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Archives of Microbiology (v.169, #1)

A 71-kDa protein from Halobacterium salinarium belongs to a ubiquitous P-loop ATPase superfamily with head-rod-tail structure by Andreas Ruepp; Gerhard Wanner; J. Soppa (pp. 1-9).

The nucleotide sequence of a genomic fragment from Halobacterium salinarium containing an open reading frame encoding a protein with a calculated molecular mass of 71 kDa was determined. Database searches revealed that this protein, Hp71, has similarities to eukaryotic cytoskeletal proteins. Heterologous production of Hp71 in Escherichia coli allowed the isolation of anti-Hp71 antibodies. The antibodies were used (1) to verify the production of Hp71 in H. salinarium and (2) to determine its cytoplasmic localization by immune electron microscopy. Homologous overproduction of Hp71 in H. salinarium and heterologous production in Haloferax volcanii resulted in modifications of cell morphology from rods to extended rods, and from pleiomorphic cells to rods, respectively. Structure prediction methods indicated that Hp71 has a head-rod-tail configuration, including an N-terminal domain with a nucleotide binding motif (P-loop), and an extended discontinuous coiled-coil domain of 330 amino acids. To identify related proteins, the complete genomes of Haemophilus influenzae, Mycoplasma genitalium, and Methanococcus jannaschii were searched for deduced proteins with extended coiled-coil domains. Only one or two proteins were found for each organism, showing that Hp71 is one of only a few prokaryotic intracellular proteins with extended coiled-coil domains. The phenotype upon overproduction and the similarity of Hp71 to the SMC superfamily of P-loop head-rod-tail proteins (named after SMC1, which is involved in the “stability of minichromosomes” in yeast) indicate that Hp71 might be involved in cytoskeleton formation and/or chromosome partitioning in H. salinarium.

Keywords: Key words Archaea; Halobacterium salinarium; Coiled coil; Cytoskeleton; Chromosome partitioning; Cell morphology; MukB; P115; SMC1

Growth at low temperature causes nitrogen limitation in the cyanobacterium Synechococcus sp. PCC 7002 by Toshio Sakamoto; D. A. Bryant (pp. 10-19).

The coloration of cells of the cyanobacterium Synechococcus sp. PCC 7002 changed from normal blue-green to yellow-green when cells were grown at 15° C in a medium containing nitrate as the sole nitrogen source. This change of coloration was similar to a general response to nutrient deprivation (chlorosis). For the chlorotic cells at 15° C, the total amounts of phycobiliproteins and chlorophyll a decreased, high levels of glycogen accumulated, and growth was arithmetic rather than exponential. These changes in composition and growth occurred in cells grown at low (50 μE m^–2 s^–1) as well as high (250 μE m^–2 s^–1) light intensity. After a temperature shift-up to 38° C, chlorotic cells rapidly regained their normal blue-green coloration and normal exponential growth rate within 7 h. When cells were grown at 15° C in a medium containing urea as the reduced nitrogen source, cells grew exponentially and the symptoms of chlorosis were not observed. The decrease in photosynthetic oxygen evolution activity at low temperature was much smaller than the decrease in growth rate for cells grown on nitrate as the nitrogen source. These studies demonstrate that low-temperature-induced chlorosis of Synechococcus sp. PCC 7002 is caused by nitrogen limitation and is not the result of limited photosynthetic activity or photodamage to the photosynthetic apparatus, and that nitrogen assimilation is an important aspect of the low-temperature physiology of cyanobacteria.

Keywords: Key words Chilling tolerance; Chlorosis; Cyanobacterium; Low-temperature acclimation; Nitrogen assimilation; Phycobiliprotein

Alteration of low-temperature susceptibility of the cyanobacterium Synechococcus sp. PCC 7002 by genetic manipulation of membrane lipid unsaturation by Toshio Sakamoto; Gaozhong Shen; Shoichi Higashi; Norio Murata; D. A. Bryant (pp. 20-28).

Cyanobacteria acclimate to low temperature by desaturating their membrane lipids. Mutant strains of Synechococcus sp. PCC 7002 containing insertionally inactivated desA (Δ12 acyl-lipid desaturase) and desB (ω3 acyl-lipid desaturase) genes were produced, and their low-temperature susceptibility was characterized. The desA mutant synthesized no linoleic acid or α-linolenic acid, and the desB mutant did not produce α-linolenic acid. The desA mutant grew more slowly than the wild-type at 22° C and could not grow at 15° C. The desB mutant could not continuously grow at 15° C, although no observable phenotype appeared at higher temperatures. It has been shown that expression of the desA gene occurs at 38° C and is up-regulated at 22° C, and that the desB gene is only expressed at 22° C. These results indicate that the expression of the desA and desB genes occurs at higher temperatures than those at which a significant decline in physiological activities is caused by the absence of their products. The temperature dependency of photosynthesis was not affected by these mutations. Since chlorosis and inability to grow at 15° C with nitrate was suppressed by the substitution of urea as a nitrogen source, it is very likely that the chilling susceptibility of the desaturase mutants is attributable to nutrient limitation.

Keywords: Key words Chilling tolerance; Cyanobacterium; Fatty acid desaturase; Low-temperature acclimation; Membrane lipid; Photosynthesis

Purification and characterization of 9-hexadecenoic acid cis-trans isomerase from Pseudomonas sp. strain E-3 by H. Okuyama; Akio Ueno; Daisuke Enari; Naoki Morita; Teruo Kusano (pp. 29-35).

A 9-hexadecenoic acid cis-trans isomerase (9-isomerase) that catalyzed the cis-to-trans isomerization of the double bond of free 9-cis-hexadecenoic acid [16:1(9c)] was purified to homogeneity from an extract of Pseudomonas sp. strain E-3 and characterized. Electrophoresis of the purified enzyme on both incompletely denaturing and denaturing polyacrylamide gels yielded a single band of a protein with a molecular mass of 80 kDa, suggesting that the isomerase is a monomeric protein of 80 kDa. The 9-isomerase, assayed with 16:1(9c) as a substrate, had a specific activity of 22.8 μmol h^–1 (mg protein)^–1 and a K _m of 117.6 mM. The optimal pH and temperature for catalysis were approximately pH 7–8 and 30° C, respectively. The 9-isomerase catalyzed the cis-to-trans conversion of a double bond at positions 9, 10, or 11, but not that of a double bond at position 6 or 7 of cis-mono-unsaturated fatty acids with carbon chain lengths of 14, 15, 16, and 17. Octadecenoic acids with a double bond at position 9 or 11 were not susceptible to isomerization. These results suggest that 9-isomerase has a strict specificity for both the position of the double bond and the chain length of the fatty acid. The enzyme catalyzed the cis-to-trans isomerization of fatty acids in a free form, and in the presence of a membrane fraction it was also able to isomerize 16:1(9c) esterified to phosphatidylethanolamine. The 9-isomerase was strongly inhibited by catecholic antioxidants such as α-tocopherol and nordihydroguaiaretic acid, but was not inhibited by 1,10-phenanthroline or EDTA or under anoxic conditions. Based on these results, the possible mechanism of catalysis by this enzyme is discussed.

Keywords: Key wordscis-trans Isomerase; Psychrophilic; bacterium; trans-Unsaturated fatty acid; Pseudomonas sp.

Degradation of p-nitrophenol by the phototrophic bacterium Rhodobacter capsulatus by M. D. Roldán; R. Blasco; F. J. Caballero; F. Castillo (pp. 36-42).

The phototrophic bacterium Rhodobacter capsulatus detoxified p-nitrophenol and 4-nitrocatechol. The bacterium tolerated moderate concentrations of p-nitrophenol (up to 0.5 mM) and degraded it under light at an optimal O₂ pressure of 20 kPa. The bacterium did not metabolize the xenobiotic in the dark or under strictly anoxic conditions or high O₂ pressure. Bacterial growth with acetate in the presence of p-nitrophenol took place with the simultaneous release of nonstoichiometric amounts of 4-nitrocatechol, which can also be degraded by the bacterium. Crude extracts from R. capsulatus produced 4-nitrocatechol from p-nitrophenol upon the addition of NAD(P)H, although at a very low rate. A constitutive catechol 1,2-dioxygenase activity yielding cis,cis-muconate was also detected in crude extracts of R. capsulatus. Further degradation of 4-nitrocatechol included both nitrite- and CO₂-releasing steps since: (1) a strain of R. capsulatus (B10) unable to assimilate nitrate and nitrite released nitrite into the medium when grown with p-nitrophenol or 4-nitrocatechol, and the nitrite concentration was stoichiometric with the 4-nitrocatechol degraded, and (2) cultures of R. capsulatus growing microaerobically produced low amounts of ¹⁴CO₂ from radiolabeled p-nitrophenol. The radioactivity was also incorporated into cellular compounds from cells grown with uniformly labeled ¹⁴C-p-nitrophenol. From these results we concluded that the xenobiotic is used as a carbon source by R. capsulatus, but that only the strain able to assimilate nitrite (E1F1) can use p-nitrophenol as a nitrogen source.

Keywords: Key words Biodegradation; Nitrophenol; Nitrocatechol; Phototrophic bacteria; Rhodobacter

Skew or third moment of bacterial generation times by W. J. Voorn; L. J. H. Koppes (pp. 43-51).

We studied two statistical hypotheses for the occurrence of cellular division and compared these hypotheses to available data. The two models were tested by observed distributions of cellular size during steady-state growth. The 30-year-old sloppy size model could be rejected, whereas the recently developed incremental size proposal could not. The latter proposition was accepted by default. We concluded that the time between successive divisions is not simply derived from extant size at cellular division, but rather from interdivisional size increment. We therefore propose that cellular division is regulated by the need of cells at birth to accumulate a certain amount of mass or something related to mass before division.

Keywords: Key wordsEscherichia coli; Kinetics of cellular; division; Cell size distributions; Statistics of size; Skewness; Kurtosis

The Alcaligenes eutrophus hemN gene encoding the oxygen-independent coproporphyrinogen III oxidase, is required for heme biosynthesis during anaerobic growth by Carola Lieb; Roman A. Siddiqui; Birgit Hippler; Dieter Jahn; Bärbel Friedrich (pp. 52-60).

The insertion mutant HF231 of Alcaligenes eutrophus H16 failed to grow anaerobically on nitrate and nitrite. When grown under oxygen limitation, mutant HF231 specifically excreted coproporphyrin III, an intermediate of heme biosynthesis. With the help of a Tn5-labeled fragment, we identified and cloned the corresponding wild-type fragment. Sequence analysis of the mutant locus revealed an open reading frame consisting of 1,473 bp, predicting a protein of 491 amino acids that corresponds to a size of 54.2 kDa. In the non-coding upstream region, consensus elements that are indicative for binding sites of the anaerobic transcriptional regulator Fnr were identified. The deduced polypeptide showed extensive sequence similarity with various bacterial oxygen-independent coproporphyrinogen III oxidases designated HemN. HemN catalyzes the oxidative decarboxylation of coproporphyrinogen III to yield protoporphyrinogen IX. Anaerobic growth on nitrate and nitrite of mutant HF231 was restored by introducing the hemN gene of A. eutrophus or of Pseudomonas aeruginosa on a broad-host-range vector. Likewise, the A. eutrophus hemN complemented heme biosynthesis of a Salmonella typhimurium hemF/hemN double mutant during anaerobic and aerobic growth. Analysis of a transcriptional lacZ gene fusion showed that expression of hemN in A. eutrophus is nitrate-independent and repressed by oxygen.

Keywords: Key wordshemN; Denitrification; Anaerobic heme biosynthesis; Alcaligenes eutrophus

Analysis of changes in congener selectivity during PCB degradation by Burkholderia sp. strain TSN101 with increasing concentrations of PCB and characterization of the bphBCD genes and gene products by G. Mukerjee-Dhar; Takashi Hatta; Minoru Shimura; Kazuhide Kimbara (pp. 61-70).

We isolated and characterized a gram-negative bacterium, Burkholderia sp. strain TSN101, that can degrade polychlorinated biphenyls (PCBs) at concentrations as high as 150 μg Kaneclor 300/ml, a PCB mixture equivalent to Aroclor 1242. Growing cells of strain TSN101 degraded most of the tri- and tetrachlorobiphenyls in medium containing 25 μg Kaneclor 300/ml. Using PCB concentrations of 50–150 μg of Kaneclor 300/ml, the congener selectivity pattern was different and the pattern of chlorine substitution strongly affected degradation of some congeners. At 25 μg Kaneclor 300/ml, strain TSN101 degraded di- and trichlorinated congeners with chlorine substitutions at both the ortho and the para positions. At higher concentrations of Kaneclor 300, di- and trichlorobiphenyls with ortho substituents in both phenyl rings were not degraded well. Trichlorobiphenyls with para and meta substitutents were degraded equally well at all concentrations studied. The ability of strain TSN101 to degrade ortho and para-substituted congeners was confirmed using a defined PCB mixture with chlorine substituents at 2′- and 4′-positions. A 5-kb DNA fragment containing the bphBCD genes was cloned and sequenced. Comparison of the deduced amino acid sequences of these genes with related proteins indicated 99 and 98% sequence similarity to the BphB and BphD of Comamonas testosteroni strain B-356, respectively. The bphC gene product showed 74% sequence similarity to the BphC of Burkholderia cepacia strain LB400 and exhibited a narrow substrate specificity with strong affinity for 2,3-dihydroxybiphenyl. A bphC-disrupted mutant of Burkholderia sp. strain TSN101, constructed by gene replacement, lost the ability to utilize biphenyl, thus supporting the role of the cloned bph gene in biphenyl metabolism.

Keywords: Key words Biodegradation; Burkholderia sp.; Polychlorinated biphenyl; Congener; bph genes

Functional expression in Escherichia coli of the Haemophilus influenzae gene coding for selenocysteine-containing selenophosphate synthetase by Reinhard Wilting; Kalliopi Vamvakidou; A. Böck (pp. 71-75).

The selenophosphate synthetases from several organisms contain a selenocysteine residue in their active site where the Escherichia coli enzyme contains a cysteine. The synthesis of these enzymes, therefore, depends on their own reaction product. To analyse how this self-dependence is correlated with the selenium status, e.g. after recovery from severe selenium starvation, we expressed the gene for the selenocysteine-containing selenophosphate synthetase from Haemophilus influenzae (selD _HI) in an E. coliΔselD strain. Gene selD _HI gave rise to a selenium-containing gene product and also supported – via its activity – the formation of E. coli selenoproteins. The results provide evidence either for the suppression of the UGA_Sec codon with the insertion of an amino acid allowing the formation of a functional product or for a bypass of the selenophosphate requirement. We also show that the selenocysteine synthesis and the insertion systems of the two organisms are fully compatible despite conspicuous differences in the mRNA recognition motif.

Keywords: Key words Selenophosphate; Selenoproteins

Amino acid degradation by the mesophilic sulfate-reducing bacterium Desulfobacterium vacuolatum by G. N. Rees; Christopher G. Harfoot; A. J. Sheehy (pp. 76-80).

Desulfobacterium vacuolatum strain IbRM was able to grow using casamino acids as a source of carbon, energy and nitrogen. Growth was accompanied by utilization of several amino acids and sulfide production. Proline and glutamate were used preferentially and to the greatest extent. Glycine, serine and alanine were used more slowly and only after proline and glutamate were used. Isoleucine, valine, leucine and aspartate decrease was slowest and occurred in a linear fashion throughout the growth phase. Amino acids used from casamino acids, excluding aspartate, were also used as single carbon, energy and nitrogen sources. As a single amino acid, aspartate could only be used as a nitrogen source. Aspartate was not used as an electron acceptor. No growth occurred on any amino acid in the absence of sulfate. As single substrates, isoleucine, proline and glutamate were oxidized without formation of acetate and with molar yields of 13.1, 9.4 and 7.7 g mol^–1, respectively.

Keywords: Key words Sulfate reduction; Desulfobacterium; vacuolatum; Amino acid oxidation; Glutamate; Proline; Isoleucine

Spontaneous mutation in a thermoacidophilic archaeon: evaluation of genetic and physiological factors by Kelly L. Jacobs; D. W. Grogan (pp. 81-83).

We used direct selection of pyrE and pyrF mutants to estimate the rates of spontaneous mutation in Sulfolobus acidocaldarius as a function of genetic background and culture conditions. Fluctuation tests were applied to several genetically marked strains, including one isolated as a putative mutator strain, and to cultures grown over a wide range of temperature and other physiological conditions. The results suggested some impact of auxotrophic markers on the apparent rate of mutation, but no obvious pattern of effect of growth conditions, including those that gave evidence of being physiologically stressful.

Keywords: Key words Archaea; Geothermal habitats; Spontaneous mutation; Genetic background; Growth conditions

Tetrahydrofolate serves as a methyl acceptor in the demethylation of dimethylsulfoniopropionate in cell extracts of sulfate-reducing bacteria by Michael Jansen; T. A. Hansen (pp. 84-87).

Tetrahydrofolate was shown to function as a methyl acceptor in the anaerobic demethylation of dimethylsulfoniopropionate to methylthiopropionate in cell extracts of the sulfate-reducing bacterium strain WN. Dimethylsulfoniopropionate-dependent activities were 0.56 μmol methyltetrahydrofolate min^–1 (mg protein)^–1 and were higher than required to explain the growth rate of strain WN on dimethylsulfoniopropionate. The reaction did not require ATP or reductive activation by titanium(III)-nitrilotriacetic acid. Preincubation of the extract under air significantly decreased the activity (35% loss in 3 h). Three other dimethylsulfoniopropionate-demethylating sulfate reducers, Desulfobacterium niacini, Desulfobacterium vacuolatum, and Desulfobacterium strain PM4, had dimethylsulfoniopropionate:tetrahydrofolate methyltransferase activities of 0.16, 0.05, and 0.24 μmol min^–1 (mg protein)^–1, respectively. No methyltransferase activity to tetrahydrofolate was found with betaine as a substrate, not even in extracts of betaine-grown cells of these sulfate reducers. Dimethylsulfoniopropionate demethylation in cell extracts of strain WN was completely inhibited by 0.5 mM propyl iodide; in the light, the inhibition was far less strong, indicating involvement of a corrinoid-dependent methyltransferase.

Keywords: Key words Dimethylsulfoniopropionate; Methylthiopropionate; Sulfate-reducing bacteria; Desulfobacterium; Tetrahydrofolate; Methyltransferase

Desulfovibrio inopinatus, sp. nov., a new sulfate-reducing bacterium that degrades hydroxyhydroquinone (1,2,4-trihydroxybenzene) by Wolfram Reichenbecher; Bernhard Schink (pp. 88-88).

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Archives of Microbiology (v.169, #1)