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Archives of Microbiology (v.168, #3)

Glycoproteins in prokaryotes by Sara Moens; J. Vanderleyden (pp. 169-175).

Rather recently it has become clear that prokaryotes (Archaea and Bacteria) are able to glycosylate proteins. A literature survey revealed the different types of glycoproteins. They include mainly surface layer (S-layer) proteins, flagellins, and polysaccharide-degrading enzymes. Only in a few cases is structural information available. Many different structures have been observed that display much more variation than that observed in eukaryotes. A few studies have given evidence for the function of the prokaryotic glycoprotein glycans. Also from the biosynthetic point of view, information is rather scarce. Due to their different cell structure, prokaryotes have to use mechanisms different from those found in eukaryotes to glycosylate proteins. However, from the fragmented data available for the prokaryotic glycoproteins, similarities with the eukaryotic system can be noticed.

Keywords: Key words Glycoprotein; Glycosylation; Bacteria; Archaea

Characterization of Cyanobacteria by SDS-PAGE of whole-cell proteins and PCR/RFLP of the 16S rRNA gene by Christina Lyra; Jarkko Hantula; Eeva Vainio; Jarkko Rapala; L. Rouhiainen; K. Sivonen (pp. 176-184).

Planktonic, filamentous cyanobacterial strains from different genera, both toxic and nontoxic strains, were characterized by SDS-PAGE of whole-cell proteins and PCR/RFLP of the 16S rRNA gene. Total protein pattern analysis revealed the mutual relationships at the genus level. Restriction fragment length polymorphism (RFLP) of the 16S rRNA gene with reference strains proved to be a good method for the cyanobacterial taxonomy. The nonheterocystous strains outgrouped from the nitrogen-fixing ones. With both methods, Aphanizomenon clustered with Anabaena, and Nodularia with Nostoc. In the RFLP study of Anabaena, the neurotoxic strains were identical, but the hepatotoxic ones formed a heterogeneous group. Genetic distances found in the RFLP study were short, confirming that close genotypic relationships underlie considerable diversity among cyanobacterial genera.

Keywords: Key words Cyanobacteria; Planktonic; Total protein; SDS-PAGE; PCR; RFLP; 16S rRNA; UPGMA

Analysis of bacterial community structure in bulk soil by in situ hybridization by Boris Zarda; D. Hahn; Antonis Chatzinotas; Wilhelm Schönhuber; Alexander Neef; Rudolf I. Amann; Josef Zeyer (pp. 185-192).

In situ hybridization with rRNA-targeted, fluorescent (Cy3-labeled) oligonucleotide probes was used to analyze bacterial community structure in ethanol- or paraformaldehyde-fixed bulk soil after homogenization of soil samples in 0.1% pyrophosphate by mild ultrasonic treatment. In ethanol-fixed samples 37 ± 7%, and in paraformaldehyde 41 ± 8% of the 4′, 6-diamidino-2-phenylindole(DAPI)-stained cells were detected with the bacterial probe Eub338. The yield could not be increased by enzymatic and/or chemical pretreatments known to enhance the permeability of bacterial cells for probes. However, during storage in ethanol for 7 months, the detectability of bacteria increased in both ethanol- and paraformaldehyde-fixed samples to up to 47 ± 8% due to an increase in the detection yield of members of the α-subdivision of Proteobacteria from 2 ± 1% to 10 ± 3%. Approximately half of the bacteria detected by probe Eub338 could be affiliated to major phylogenetic groups such as the α-, β-, γ-, and δ-subdivisions of Proteobacteria, gram-positive bacteria with a high G+C DNA content, bacteria of the Cytophaga-Flavobacterium cluster of the CFB phylum, and the planctomycetes. The analysis revealed that bacteria of the α- and δ-subdivision of Proteobacteria and the planctomycetes were predominant. Here, members of the α-subdivision of Proteobacteria accounted for approximately 10 ± 3% of DAPI-stained cells, which corresponded to 44 ± 16 × 10⁸ cells (g soil, dry wt.)^–1, while members of the δ-subdivision of Proteobacteria made up 4 ± 2% of DAPI-stained cells [17 ± 9 × 10⁸ cells (g soil, dry wt.)^–1]. A large population of bacteria in bulk soil was represented by the planctomycetes, which accounted for 7 ± 3% of DAPI-stained cells [32 ± 12 × 10⁸ cells (g soil, dry wt.)^–1]. The detection of planctomycetes in soil confirms previous reports on the occurrence of planctomycetes in soil and indicates a yet unknown ecological significance of this group, which to date has never been isolated from terrestrial environments.

Keywords: Key words Fluorescent oligonucleotide probes; Planctomycetes; rRNA; Whole-cell hybridization

Nodulation of Trifolium repens at low pH by single and paired strains of Rhizobium leguminosarum biovar trifolii by C. E. Stone; J. E. Cooper (pp. 193-198).

Detailed individual nodulation profiles were obtained for five strains of Rhizobium leguminosarum biovar trifolii inoculated onto roots of Trifolium repens seedlings growing on an agar medium of pH 4.5. The time of appearance and the location of every nodule were noted for a period of 10 days after inoculation. Using these nodulation frequency profiles, pairings of strains were identified and six mixed-strain inoculation (1:1 ratio) experiments were subsequently performed at pH 4.5. Results from the mixed-inoculum experiments showed that the performance of a Rhizobium strain in single culture could not be reliably used to predict the outcome of a paired-inoculation study and that some seedlings were exclusively nodulated by rhizobia that performed poorly at low pH in single-culture inoculations.

Keywords: Key words Competition; Nodulation; Rhizobium; leguminosarum bv. trifolii; Trifolium repens; Acidity

Anaerobic degradation of cyclohexane-1,2-diol by a new Azoarcus species by J. Harder (pp. 199-204).

A bacterium, strain 22Lin, was isolated on cyclohexane-1,2-diol as sole electron donor and carbon source and nitrate as electron acceptor. Cells are motile rods and are facultatively anaerobic. A phylogenetic comparison based on the total 16S rRNA gene sequence allowed the assignment of the isolate to the genus Azoarcus. Cyclohexanol, cyclohexanone, cyclohexane-1,3-diol, and cyclohexane-1,3-dione, which are oxidized by a different denitrifying strain, did not support denitrifying growth of isolate 22Lin. On the contrary, cyclohexanol (I₅₀ = 37 μM) and cyclohexanone (I₅₀ = 28 μM) inhibited growth on cyclohexane-1,2-diol, but not on acetate. NAD was reduced by crude extracts of strain 22Lin in the presence of cyclohexane-1,2-dione, but not in the presence of cyclohexanone or cyclohexane-1,3-dione. The formation of 6-oxohexanoate from cyclohexane-1,2-dione and of adipate during NAD reduction suggests that strain 22Lin possesses a carbon–carbon hydrolase that transforms cyclohexane-1,2-dione into 6-oxohexanoate. This pathway was once observed in an aerobic pseudomonad that was lost and could not be reisolated. Here, the application of strictly anoxic enrichment conditions enabled the reisolation of another strain (22Lin) that uses this pathway.

Keywords: Key wordsAzoarcus; Diol dehydratase; Acetoin; dehydrogenase; Carbon; carbon hydrolase; Denitrification

Characterization of a K+-ATPase from Lactobacillus helveticus ATCC 15009 by Cristina Solari; Isabella Panfoli; A. Morelli; Denise Cassandrini; Piersandro Cocconcelli; Lorenzo Morelli (pp. 205-209).

Lactobacillus helveticus ATCC 15009 (wild-type) membrane preparations hydrolyzed Mg²⁺-ATP as a function of K⁺ concentration (2–200 mM). Mg²⁺-ATP hydrolysis by L. helveticus membranes was strongly inhibited in the absence of exogenous K⁺, while it amounted to 6 nmol ATP hydrolyzed min^–1 (mg membrane protein)^–1 at 50 mM KCl (saturating conditions) and pH 7.2. The K⁺-dependent ATPase of L. helveticus displayed a relatively high affinity for potassium ions (K _m = 800 μM) and was not affected by pretreatment of membranes with N,N’-dicyclohexylcarbodiimide. Membrane preparations were subjected to hypotonic shock to obtain a maximum yield of open profiles. The formation of a maximum level of enzyme-phosphate complex with a molecular mass of approximately 82 kDa was induced upon treatment of L. helveticus membrane preparations with low concentrations of [γ-³²P]ATP in the presence of K⁺ and La³⁺ ions and was visualized by acidic SDS-PAGE. It was concluded that L. helveticus membranes contain an inwardly directed K⁺ pump whose presence is discussed in terms of its putative role in cytoplasmic pH regulation.

Keywords: Key words K+-ATPase; Lactobacilli; Potassium pump; 2; 3-Butanedione; Enzyme-phosphate complex

Fermentation of cysteate by a sulfate-reducing bacterium by Heike Laue; Karin Denger; A. M. Cook (pp. 210-214).

We isolated a strictly anaerobic bacterium, strain GRZCYSA, from a sludge digestor for its ability to ferment cysteate (2-amino-3-sulfopropionate). The organism also fermented the organosulfonates isethionate (2-hydroxyethanesulfonate) and aminomethanesulfonate, but taurine (2-aminoethanesulfonate) was not a substrate. Strain GRZCYSA, a gram-negative, oxidase-negative and catalase-positive vibrio that could reduce sulfate and contained desulfoviridin, was tentatively identified as Desulfovibrio sp. Utilization of cysteate as a substrate for fermentative growth led to the formation of four products identified as acetate, ammonia, and equimolar amounts of sulfide and sulfate. The fermentation was in balance. Some reactions involved in this novel process were detected in cell-free extracts in which ammonia and acetate were formed from cysteate.

Keywords: Key words Anaerobic desulfonation; Desulfonation; Sulfonate fermentation; Sulfide; Sulfate; Sulfate-reducing bacteria; Desulfovibrio

In vitro and in vivo regulation of assimilatory nitrite reductase from Candida utilis by S. Sengupta; Melkote Subbarao Shaila; Gannamani Ramananda Rao (pp. 215-224).

The nitrate assimilation pathway in Candida utilis, as in other assimilatory organisms, is mediated by two enzymes: nitrate reductase and nitrite reductase. Purified nitrite reductase has been shown to be a heterodimer consisting of 58- and 66-kDa subunits. In the present study, nitrite reductase was found to be capable of utilising both NADH and NADPH as electron donors. FAD, which is an essential coenzyme, stabilised the enzyme during the purification process. The enzyme was modified by cysteine modifiers, and the inactivation could be reversed by thiol reagents. One cysteine was demonstrated to be essential for the enzymatic activity. In vitro, the enzyme was inactivated by ammonium salts, the end product of the pathway, proving that the enzyme is assimilatory in function. In vivo, the enzyme was induced by nitrate and repressed by ammonium ions. During induction and repression, the levels of nitrite reductase mRNA, protein, and enzyme activity were modulated together, which indicated that the primary level of regulation of this enzyme was at the transcriptional level. When the enzyme was incubated with ammonium salts in vitro or when the enzyme was assayed in cells grown with the same salts as the source of nitrogen, the residual enzymatic activities were similar. Thus, a study of the in vitro inactivation can give a clue to understanding the mechanism of in vivo regulation of nitrite reductase in Candida utilis.

Keywords: Key words Candida utilis; Nitrite reductase; Electron; donors; Cysteine modification; Transcriptional control

Autotrophic growth on carbon disulfide is a property of novel strains of Paracoccus denitrificans by Sarah L. Jordan; I. R. McDonald; Anna J. Kraczkiewicz-Dowjat; Donovan P. Kelly; Frederick A. Rainey; J. Colin Murrell; A. P. Wood (pp. 225-236).

Three distinct strains (KL1, KS1, and KS2) of facultatively chemolitho-autotrophic bacteria able to use carbon disulfide or carbonyl sulfide as sole energy substrates were identified as novel strains of Paracoccus denitrificans. Evidence for their identity as biovars of P. denitrificans and as close relatives of Paracoccus versutus is based on their DNA composition, total sequencing of the genes for their 16S rRNA, muropeptide profiles, amino acid composition of peptidoglycan, kinetics of murein degradation by lysozyme, possession of large plasmids (91–98 kb) and megaplasmids (> 450 kb), and plasmid transfer between the strains and with P. denitrificans and P. versutus. No functions have been identified for the 91- to 98-kb plasmids of strains KL1 and KS2, but curing strain KL1 of its plasmid did not affect growth on carbon disulfide, thiosulfate or succinate. Emendation of the formal description of Paracoccus denitrificans is presented. Autotrophic growth on carbon disulfide and thiosulfate was confirmed by ¹⁴CO₂ fixation. Evidence is presented for initiation of carbon disulfide oxidation by an NADH-dependent oxygenase. Cell-free extracts catalyzed (1) NADH-stimulated uptake of oxygen in the presence of carbon disulfide, and (2) carbon-disulfide-stimulated oxidation of NADH. The activity was not sedimented at 50,000 ×g. Intermediates in aerobic carbon disulfide metabolism were shown by GC and GC/MS to include carbonyl sulfide and hydrogen sulfide, but anaerobic production of COS and H₂S from carbon disulfide did not occur. SDS-PAGE of cell-free extracts showed polypeptides that were unique to growth on carbon disulfide, common to carbon disulfide and carbonyl sulfide, or found after growth on carbon disulfide, carbonyl sulfide or thiosulfate. The possible identity of these as proteins involved in sulfur compound metabolism is discussed.

Keywords: Key words Paracoccus denitrificans; Paracoccus; versutus; CS2 oxidation; CS2 oxygenase; Autotrophy; 16S rRNA phylogeny; Plasmids; Megaplasmids; Murein; Gas chromatography; SDS-PAGE profiles

Reductive catabolism of uracil and thymine by Burkholderia cepacia by T. P. West (pp. 237-239).

Catabolism of uracil and thymine in Burkholderia cepacia ATCC 25416 was shown to occur using a reductive pathway. The first pathway enzyme, dihydropyrimidine dehydrogenase, was shown to utilize NADPH as its nicotinamide cofactor. Growth of B. cepacia on pyrimidine bases as the nitrogen source instead of on ammonium sulfate increased dehydrogenase activity at least 32-fold. The second and third reductive pathway enzymes, dihydropyrimidinase and N-carbamoyl-β-alanine amidohydrolase, respectively, exhibited activities elevated more than 21-fold when pyrimidine or dihydropyrimidine bases served as the nitrogen source rather than ammonium sulfate. The pathway enzyme activities were induced after growth on 5-methylcytosine.

Keywords: Key words Pyrimidine catabolism; Burkholderia; cepacia; Induction; Reductive pathway; 5-Methylcytosine; NADPH

Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein by K. Tyson; Steve Busby; J. Cole (pp. 240-244).

The Escherichia coli nir and nrf operons, which encode alternative nitrite reductases expressed during anaerobic growth, are subject to catabolite regulation. Transcription from the nir promoter is maximal when bacteria are grown in rich media such as Lennox broth supplemented with glucose. Conversely, expression of the nrf operon is suppressed by rich media, but stimulated during growth in minimal medium with glycerol and fumarate. The role of the catabolite repressor-activator (Cra) protein in catabolite regulation of the nir and nrf promoters was investigated. Transcription from the nir promoter was repressed by Cra when cells were grown in minimal medium with glycerol and fumarate. Crude protein extracts from a strain overproducing Cra encoded on a multicopy plasmid retarded a nir promoter fragment in a mobility shift assay, confirming that the observed Cra-dependent repression was due to the direct interaction of Cra with the regulatory region of the nir operon. Furthermore, the inclusion of fructose 1-phosphate, an effector of Cra DNA-binding activity, in the assay decreased the ability of Cra to retard the nir promoter fragment. In contrast, transcription from the nrf promoter was not regulated by Cra under any of the growth conditions tested.

Keywords: Key words Catabolite regulation; Cra protein; Nitrite; reductase regulation; Escherichia coli; Catabolite; repression

The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: a proposal that AN1 represents a new species, Thermococcus zilligii sp. nov. by R. S. Ronimus; A.-L. Reysenbach; D. R. Musgrave; H. W. Morgan (pp. 245-248).

The 16S rRNA gene from the Thermococcus New Zealand isolate AN1 was cloned and sequenced. Analysis of the gene revealed the presence of signature sequences, indicating that strain AN1 represents a new species of the genus Thermococcus. Since the isolate AN1 differed from other thermococci in both its lower optimal NaCl concentration and generally lower optimal temperature for growth, in its unusual lipid membrane composition, and in its sensitivity to antibiotics, we propose that strain AN1 represents a new species of Thermococcus. The proposed name is Thermococcus zilligii, and the type strain is DSM 2770.

Keywords: Key words Thermophile; Thermococcus; Pyrococcus; 16S rRNA; Archaea; Euryarchaeota; Extremophile; Phylogeny; Taxonomy

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Archives of Microbiology (v.168, #3)