species for which the name Aquincola tertiaricarbonis gen. nov., sp. nov., is proposed. The type strain is strain L10T (=DSM 18512T=CIP 109243T).

Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees

Bacteria were isolated from flowers and bark of apple and pear trees at three places in Australia. In Victoria, Tasmania and Queensland, strains with white colonies on nutrient agar were screened for dome-shaped colony morphology on agar with sucrose and were found to be closely related by several criteria. The isolates were not pathogenic on apples or pears. They were characterized by a polyphasic approach including microbiological and API assays as well as fatty acid methyl ester analysis, DNA-DNA hybridization and DNA sequencing. For molecular classification, the 16S rRNA cistron and the conserved genes gpd and recA of these bacteria were investigated. Together with other taxonomic criteria, the results of these studies indicate that the bacteria belong to a novel separate species, which we propose to name Erwinia tasmaniensis sp. nov., with the type strain Et1/99(T) (=DSM 17950(T)=NCPPB 4357(T)). From DNA-DNA hybridization kinetics, microbiological characteristics and nucleotide sequence analyses, this species is related to pathogenic Erwinia species, but also to the epiphytic species Erwinia billingiae.

High-level resistance to cobalt and nickel but probably no transenvelope efflux: Metal resistance in the Cuban Serratia marcescens strain C-1

Molecular mechanisms underlying inducible cobalt and nickel resistance of a bacterial strain isolated from a Cuban serpentine deposit were investigated. This strain C-1 was assigned to Serratia marcescens by 16S rDNA analysis and DNA/DNA hybridization. Genes involved in metal resistance were identified by transposon mutagenesis followed by selection for cobalt- and nickel-sensitive derivatives. The transposon insertion causing the highest decrease in metal resistance was located in the ncrABC determinant. The predicted NcrA product was a NreB ortholog of the major facilitator protein superfamily and central for cobalt/nickel resistance in S. marcescens strain C-1. NcrA also mediated metal resistance in Escherichia coli and caused decreased accumulation of Co(II) and Ni(II) in this heterologous host. NcrB may be a regulatory protein. NcrC was a protein of the nickel-cobalt transport (NiCoT) protein family and necessary for full metal resistance in E. coli, but only when NcrA was also present. Without NcrA, NcrC caused a slight decrease in metal resistance and mediated increased accumulation of Ni(II) and Co(II). Because the cytoplasmic metal concentration can be assumed to be the result of a flow equilibrium of uptake and efflux processes, this interplay between metal uptake system NcrC and metal efflux system NcrA may contribute to nickel and cobalt resistance in this bacterium.

S434F in NrdE Generates the Thermosensitive Phenotype of Corynebacterium ammoniagenes CH31 and Enhances Thermolability by Increasing the Surface Hydrophobicity of the NrdE(Ts) Protein

The thermosensitive phenotype of strain CH31, a derivative of Corynebacterium ammoniagenes ATCC 6872, was allocated by cloning, sequencing, and genetic complementation to a single C→T exchange in the nrdE ( n ucleotide r e d uction) gene at nucleotide 1301. Protein modeling indicates the impaired surface hydrophobicity of NrdE(Ts) due to the S434F transition.

Plant-microbe interactions: identification of epiphytic bacteria and their ability to alter leaf surface permeability

Bacteria were either isolated from leaf surfaces of Hedera helix or obtained from a culture collection in order to analyse their effect on barrier properties of isolated Hedera and Prunus laurocerasus cuticles. On the basis of the 16S rDNA sequences the genera of the six bacterial isolates from Hedera were identified as Pseudomonas sp., Stenotrophomonas sp. and Achromobacter. Water permeability of cuticles isolated from H. helix was measured before and after inoculation with the six bacterial strains. In addition water permeability of cuticles isolated from P. laurocerasus was measured before and after inoculation with the three bacterial strains Pseudomonas aeruginosa, Xanthomonas campestris and Corynebacterium fascians. Rates of water diffusing across isolated cuticles of both species significantly increased by up to 50% after inoculation with all bacterial strains. Obtained results show that epiphytic bacteria have the ability of increasing water permeability of Hedera and Prunus cuticles, which in turn should increase the availability of water and dissolved compounds in the phyllopshere. Consequently, living conditions in the habitat phyllosphere are improved. It can be concluded that the ability to change leaf surface properties will improve epiphytic fitness of leaf surface bacteria.

Overproduction of NAD+ and 5'-inosine monophosphate in the presence of 10 microM Mn2+ by a mutant of Corynebacterium ammoniagenes with thermosensitive nucleotide reduction (nrd(ts)) after temperature shift

Corynebacterium ammoniagenes strain CH31 is thermosensitive due to a mutation in nucleotide reduction ( nrd(ts)). The strain was examined for nucleotide overproduction upon shifting the culture temperature to a range of elevated temperatures. No overproduction of NAD(+) was detected in the control maintained at 27 degrees C whereas NAD(+) was accumulated extracellularily by strain CH31 at 37 degrees C and at 40 degrees C. As a result of the temperature shift, division-inhibited cells displayed only limited elongation. This is a characteristic morphological feature of cell-cycle-arrested coryneform bacteria. Ribonucleotide reductase (RNR) activity was inactivated immediately after the temperature shift in the NAD(+)-proficient cultures, leading presumably to an exhaustion of deoxyribonucleotide pools and impairment of DNA replication. In contrast to the low extracellular accumulation of NAD(+), at the non-permissive temperature of 35 degrees C a distinct capacity for intracellular nucleotide overproduction was revealed by a new method using nucleotide-permeable cells. The approach of shifting the culture temperature was applied successfully to the overproduction of taste-enhancing nucleotides in the presence of 10 microM Mn(2+). Concomitant with a dramatic loss of viability, the thermosensitive mutant CH31 accumulated 5.3 g 5'-inosine monophosphate per liter following the addition of hypoxanthine as precursor for the salvage pathway.

Arrest of cell cycle by inhibition of ribonucleotide reductase induces accumulation of NAD+ by Mn2+-supplemented growth of Corynebacterium ammoniagenes

Cell division of the wild type strain Corynebacterium (formerly Brevibacterium) ammoniagenes ATCC 6872 which requires 1 microM Mn2+ for balanced growth was inhibited by addition of 20 mM hydroxyurea (HU) or 10 mM p-methoxyphenol (MP) to a Mn2+-supplemented fermentation medium at an appropriate time. Scanning electron microscopy (SEM) showed a restricted elongation characteristic of arrest of the cell cycle in coryneform bacteria. The cultures treated with HU or MP had, respectively, a fourfold or sixfold enhanced accumulation of NAD+ by a salvage biosynthetic pathway. An assay of nucleotide-permeable cells for ribonucleotide reductase activity using [3H-CDP] as substrate revealed a pre-early and complete decline of DNA precursor biosynthesis not found in the untreated control. Overproduction of NAD+ is an alternative to the conventional fermentation process using Mn2+ deficiency. A simple model is presented to discuss the metabolic regulation of the new process based on the presence of a manganese ribonucleotide reductase (Mn-RNR) in the producing strain.

Isolation of toxigenic Nocardiopsis strains from indoor environments and description of two new Nocardiopsis Species, N. exhalans sp. nov. and N. umidischolae sp. nov

Nocardiopsis strains were isolated from water-damaged indoor environments. Two strains (N. alba subsp. alba 704a and a strain representing a novel species, ES10.1) as well as strains of N. prasina, N. lucentensis, and N. tropica produced methanol-soluble toxins that paralyzed the motility of boar spermatozoa at <30 microg of crude extract (dry weight) x ml(-1). N. prasina, N. lucentensis, N. tropica, and strain ES10.1 caused cessation of motility by dissipating the mitochondrial membrane potential, Deltapsi, of the boar spermatozoa. Indoor strain 704a produced a substance that destroyed cell membrane barrier function and depleted the sperm cells of ATP. Indoor strain 64/93 was antagonistic towards Corynebacterium renale. Two indoor Nocardiopsis strains were xerotolerant, and all five utilized a wide range of substrates. This combined with the production of toxic substances suggests good survival and potential hazard to human health in water-damaged indoor environments. Two new species, Nocardiopsis exhalans sp. nov. (ES10.1T) and Nocardiopsis umidischolae sp. nov. (66/93T), are proposed based on morphology, chemotaxonomic and physiological characters, phylogenetic analysis, and DNA-DNA reassociations.

Diversity of polyamine patterns in soft rot pathogens and other plant-associated members of the Enterobacteriaceae

Polyamine profiles of 91 pectolytic and other plant-associated strains from 30 taxa of the Enterobacteriaceae were obtained by gradient high performance liquid chromatography (HPLC). Pectobacterium carotovorum, basonym Erwinia carotovora, contained a high amount of putrescine and less diaminopropane. Diaminopropane was absent in Pectobacterium chrysanthemi, basonym E. chrysanthemi, whereas cadaverine was present in addition to the major compound putrescine. This chemotaxonomic difference reflects the deepest phylogenetic branching point within the recently emended genus Pectobacterium which lies between the two species P. carotovorum and P. chrysanthemi. Both important soft rot pathogens are easily distinguishable from each other and from the type species of the genus Erwinia as diaminopropane is the only major polyamine compound in E. amylovora. Chemotaxonomic heterogeneity is also emerging with respect to DYE's Amylovora group proposed in an early phytopathological concept.

Isolation and characterization of highly thermophilic xylanolyticThermus thermophilusstrains from hot composts

This is the first detailed report of xylanolytic activity in Thermus strains. Two highly thermophilic xylanolytic bacteria, very closely related to non-xylanolytic T. thermophilus strains, have been isolated from the hottest zones of compost piles. Strain X6 was investigated in more detail. The growth rate (optical density monitoring) on xylan was 0.404·h-1at 75°C. Maximal growth temperature was 81°C. Xylanase activity was mainly cell-bound, but was solubilized into the medium by sonication. It was induced by xylan or xylose in the culture medium. The temperature and pH optima of the xylanases were determined to be around 100°C and pH 6, respectively. Xylanase activity was fairly thermostable; only 39% of activity was lost after an incubation period of 48 h at 90°C in the absence of substrate. Xylanolytic T. thermophilus strains could contribute to the degradation of hemicellulose during the thermogenic phase of industrial composting.Key words: Thermus, thermophilic aerobic bacteria, xylanase, thermostable enzyme, compost.

Isolation and characterization of highly thermophilic xylanolytic Thermus thermophilus strains from hot composts

This is the first detailed report of xylanolytic activity in Thermus strains. Two highly thermophilic xylanolytic bacteria, very closely related to non-xylanolytic T. thermophilus strains, have been isolated from the hottest zones of compost piles. Strain X6 was investigated in more detail. The growth rate (optical density monitoring) on xylan was 0.404.h-1 at 75 degrees C. Maximal growth temperature was 81 degrees C. Xylanase activity was mainly cell-bound, but was solubilized into the medium by sonication. It was induced by xylan or xylose in the culture medium. The temperature and pH optima of the xylanases were determined to be around 100 degrees C and pH 6, respectively. Xylanase activity was fairly thermostable; only 39% of activity was lost after an incubation period of 48 h at 90 degrees C in the absence of substrate. Xylanolytic T. thermophilus strains could contribute to the degradation of hemicellulose during the thermogenic phase of industrial composting.

Ribonucleotide reductase (RNR) of Corynebacterium glutamicum ATCC 13032--genetic characterization of a second class IV enzyme

Ribonucleotide reductases (RNRs) encoded by nrd (nucleotide reduction) genes are unique enzymes providing the DNA precursors in all living organisms and several viruses. The designation of four classes of RNRs reflects their use of diverse metallo-cofactors. Using oligonucleotide primers derived from conserved domains of the primary structure of known NrdA and NrdE proteins, an internal 938 bp fragment of the nrdE gene was amplified from genomic DNA of Corynebacterium glutamicum. With this PCR product a 4.36 kb fragment was identified and cloned containing the nrdHIE genes of C. glutamicum. A probe derived from nrdF2 of Mycobacterium tuberculosis allowed the cloning and sequencing of the nrdF gene located 3.1 kb further downstream, encoding the small subunit of the C. glutamicum RNR. Conjugative introduction of nrdE from C. glutamicum complemented thermosensitive mutants of Corynebacterium ammoniagenes which had a defective catalytic subunit of the Mn-RNR. The authors provide arguments for allocation of the C. glutamicum NrdEF proteins to class IV in the RNR classification scheme of Stubbe & van der Donk (1995) [Chem Biol 2, 793-801].

Thauera mechernichensis sp. nov., an aerobic denitrifier from a leachate treatment plant

A heterotrophic bacterial strain TL1T capable of aerobic denitrification was previously enriched in continuous culture from a landfill leachate treatment plant and isolated as a pure culture. The taxonomic position of this isolate within the beta-subclass of the Proteobacteria was determined by 16S rDNA sequence analysis and by conventional taxonomy including substrate spectrum, quinone type (ubiquinone Q-8) and cellular fatty acid composition. Detection of the specific polyamine 2-hydroxyputrescine supports the membership of strain TL1T in the beta-subclass of the Proteobacteria. The results of 16S rDNA sequencing showed that the strain clustered with, but was separate from, Thauera aromatica and Thauera selenatis. DNA-DNA hybridization experiments indicated that the new isolate represents a new species of the genus, for which the name Thauera mechernichensis is proposed; the type strain is DSM 12266T.

Defluvibacter lusatiae gen. nov., sp. nov., a new chlorohenol-degrading member of the alpha-2 subgroup of proteobacteria

The two Gram-negative bacterial strains S1 and S4 were isolated from activated sludge of an industrial waste water treatment plant and exhibited a stable capability to degrade 2,4-dichlorophenol, 4-chloro-2-methylphenol, 4-chlorophenol and phenol. The cells were short rods with a polar flagellum, being mesophilic, strictly aerobic, oxidase-positive, and chemoorganotrophic. They utilized a range of amino acids, but only a restricted number of carbohydrates. Reassociation experiments with DNA from strains S1 and S4 revealed high interstrain similarity, indicating, that both strains belong to the same species. The phylogenetic position was determined by comparison of the almost complete 16S rDNA sequence of strain S1 with sequences of related bacteria. Strain S1 clustered with members of the alpha-2 subgroup of the Proteobacteria by forming a separate lineage within the radiation of Mesorhizobium, Phyllobacterium and Sinorhizobium. Both strains can be differentiated from members of related taxa by a set of physiological and chemotaxonomic properties including the ability to grow with norvaline, L-tryptophan, putrescine, glutarate and malonate, and by the presence of spermidine as major polyamine and of 12:0 3OH as fatty acid. Strain S1 is described as type strain of a new species and assigned to a new genus with the proposed name Defluvibacter lusatiae.

Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov

An aerobic bacterium, strain BN12T, which degrades substituted naphthalenesulfonates and substituted salicylates was isolated from a 6-aminonaphthalene-2-sulfonate-degrading microbial consortium originating from the River Elbe, Germany. Chemotaxonomic investigations of quinones, polyamines and polar lipids allowed allocation of this strain to the alpha-subclass of the Proteobacteria and revealed similarity to species of the genera Aminobacter, Chelatobacter and Mesorhizobium. This was confirmed by typing with 16S rRNA-targeted oligonucleotide probes and 16S rDNA sequencing and phylogenetic analysis, indicating that BN12T clusters most closely with a strain 'Thiobacillus' THI 051T and with the above genera but comprising a separate branch. DNA-DNA hybridizations demonstrated that strain BN12T is different from all species of Aminobacter currently described and recognized. The fatty acid patterns, substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of Aminobacter and Chelatobacter species. 'Thiobacillus' THI 051T, however, revealed phenotypic similarities to BN12T. Furthermore, 16S rRNA sequences of Chelatobacter heintzii showed a high similarity to the 16S rRNA sequences of all currently recognized Aminobacter species. On the basis of these and previously published results, the new genus Pseudaminobacter is proposed, harbouring the two new species Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. The type strains are BN12T (= DSM 6986T) and THI 051T (= IFO 14570T), respectively.

Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales

The 16S rDNA sequences of 20 novel isolates of members of the order Planctomycetales were compared to those of the type strains of described planctomycete species and 22 planctomycete isolates for which the 16S rDNA sequences had been previously determined. The novel isolates could be assigned to several phylogenetically broad groups, four of which are defined by the genera Gemmata, Isosphaera, Planctomyces and Pirellula. To evaluate polyamines as a chemotaxonomic marker within this order, the polyamine pool was determined for six planctomycete reference species and for 20 planctomycete isolates. All analysed members of the order Planctomycetales contained significant amounts of polyamines. sym-Homospermidine (HSPD) is present in all strains except Planctomyces limnophilus and related strains, which had high amounts of putrescine (PUT) as the dominant polyamine component. The distribution of PUT, HSPD and spermidine reflects the phylogenetic diversity within the Planctomycetales as closely related representatives of the phylogenetic groups defined by described species and novel isolates exhibit similar polyamine patterns. Determination of the DNA base composition revealed G + C contents of > 60 mol% for members of Gemmata and Isosphaera whereas, except for two isolates, strains which are phylogenetically associated with Planctomyces and Pirellula had G + C contents of 51-57 mol%.

A divalent metal site in the small subunit of the manganese-dependent ribonucleotide reductase of Corynebacterium ammoniagenes

Based on its metallo-cofactor, the manganese-dependent ribonucleotide reductase (Mn-RRase) responsible for delivery of DNA precursors in the Mn-requiring Gram-positive bacterium Corynebacterium (formerly Brevibacterium) ammoniagenes ATCC 6872 is no longer considered as a simple analogue of the aerobic Fe-RRase of Escherichia coli but as the prototype of the class IV enzymes (1). Deliberate dissociation of the Mn-RRase holoenzyme and an improved sample preparation of the dimeric CA2 protein allowed further characterization of the inherent metallo-cofactor by Q-band electron paramagnetic resonance (EPR) spectroscopy. At 40 K, a distinct hyperfine sextet (I = 5/2,55Mn) pattern with a weak zero-field splitting was detected in the CA2 protein prepared from manganese-sufficient cells displaying high RRase activity as expected. This Q-band Mn(II) signal was absent in the apo-CA2 protein obtained from manganese-depleted cells devoid of this enzymatic activity. The presence of a mixed valence manganese cluster in the C. ammoniagenes RRase is excluded since no complex multiline EPR signals were detected in the CA2 protein even at very low (8 K) temperature. The observed Mn(II) spectrum indicates a protein-bound manganese which was modified in the presence of 5.7 mM p-methoxyphenol, but is insensitive toward 10 mM EDTA. Thus, the manganese appeared to be either strictly bound or buried within a hydrophobic pocket of the CA2 protein, inaccessible for EDTA.

Ribonucleotide reductase in Bacillus subtilis--evidence for a Mn-dependent enzyme

The reduction of 2'-ribonucleotides to 2'-deoxyribonucleotides, a unique step in DNA formation, is catalyzed by ribonucleotide reductase (RRase), an allosterically regulated, cell cycle-dependent enzyme. This work reports a reversible impairment of DNA formation and ribonucleotide reduction upon manganese depletion in Bacillus subtilis demonstrated through in vivo labeling with necleic acid precursors and enzyme assays with ether-permeabilized cells. No deoxyadenosylcobalamin-dependent reduction of ribonucleotides was detected in the cytosol, and the properties of a partially purified enzyme fraction, i.e., sensitivity towards EDTA and hydroxyurea (HU), indicated a metal-dependent type of RRase. The enzyme was enriched by gel filtration on Superose 12 from glycerol- or fumarate-grown cells and submitted to Q-band electron paramagnetic resonance (EPR) spectroscopy for further characterization of the metal center. A distinct Mn(II) signal was obtained in both preparations characteristic of a protein-bound mangaenese in a mononuclear metal center with axial symmetry. The intensity of this Mn signal was not affected by addition of the radical scavenger HU (10 mM) but reduced in the presence of 2.5 mM EDTA. On the basis of these results, we suggest that Bacillus subtilis has a Mn-dependent ribonucleotide reductase.

Temperature-sensitive mutants of Corynebacterium ammoniagenes ATCC 6872 with a defective large subunit of the manganese-containing ribonucleotide reductase

Chemical mutagenesis of the nucleotide-producing strain Corynebacterium ammoniagenes ATCC 6872 with N-methyl-N-nitro-N-nitrosoguanidine followed by an enrichment protocol yielded 46 temperature-sensitive (ts) clones. A rapid assay for the allosterically regulated Mn-ribonucleotide reductase (RRase) was developed with nucleotide-permeable cells of C. ammoniagenes in order to screen for possible defects in DNA precursor biosynthesis at elevated temperature. Three mutants (CH 31, CH 32, and CH 33) grew well at 30 degrees C but did not proliferate at 40 degrees C because they did not reduce ribonucleotides to 2'-deoxyribonucleotides. They were designated nrdts (nucleotide reduction defective). When the cultures were shifted from 30 to 40 degrees C, the nrdts mutants immediately ceased to incorporate radiolabeled nucleic acid precursors into the DNA fraction, while DNA chain elongation was barely affected. Thus, exhaustion of the deoxyribonucleotide pool ultimately inhibited cell division, leading to a filamentous growth morphology. In contrast to the wild-type, all three nrdts mutants displayed a distinctly enhanced sensitivity of ribonucleotide reduction towards hydroxyurea (in permeabilized cells and in vitro) at 30 degrees C. The results from assays for biochemical complementation of heat-inactivated (2 min, 37 degrees C) mutant enzyme with either the small or the large subunit of wild-type Mn-RRase located the mutational defect on the large subunit.

Detection of a stable free radical in the B2 subunit of the manganese ribonucleotide reductase (Mn-RRase) of Corynebacterium ammoniagenes

Ribonucleotide reductases catalyze the irreversible reductive formation of 2'-deoxyribonucleotides required for DNA replication and cell proliferation, and a radical mechanism was assumed to be involved in this reaction. In order to search for a radical in the aerobic manganese ribonucleotide reductase (Mn-RRase) by electron paramagnetic resonance (EPR) the native metal-containing 100 kDa B2 subunit was deliberately prepared from the wild type strain Corynebacterium ammoniagenes ATCC 6872. Enrichment by 2'5'-ADP Sepharose 4B affinity chromatography, fast protein liquid chromatography (FPLC) with SuperoseTM12 and concentration by vacuum evaporation allowed for the first time the detection of a stable free radical by EPR spectroscopy at 77 K. The EPR spectrum exhibits an easily saturable doublet of 1.8 mT splitting and a line width of 1.3 mT at g = 2.0040. The EPR signal intensity showed a clear correlation with the enzymatic activity upon long-time storage at ambient temperature (294 K) and inactivation by the specific RRase inhibitor hydroxyurea (HU). This leads to the assumption of a protein-linked radical, with functional significance, in the metal-containing 100 kDa B2 subunit of the MnRRase of Corynebacterium ammoniagenes.

Degradation of 4-chloro-2-methylphenol by an activated sludge isolate and its taxonomic description

The Gram-negative strain S1, isolated from activated sludge, metabolized 4-chloro-2-methylphenol by an inducible pathway via a modified ortho-cleavage route as indicated by a transiently secreted intermediate, identified as 2-methyl-4-carboxymethylenebut-2-en-4-olide by gas chromatography/mass spectrometry. Beside 4-chloro-2-methylphenol only 2,4-dichlorophenol and 4-chlorophenol were totally degraded, without an accumulation of intermediates. The chlorinated phenols tested induced activities of 2,4-dichlorophenol hydroxylase and catechol 1,2-dioxygenase type II. Phenol itself appeared to be degraded more efficiently via a separate, inducible ortho-cleavage pathway. The strain was characterized with respect to its physiological and chemotaxonomic properties. The fatty acid profile, the presence of spermidine as main polyamine, and of ubiquinone Q-10 allowed the allocation of the strain into the alpha-2 subclass of the Proteobacteria. Ochrobactrum anthropi was indicated by fatty acid analysis as the most similar organism, however, differences in a number of physiological features (e.g. absence of nitrate reduction) and pattern of soluble proteins distinguished strain S1 from this species.

Characterization of Aeromonas genomic species by using quinone, polyamine, and fatty acid patterns

A chemotaxonomic study was carried out on representative strains of 13 Aeromonas genomic species. Quinone, polyamine, and fatty acid patterns were found to be very useful for an improved characterization of the genus and an improved differentiation from members of the families Enterobacteriaceae and Vibrionaceae. The Q-8-benzoquinone was the predominant ubiquinone, and putrescine and diaminopropane were the major polyamines of the genus. The fatty acid patterns of 181 strains, all characterized by DNA-DNA hybridization, showed a great homogeneity within the genus, with major amounts of hexadecanoic acid (16:0), hexadecenoic acid (16:1), and octadecenoic acid (18:1), and minor amounts of the hydroxylated fatty acids (3-OH 13:0, 2-OH 14:0, 3-OH 14:0) in addition to some iso and anteiso branched fatty acids (i-13:0, i-17:1, i-17:0, and a-17:0). Although some differences in fatty acid profiles between the genomic species could be observed, a clearcut differentiation of all species was not possible.

Thauera selenatis gen. nov., sp. nov., a member of the beta subclass of Proteobacteria with a novel type of anaerobic respiration

A recently isolated, selenate-respiring microorganism (strain AXT [T = type strain]) was classified by using a polyphasic approach in which both genotypic and phenotypic characteristics were determined. Strain AXT is a motile, gram-negative, rod-shaped organism with a single polar flagellum. On the basis of phenotypic characteristics, this organism can be classified as a Pseudomonas sp. However, a comparison of the 16S rRNA sequence of strain AXT with the sequences of other organisms indicated that strain AXT is most similar to members of the beta subclass (level of similarity, 86.8%) rather than to members of the gamma subclass (level of similarity, 80.2%) of the Proteobacteria. The presence of the specific polyamine 2-hydroxyputrescine and the presence of a ubiquinone with eight isoprenoid units in the side chain (ubiquinone Q-8) excluded strain AXT from the authentic genus Pseudomonas and allowed placement in the beta subclass of the Proteobacteria. Within the beta subclass, strain AXT is related to Iodobacter fluvatile. The phylogenetic distance (level of similarity, less than 90%), as well as a lack of common phenotypic characteristics between these organisms, prevents classification of strain AXT as a member of the genus Iodobacter. In addition, strain AXT possesses a unique mechanism for anaerobic respiration, which allows it to utilize selenate as an electron acceptor without interference by nitrate. Therefore, we propose that strain AXT should be the first member of a new genus and species, Thauera selenatis.

Identification of Xenobiotic-Degrading Isolates from the Beta Subclass of the Proteobacteria by a Polyphasic Approach Including 16S rRNA Partial Sequencing

Nineteen gram-negative, aerobic, biodegradative isolates were identified by using a polyphasic taxonomic approach. The presence of the specific polyamine 2-hydroxyputrescine and the presence of a ubiquinone with eight isoprenoid units in the side chain (ubiquinone Q-8) allowed allocation of these organisms to the beta subclass of the Proteobacteria. On the basis of the results of additional characterization experiments (i.e., API 20NE tests, determinations of soluble protein patterns, and DNA-DNA hybridization experiments), we classified six isolates as either Comamonas testosteroni, Comamonas acidovorans, or Alcaligenes xylosoxidans subsp. denitrificans. By using the same criteria we allocated two additional isolates to the genus Alcaligenes. A comparison of a 16S rRNA fragment (positions 1220 to 1377; Escherichia coli nomenclature) indicated that the remaining isolates should be allocated as follows: one is a member of C. testosteroni and one is a member of Acidovorax facilis, as confirmed by the results of additional DNA-DNA hybridizations; two others probably belong to the family Alcaligenaceae; six are related to "Alcaligenes eutrophus"; and one, strain NRRL 12228, occupies an isolated position.

Analysis of the polyphosphate-accumulating microflora in phosphorus-eliminating, anaerobic-aerobic activated sludge systems by using diaminopropane as a biomarker for rapid estimation of Acinetobacter spp

Polyphosphate-accumulating gram-negative bacteria were isolated from different anaerobic-aerobic activated sludge systems with diverse processes for enhanced biological phosphorus (P) elimination. Of 22 isolates, 10 were allocated to the genus Acinetobacter by using multiple-test systems and soluble protein and polyamine patterns. As diaminopropane (DAP) appears to be the characteristic main polyamine compound produced by Acinetobacter spp., it was used as a biomarker for the genus. The high DAP contents of representative samples from municipal wastes with enhanced biological P elimination indicated that Acinetobacter spp. can be dominant organisms in sewage treatment plants with low organic loading and nitrification and denitrification steps. Contrary to accepted opinion, sludge from treatment plants with efficient P removal and high organic loading had a low DAP content, indicating that bacteria other than Acinetobacter spp. are responsible for enhanced biological P elimination in these plants.

Isolation and growth of a bacterium able to degrade nitrilotriacetic acid under denitrifying conditions

A Gram-negative bacterium was isolated from river sediment which was able to grow with nitrilotriacetic acid as a combined carbon, nitrogen and energy source in the absence of molecular oxygen using nitrate as the terminal electron acceptor. Batch growth parameters and mass balances are reported for growth under both aerobic and denitrifying conditions. The strain was characterized with respect to its substrate spectrum and other physiological properties. This denitrifying isolate is serologically unrelated to the comprehensively described Gram-negative obligately aerobic NTA-degrading bacteria all of which belong to the alpha-subclass of Proteobacteria. Chemotaxonomic characterization, which revealed the presence of spermidine as the main polyamine and ubiquinone Q-8, excludes the new isolate from the phylogenetically redefined genus Pseudomonas and indicates a possible location within the gamma-subclass of Proteobacteria close to, but separate from the genus Xanthomonas.

Evaluation of different approaches for identification of xenobiotic- degrading pseudomonads

Different approaches were evaluated to identify aerobic, gram-negative, biodegradative isolates assumed to be pseudomonads. Quinone and polyamine analysis allowed rapid identification to the genus level, i.e., allocation of those isolates belonging to the Pseudomonas fluorescens complex which represents the phylogenetically defined core of the heterogeneous genus Pseudomonas. Subsequent studies concentrated only on these true pseudomonads. The multiple-test system API 20NE, determination of the moles percent G+C content, and polyacrylamide gel electrophoresis of soluble proteins aided in identification on the species level. Polyacrylamide gel electrophoresis of both soluble proteins and whole-cell lipopolysaccharides allowed recognition of identical strains and double isolates, which were confirmed by DNA-DNA hybridization.

Lipid A with 2,3-diamino-2,3-dideoxy-glucose in lipopolysaccharides from slow-growing members of Rhizobiaceae and from "Pseudomonas carboxydovorans"

Lipid A's from two Bradyrhizobium species and from the phylogenetically closely related species "Pseudomonas carboxydovorans" were found to contain 2,3-diamino-2,3-dideoxy-glucose as lipid A backbone sugar. In contrast, three representatives of the genus Rhizobium, as well as the phylogenetically related species Agrobacterium tumefaciens, contain solely glucosamine as lipid A backbone sugar. These findings support independent studies on the phylogenetical relatedness based on 16S rRNA-data of the genus Bradyrhizobium with "Pseudomonas carboxydovorans" and Rhodopseudomonas palustris, which form a tight phylogenetical cluster and which all contain the 2,3-diamino-2,3-dideoxy-glucose-containing lipid A. The relatedness of these species to the glucosamine-containing species of the genus Rhizobium and to Agrobacterium tumefaciens is rather distant as documented by 16S rRNA studies.

Nucleotide and thioredoxin specificity of the manganese ribonucleotide reductase from Brevibacterium ammoniagenes

The manganese-containing ribonucleotide reductase previously identified in gram-positive bacteria has been purified and its nucleotide specificity and other requirements were determined. The enzyme isolated from Brevibacterium ammoniagenes is a ribonucleoside-diphosphate reductase which, in the presence of allosteric effectors, reduces all four common substrates at comparable rates; very little activity is observed in the absence of effector nucleotides. Ribonucleoside triphosphates are reduced at 20% the rate of the diphosphates. Cytidine and uridine nucleotide reduction is specifically stimulated by ATP and dATP, adenylate reduction by dGTP, and guanosine nucleotide reduction by dTTP. Unlike the iron-containing ribonucleotide reductase systems, high concentrations of dATP do not inhibit substrate reduction. The new bacterial enzyme tolerates high salt concentrations (up to 250 mM ionic strength) and does not require divalent metal ions for activity in vitro. The presence of thioredoxin has been demonstrated in heat- and acid-treated protein extracts of B. ammoniagenes and the protein was purified to homogeneity. It is very similar to the thioredoxins isolated from other organisms in relative molecular mass (12,000), isoelectric point (4.3) and enzyme-activating properties. In the presence of 0.3 mM dithiothreitol, the bacterial thioredoxin can serve as hydrogen donor for B. ammoniagenes ribonucleotide reductase in vitro, indicating the presence of a functional ribonucleotide reductase-thioredoxin system in these bacteria. The properties described in this and in our preceding paper in this journal [Eur. J. Biochem. 170, 603-611 (1988)] suggest that the B. ammoniagenes ribonucleotide reductase is intermediate in structure and specificity between the deoxyadenosylcobalamin-dependent and the iron-containing enzyme classes and that it is adapted to the specific requirements of deoxyribonucleotide synthesis in this organism.