- Volume 143, Issue 4, 1997
Volume 143, Issue 4, 1997
- Review Article
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- Microbiology Comment
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- Antigens And Immunity
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Antigenic polymorphism of the lipopolysaccharides from human and animal isolates of Bordetella bronchiseptica
More LessSix monoclonal antibodies (mAbs) against lipopolysaccharides (LPS) from Bordetella pertussis (P1P3, 60.5), B. parapertussis (PP2, PP6, PP8) and B. bronchiseptica (BRg1) were used to examine the presence of antigenic determinants of LPS on B. bronchiseptica cells. Forty-eight clinical isolates of this Gram-negative bacterium (4 canine, 3 equine, 6 porcine, 4 rabbit and 31 human) were examined. Significant cross-reactivities with the heterologous anti-pertussis and anti-parapertussis mAbs were observed. The isolates also exhibited marked antigenic polymorphism. The 48 isolates could be classified in six immunogroups. Purified LPS preparations extracted from some isolates were analysed by ELISA, thin-layer chromatography, and tricine-SDS-PAGE. The results show that four main types of antigenic polymorphism of B. bronchiseptica LPSs exist: (a) heterogeneity of the core, (b) presence or absence of O-chains, (c) differences in the hinge region between O-chain and core, and (d) differences in interactions of LPS with other cell-surface constituents. Smooth-type LPS molecules, detectable with mAb PP6, were more frequently observed in animal isolates (94%) than in human isolates (52%). Reverse frequencies were found with mAb 60.5 (48% of human isolates, 18% of animal isolates), which is unable to react with long-chain LPSs. This observation could be due to the general absence of some lectin-like receptor, specific to the O-chain, on human bronchoalveolar tissues.
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- Biochemistry
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Purification of two Bacillus subtilis proteins which cross-react with antibodies directed against eukaryotic protein kinase C, the His HPr kinase and trigger factor
More LessAs in eukaryotes, phosphorylation of Ser and Thr residues in proteins appears to be a common phenomenon in bacteria. Surprisingly, however, very few Ser/Thr protein kinases have been identified and in this study antibodies directed against mammalian protein kinase C (PKC) have been used in attempts to isolate conserved Ser/Thr protein kinases. Using the mAb M7 against rat brain PKC, a single 70 kDa band was identified in total cell extracts of Bacillus subtilis by Western blotting after SDS-PAGE, whilst using polyclonal antibody α-PKC1p against Saccharomyces cerevisiae PKC a single 67 kDa band was identified by the same procedure. The two proteins were purified independently on the basis of antibody recognition employing two-dimensional gel electrophoresis as a final step, which allowed subsequent microsequencing. The 70 kDa band was thus identified as the phosphoenolpyruvate-dependent His HPr kinase, Enzyme I of the phosphotransferase system. This identity was confirmed using a mutant deleted for ptsl, encoding Enzyme I. The 67 kDa protein was identified as a previously unknown B. subtilis ‘trigger factor’, homologous to an Escherichia coli protein-folding enzyme, peptidylprolyl cis-trans-isomerase implicated in cell division.
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Isolation and characterization of the gene encoding single-stranded-DNA-binding protein (SSB) from four marine Shewanella strains that differ in their temperature and pressure optima for growth
More LessThe ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of eight amino acids were identified which could contribute to either the temperature or pressure adaptation of the proteins. The SSBs from all four Shewanella strains were overproduced and partially purified based upon their ability to bind single-stranded DNA. The differences found among the Shewanella SSBs suggest that these proteins will provide a useful system for exploring the adaptation of protein-protein and protein-DNA interactions at low temperature and high pressure.
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Tellurite reductase activity of nitrate reductase is responsible for the basal resistance of Escherichia coli to tellurite
Tellurite and selenate reductase activities were identified in extracts of Escherichia coli. These activities were detected on non-denaturing polyacrylamide gels using an in situ methyl viologen activity-staining technique. The activity bands produced from membrane-protein extracts had the same RF values as those of nitrate reductases (NRs) A and Z. Tellurite and selenate reductase activities were absent from membranes obtained from mutants deleted in NRs A and Z. Further evidence of the tellurite and selenate reductase activities of NR was demonstrated using rocket immunoelectrophoresis analysis, where the tellurite and selenate reductase activities corresponded to the precipitation arc of NR. Additionally, hypersensitivity to potassium tellurite was observed under aerobic growth conditions in nar mutants. The tac promoter expression of NR A resulted in elevated tellurite resistance. The data obtained also imply that a minimal threshold level of NR A is required to increase resistance. Under anaerobic growth conditions additional tellurite reductase activity was identified in the soluble fraction on non-denaturing gels. Nitrate reductase mutants were not hypersensitive under anaerobic conditions, possibly due to the presence of this additional reductase activity.
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- Biotechnology
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Chemical characterization and spectroscopic analysis of the solubilization products from wheat straw produced by Streptomyces strains grown in solid-state fermentation
The effects of two extraction procedures on the yield and properties of APPL (acid-preciμltable polymeric lignin, or solubilized lignocellulose) produced by four streptomycetes during growth in solid-state fermentation were examined. When APPL was extracted with NaOH (0.1 M) rather than distilled water, yields increased threefold, with Streptomyces chattanoogensis exhibiting maximum solubilization levels [163 mg product (g straw)-1]. Alterations in the characteristics of APPL obtained during extraction with NaOH were detected using cross-polarization and magic-angle sμlnning (CPMAS) 13C NMR and IR spectroscopy and by GC-MS analysis after CuO oxidation, with the most significant changes detected in the cinnamic acid and lignin moieties. When APPL was extracted with NaOH, ester links between hemicellulose and lignin and between hemicellulose and cinnamic acid were cleaved, resulting in a decrease in the alkyl and carbonyl groups attached to lignin, enabling greater solubilization. Yields of APPL extracted with water were lower, but spectral characterization of this APPL suggested a possible role for actinomycete peroxidases and phenolic acid esterases in lignin solubilization. For industrial solubilization of lignocellulose, a possible role for the application of streptomycetes, or their enzymes, in alkali extraction is suggested as a means of increasing solubilization levels.
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- Development And Structure
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Membrane topology analysis of the Bacillus subtilis BofA protein involved in pro-σ K processing
More LessThe Bacillus subtilis BofA protein is involved in regulation of pro-σ K processing in the mother cell during the late stages of sporulation. A computer analysis of the BofA amino acid sequence indicates that it is an integral membrane protein. To determine the membrane topology of the protein, a series of gene fusions of bofA with lacZ or phoA reporter genes in Escherichia coli were analysed. A BofA topological model with two membrane-spanning segments, and with the N- and the C-terminal domains located in the region between the inner and outer membranes surrounding the forespore is presented. The analysis of different modifications of the last five amino acid residues of the BofA protein, obtained by PCR site-directed mutagenesis, suggests a possible role of the C-terminal domain in the regulation of pro-σ K processing.
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Contact with a solid substratum induces cysts in axenic cultures ofPhysarum polycephalum amoebae: mannitol-induced detergent-resistant cells are not true cysts
More LessPrevious workers reported thatPhysarum polycephalum amoebae cultured in liquid axenic medium were induced to form cysts by the addition of mannitol. Their criterion for encystment was the formation of detergent (Triton)-resistant cells (TRC). In this study the frequencies of TRC in suspensions of amoebae from various treatments were compared with counts of cell types identified by transmission electron microscopy. Amoebae treated with mannitol in axenic liquid culture formed 50% TRC after 17 h but no walled cysts were found. It was concluded that TRC induced by mannitol were dense, rounded cells without walls. In contrast, TRC formed after growth to stationary phase on bacterial lawns were walled cells. When resuspended in growth medium, most mannitol-induced TRC reverted to active amoebae within a few minutes, whereas TRC formed on bacteria remained Triton resistant for many hours. It was concluded that delayed reversion of TRC was a more reliable indication of wall formation than Triton resistance alone. Transfer of amoebae from liquid culture to the surface of diluted axenic agar medium resulted in the formation of walled cysts identical in appearance with those formed on bacterial lawns. The results indicated that efficient encystment requires a solid substratum as well as nutrient deprivation.
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- Genetics And Molecular Biology
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Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli
More LessThe genes of the biosynthetic pathway of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) from the Gram-positive moderate halophile Marinococcus halophilus were cloned by functional expression in Escherichia coli. These genes were not only expressed, but also osmoregulated in E. coli, as demonstrated by increasing cytoplasmic ectoine concentration in response to medium salinity. Sequencing of a 4∙4 kb fragment revealed four major ORFs, which were designated ectA, ectB, ectC and orfA. The significance of three of these genes for ectoine synthesis was proved by sequence comparison with known proteins and by physiological experiments. Several deletion derivatives of the sequenced fragment were introduced into E. coli and the resulting clones were investigated for their ability to synthesize ectoine or one of the intermediates in its biosynthetic pathway. It was demonstrated that ectA codes for l -2,4-diaminobutyric acid acetyltransferase, ectB for l -2,4-diaminobutyric acid transaminase and ectC for l -ectoine synthase. A DNA region upstream of ectA was shown to be necessary for the regulated expression of ectoine synthesis in response to the osmolarity of the medium.
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Copper-inducible transcriptional regulation at two promoters in the Escherichia coli copper resistance determinant pco
More LessThe pco determinant of Escherichia coli plasmid pRJ1004 encodes inducible resistance to the trace element copper. The identification of two copper-dependent transcriptional initiation regions within pco that each contain a similar upstream hyphenated dyad motif is described. Deletion constructs showed that this “copper box” motif was essential for copper-inducible activity at both pco promoters, PpcoA and PpcoE. The placement of the motif differs in the two promoters, and PpcoA contains an extended -10 nonamer typical of promoters for which RNA polymerase does not bind specifically to -35 sequences. PpcoE does not contain this motif and is the more strongly expressed promoter. The transcript from PpcoA contains the pcoABCDRS genes, while PpcoE expresses only pcoE. The induction profiles for PpcoA- and PpcoE-lacZ fusions were flattened sigmoidal curves with a gradual response to increasing copper concentration. On high-copy-number plasmids, zinc was found also to induce transcription from both promoters in vivo. Both promoters showed inducible activity in the absence of pcoRS, the plasmid-borne two-component regulatory system, indicating that a second trans-acting regulatory system is present on the chromosome. The pcoR product showed repressor action in the absence of pcoS, while still allowing induction, suggesting the chromosome encoded a similar two-component system to pco. TnphoA insertion mutagenesis identified chromosomal genes which affected promoter expression, including ptsH, ptsl (sugar phosphotransferase system) and cya (adenylate cyclase). The results support that idea that pco-encoded copper resistance is an auxiliary mechanism for handling copper, the regulation of which is integrated with the chromosomal regulation of cellular copper metabolism.
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Expression of a Butyrivibrio fibrisolvens E14 gene (cinB) encoding an enzyme with cinnamoyl ester hydrolase activity is negatively regulated by the product of an adjacent gene (cinR)
More LessA second cinnamoyl ester hydrolase (CEH) encoding gene (cinB) has been characterized from the ruminal bacterium Butyrivibrio fibrisolvens E14. CinB is more similar to CinA (previously named Cinl) (28% amino acid identity), the first CEH described from B. fibrisolvens E14, than either of the enzymes are to any other member of the family of hydrolases to which they belong. Upstream of cinB, and in the opposite orientation, is a gene (cinR) encoding a protein with substantial similarity to members of the MarR family of negative regulators of bacterial gene expression. By alignment of these sequences, a possible helix-turn-helix DNA-binding domain has been identified. CinR was expressed at a high level in Escherichia coli using the lac promoter. In E. coli CinR repressed the expression of CinB, but had no effect on the expression of CinA. In gel mobility-shift assays, CinR bound specifically to the cinR-cinB intergenic region. Two identical 16 nucleotide inverted repeats adjacent to the putative PcinR and PcinB promoters are likely binding sites for CinR. The addition of FAXX (O-[5-O-(trans-feruloyl)-α-L-arabinofuranosyl]-(1,3)-O-ß-D-xylopyranosyl-(1,4)-D-xylopyranose) and Fara [5-O-(trans-feruloyl)-arabinofuranose], but not xylobiose, ferulic acid and a number of other soluble components of hemicellulose, inhibited the binding of CinR to DNA.
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Characterization and overexpression of the Aspergillus niger gene encoding the cAMP-dependent protein kinase catalytic subunit
More LessThe gene pkaC encoding the catalytic subunit of cAMP-dependent protein kinase has been isolated from the industrially important filamentous fungus Aspergillus niger. A probe for screening A. niger phage libraries was generated by a polymerase chain reaction using degenerate primers. cDNA and genomic DNA clones were isolated and sequenced. An open reading frame of 1440 bp, interrupted by three short introns, encodes a polypeptide of 480 amino acids with a calculated molecular mass of 53813 Da. The cAMP-dependent protein kinase catalytic subunit (PKA-C) from A. niger has a 126 amino acid extension at the N-terminus compared to the PKA-C of higher eukaryotes that - except for the first 15 amino acids, which are homologous to the Magnaporthe grisea PKA-C - shows no significant similarity to the N-terminal extension of PKA-C of other lower eukaryotes. The catalytic core of PKA-C of A. niger shows extensive homology with the PKA-C isolated from all other eukaryotes. Low-stringency hybridization did not reveal any other pkaC homologue in A. niger. The cloned pkaC was used for transformation of A. niger, leading to increased levels of pkaC mRNA and PKA-C activity. Transformants overexpressing pkaC were phenotypically different with respect to growth, showing a more compact colony morphology, accompanied by a more dense sporulation, especially on media containing trehalose and glycerol. A number of transformants also showed a strongly reduced or complete absence of sporulation. This phenotype was quickly lost upon propagation of the strains.
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A carboxy-terminal processing protease gene is located immediately upstream of the invasion-associated locus from Bartonella bacilliformis
More LessA gene with homology to those encoding an unusual class of C-terminal processing proteases that flanks the invasion-associated locus iaIAB of Bartonella bacilliformis has been identified. The 1302 bp gene, termed ctpA, is located immediately upstream of the ialA gene and encodes a predicted nascent product of 434 amino acids, producing a mature protein of 411 amino acid residues. The Bartonella CtpA appears to undergo autolysis in vitro, producing multiple products of 43-46 kDa, and a second group of products of 36-37 kDa. Production of CtpA in vivo gives a single product of 41.8 kDa. In addition to a computer-predicted N-terminal secretory signal sequence, the molecular mass difference in vivo versus in vitro indicates that CtpA is likely to be secreted and post-translationally modified. The full-length CtpA protein shows 30% identity to the CtpA protein of Synechocystis sp. 6803 (69% overall sequence similarity). The mature CtpA protein also has significant homology to the tail-specific protease (Tsp) of Escherichia coli, with 22% identity and 62% similarity to an internal region of the 660 amino acid Tsp. The CtpA protein does not appear to exhibit haemolysin, collagenase, or caseinase activity. The ctpA gene is conserved in all Bartonella species examined, as determined by hybridization analyses, but it was not found in Brucella abortus or E. coli. The ctpA gene does not directly affect the erythrocyte-invasion phenotype conferred by iaIAB, but its homology to other stress-response processing proteases implies an important role in survival of this intracellular pathogen.
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Squalene-hopene cyclase from Bradyrhizobium japonicum: cloning, expression, sequence analysis and comparison to other triterpenoid cyclases
More LessWith the help of a PCR-based screening method, the gene encoding squalene-hopene cyclase (SHC) of Bradyrhizobium japonicum USDA 110 was isolated from a cosmid library. The SHC catalyses the cyclization of squalene to hopanoids, a class of triterpenoid lipids recently discovered in nitrogen-fixing, root-nodule-forming Bradyrhizobium bacteria. Hybridization experiments showed that the gene is present in bacteria of all Bradyrhizobium strains tested and in photosynthetic bacteria forming stem nodules on tropical legumes of the genus Aeschynomene. The Bradyrhizobium shc gene is 1983 bp in length and encodes a protein of 660 amino acid residues with a calculated molecular mass of 73671 Da. Comparison of the deduced amino acid sequence with the sequences of other SHCs revealed highest similarity (70%) to the SHC from the Gram-negative Zymomonas mobilis and lower similarity (48%) to the SHCs from the Gram-positive Alicyclobacillus acidocaldarius and Alicyclobacillus acidoterrestris. Bradyrhizobium SHC also showed similarity (38-43%) to eukaryotic oxidosqualene cyclases. The B. japonicum shc gene was expressed in Escherichia coli. The recombinant SHC catalysed the cyclization of squalene to the hopanoids hopene and diplopterol in vitro. However, the formation of the gammacerane derivative tetrahymanol, which is produced in addition to hopanoids in B. japonicum strains in vivo, could not be detected in vitro. Therefore, the presence of a second squalene cyclase in B. japonicum can be assumed. Sequence analysis of 0.5 kb upstream from the shc gene identified a partial ORF with significant similarity to the C-terminus of an ORF located immediately upstream from the shc gene in Z. mobilis. Both ORFs also showed similarity to phytoene desaturases from cyanobacteria and plants. The 3'-end of this ORF from B. japonicum overlaps with 13 bp at the 5'-end of shc. The close proximity of this ORF to shc suggests that shc and this ORF may be part of an operon.
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Identification of genes in Rhizobium leguminosarum bv. trifolii whose products are homologues to a family of ATP-binding proteins
More LessThe wild-type Streptomyces lividans 66 genome contains a 4.3 kb amplifiable DNA unit (AUD), and its four ORFs encode proteins that could not be identified by sequence comparison with databases. One of the gene products (encoded by orf-2) was purified and determined to be a novel 23 kDa protein. This protein is synthesized by the wild-type strain, absent in a variant lacking the AUD and overproduced in a variant in which the AUD is amplified (ADS). Immunological studies and analyses by confocal laser microscopy showed that the 23 kDa protein is associated with the substrate hyphae of the wild-type and the ADS-containing variant. Examination by microscopy revealed that the strain carrying the ADS forms bulges within the substrate hyphae and apical vesicles. These bulges have high levels of associated 23 kDa protein and contain storage-like material.
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Use of an excision reporter plasmid to study the intracellular mobility of the conjugative transposon Tn916 in Gram-positive bacteria
More LessAn excision reporter plasmid was constructed to characterize the intracellular mobility of Tn916 in various Gram-positive bacteria. The reporter component of this plasmid is a chloramphenicol-resistance gene which has been insertionally inactivated with the integrative vector pAT112 containing the attachment site of Tn916. Tn916-mediated excision of pAT112, to produce clones resistant to chloramphenicol, was detected in Enterococcus faecalis BM4110, Listeria monocytogenes L028-Str and Streptococcus gordonii BM120, but not in Lactococcus lactis MG1363-RF or in Streptococcus pneumoniae BM124, and always depended upon the ability of the bacterial host to generate circular forms of the transposon. The results suggest that (i) the excision event, although required, is not sufficient for conjugal transfer to occur and (ii) there is no linear relationship between the donor potential of E. faecalis strains and either the excision frequency of pAT112 or the copy number of Tn916 circular intermediates per cell in these hosts. Excision of pAT112 occurred mainly during the late exponential phase of growth of E. faecalis and L. monocytogenes and this recombination event was not stimulated by heat shock, salt and alcohol stresses or by the presence of tetracycline in the medium.
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The TBP gene from Aspergillus nidulans -structure and expression in Saccharomyces cerevisiae
More LessThe genomic and cDNA copy of the TATA-binding protein (TBP) gene from the filamentous fungus Aspergillus nidulans have been cloned. The gene is interrupted by four introns, one of which is in the long 5' untranslated region of 615 bp. The transcription initiation site was established and the levels of mRNA were analysed under diverse growth conditions and found to vary severalfold. The gene encodes a protein of 268 amino acids composed of an N-terminal domain of 88 amino acids with no significant homology to other TBPs and a C-terminal domain of 180 amino acids with about 95% homology to other fungal TBPs. A cDNA clone under the yeast ADH1 promoter was able to substitute for the yeast TBP gene in vivo; however, the transformants obtained grew poorly at 35°C and on galactose and glycerol at 30°C, though they could grow in the presence of copper ions or aminotriazole at this temperature. This phenotype may be the result of altered function of A. nidulans TBP in certain yeast transcription activation pathways.
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Genes encoding the NAD-reducing hydrogenase ofRhodococcus opacus MR11
More LessThe dissociation of the soluble NAD-reducing hydrogenase of Rhodococcus opacus MR11 into two dimeric proteins with different catalytic activities and cofactor composition is unique among the NAD-reducing hydrogenases studied so far. The genes of the soluble hydrogenase were localized on a 7.4 kbp AsnI fragment of the linear plasmid pHG201 via heterologous hybridization. Analysis of the nucleotide sequence of this fragment revealed the seven open reading frames ORF1, hox F, -U, -Y, -H, -W and ORF7. The six latter ORFs belong to the gene cluster of the soluble hydrogenase. Their gene products are highly homologous to those of the NAD-reducing enzyme of Alcaligenes eutrophus H16. The genes hox F, -U, -Y and -H encode the subunits α, γ, δ and ß, respectively. The gene hoxW encodes a putative protease, which may be essential for C-terminal processing of the ß subunit. Finally, ORF7 encodes a protein which has similarities to cAMP- and cGMP-binding protein kinases, but its function is not known. 0RF1, which lies upstream of the hydrogenase gene cluster, encodes a putative transposase found in IS elements of other bacteria. Northern hybridizations and primer extensions using total RNA of autotrophically and heterotrophically grown cells of R. opacus MR11 indicated that the hydrogenase genes are under control of a α70-like promoter located at the right end of ORF1 and are even transcribed under heterotrophic conditions at a low level. Furthermore, this promoter was shown to be active in the recombinant Escherichia coli strain LHY1 harbouring the 7.4 kbp AsnI fragment, resulting in overexpression of the hydrogenase genes. Although all four subunits of the soluble hydrogenase were shown via Western immunoblots to be synthesized in E. coli, no active enzyme was detectable.
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Structure and gene-polypeptide relationships of the region encoding glycerol diffusion facilitator (glpF) and glycerol kinase (glpk) of Pseudomonas aeruginosa
More LessThe glycerol facilitator is one of the few known examples of bacterial solute transport proteins that catalyse facilitated diffusion across the cytoplasmic membrane. A second protein, glycerol kinase, is involved in entry of external glycerol into cellular metabolism by trapping glycerol in the cytoplasm as sn-glycerol 3-phosphate. Evidence is presented that glycerol transport in Pseudomonas aeruginosa is mediated by a similar transport system. The genes encoding the glycerol facilitator, glpF, and glycerol kinase, glpK, were isolated on a 4.5 kb EcoRI fragment from a chromosomal mini-library by functional complementation of an Escherichia coli glpK mutant after establishing a map of the chromosomal glpFK region with the help of a PCR-amplified glpK segment. The nucleotide sequence revealed that glpF is the promoter-proximal gene of the glpFK operon. The glycerol facilitator and glycerol kinase were identified in a T7 expression system as proteins with apparent molecular masses of 25 and 56 kDa, respectively. The identities of the glycerol facilitator and glycerol kinase amino acid sequences with their counterparts from Escherichia coli were 70 and 81%, respectively; this similarity extended to two homologues in the genome sequence of Haemophilus influenzae. A chromosomal δglpFK mutant was isolated by gene replacement. This mutant no longer transported glycerol and could no longer utilize it as sole carbon and energy source. Two ORFs, orfX and orfY, encoding a putative regulatory protein and a carbohydrate kinase of unknown function, were located upstream of the glpFK operon.
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The temperature sensitivity of Bacillus subtilis DB1005 is due to insufficient activity, rather than insufficient concentration, of the mutant σA factor
More LessThe σA factor of Bacillus subtilis DB1005 contains two amino acid substitutions (1198A and 1202A) in the promoter –10 binding region. It has been confirmed that this σ factor is responsible for the temperature sensitivity of B. subtilis DB1005. An investigation was conducted into how the mutantσA could cause temperature-sensitive (Ts) cell growth by analysing its structural stability, cellular concentration and transcriptional activity. The mutant σA was unstable even at the permissive temperature of 37°C (t1/2 59 min), whereas the wild-type counterpart was fairly stable under the same conditions (t 1/2 600 min). However, neither wild-type σA nor mutant σA was stable at 49°C (t 1/2 34 min and 23 min, respectively). Analyses of the rates of σA synthesis revealed that B. subtilis DB1005 was able to compensate for unstable σ by elevating the level of σA at 37°C but not at 49°C. Moreover, overexpression of the mutant σA at 49°C could not suppress the Ts phenotype of B. subtilis DB1005. This indicates that the temperature sensitivity of B. subtilis DB1005 is not due to insufficient σA concentration in the cell. The greater decline of an already reduced activity of the mutant σA at 49°C suggests that the temperature sensitivity of B. subtilis DB1005 is instead the result of a very low activity of σ A probably below a critical level necessary for cell growth.
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The Bacillus subtilis clpC operon encodes DNA repair and competence proteins
More LessClpC of Bacillus subtilis, controlling competence gene expression and survival under stress conditions, is encoded by the fourth gene of a six-gene operon. The product of orf1 contains a potential helix-turn-helix motif, but shows no significant similarities with known protein sequences. The second and third genes encode proteins with similarities to zinc-finger proteins (orf2) and arginine kinases (orf3), respectively. The product of orf5 contains a zinc-finger motif and an ATP-binding domain, and is highly similar to the product of the Escherichia coli sms gene. A strain bearing a disruption of orf5 showed increased sensitivity to the alkylating agent methyl methanesulfonate. Furthermore, this mutant strain displayed decreased capacity for genetic recombination as measured by transformation experiments. The last open reading frame, orf6, encodes a protein with limited similarity in its C-terminal part to the B. subtilis comEA gene product and to the UvrC DNA repair excinuclease. Inactivation of orf5 resulted in strongly diminished transformation with all types of DNA. Mutations affecting either orf5 or orf6 resulted in strains with decreased resistance to UV-irradiation in the stationary phase, indicating that these proteins play a role in the development of a nonspecific stationary-phase resistance to UV-irradiation. Moreover, these results suggest an involvement of both proteins in transformation and presumably in DNA repair.
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Molecular characterization of the bet genes encoding glycine betaine synthesis in Sinorhizobium meliloti 102F34
As a first step towards the elucidation of the molecular mechanisms responsible for the utilization of choline and glycine betaine (betaine) either as carbon and nitrogen sources or as osmoprotectants in Sinorhizobium meliloti, we selected a Tn5 mutant, LTS23-1020, which failed to grow on choline but grew on betaine. The mutant was deficient in choline dehydrogenase (CDH) activity, failed to oxidize [methyl-14C]choline to [methyl-14C]betaine, and did not use choline, but still used betaine, as an osmoprotectant. The Tn5 mutation in LTS23-1020 was complemented by plasmid pCH034, isolated from a genomic bank of S. meliloti 102F34. Subcloning and DNA sequencing showed that pCH034 harbours two ORFs which showed 60% and 57% identity with the Escherichia coli betB gene encoding betaine-aldehyde dehydrogenase (BADH) and betA gene encoding CDH, respectively. In addition to the homology with E. coli genes, the deduced sequence of the sinorhizobial BADH protein displays consensus sequences also found in plant BADHs. The deduced sequence of the sinorhizobial CDH protein shares only 21% identical residues with choline oxidase from Arthrobacter globiformis. The structural organization of the betBA genes in S. meliloti differs from that described in E. coli: (i) the two ORFs are separated by a 210 bp sequence containing inverted repeats ressembling a putative rho-independent transcription terminator, and (ii) no sequence homologous to betT (high-affinity choline transport system) or betI (regulator) was found in the vicinity of the sinorhizobial betBA genes. Evidence is also presented that the S. meliloti betBA genes are not located on the megaplasmids.
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- Pathogenicity And Medical Microbiology
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The ability of Escherichia coli O157:H7 to decrease its intracellular pH and resist the toxicity of acetic acid
More LessBatch cultures of Escherichia coli K-12 grew well in an anaerobic glucose medium at pH 5.9, but even small amounts of acetate (20 mM) inhibited growth and fermentation. E. coli O157:H7 was at least fourfold more resistant to acetate than K-12. Continuous cultures of E. coli K-12 (pH 5.9, dilution rate 0.085 h-1) did not wash out until the sodium acetate concentration in the input medium was 80 mM, whereas E. coli O157:H7 persisted until the sodium acetate concentration was 160 mM. E. coli K-12 cells accumulated as much as 500 mM acetate, but the intracellular acetate concentration of O157:H7 was never greater than 300 mM. Differences in acetate accumulation could be explained by intracellular pH and the transmembrane pH gradient (δpH). E. coli K-12 maintained a more or less constant δpH (intracellular pH 6.8), but E. coli O157:H7 let its δpH decrease from 0.9 to 0.2 units as sodium acetate was added to the medium. Sodium acetate increased the rate of glucose consumption, but there was little evidence to support the idea that acetate was creating a futile cycle of protons. Increases in glucose consumption rate could be explained by increases in D-lactate production and decreases in ATP production. Intracellular acetate was initially lower than the amount predicted by ∆pH, but intracellular acetate and δpH were in equilibrium when the external acetate concentrations were high. Based on these results, the acetate tolerance of O157:H7 can be explained by fundamental differences in metabolism and intracellular pH regulation. By decreasing the intracellular pH and producing large amounts of D-lactate, O157:H7 is able to decrease δpH and prevent toxic accumulations of intracellular acetate anion.
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Homologous regions of the Salmonella enteritidis virulence plasmid and the chromosome of Salmonella typhi encode thiol: disulphide oxidoreductases belonging to the DsbA thioredoxin family
More LessThe nucleotide sequence relatedness between the chromosome of Salmonella typhi and the virulence plasmid of Salmonella enteritidis was investigated using short DNA probes of < 2 kb covering the whole virulence plasmid sequence. Only one homologous region was detected. This region was subsequently cloned and partially sequenced. Sequences closely related to the pefl gene and the ORFs orf7, orf8 and orf9, which are located downstream of the fimbrial pef operon of the Salmonella typhimurium virulence plasmid, were detected. Sequencing of the cloned S. typhi DNA fragment also revealed identity with genes of the fimbrial sef operon characterized in the chromosome of S. enteritidis. These nucleotide sequences mapped upstream of the S. typhi chromosomal region homologous to the S. enteritidis virulence plasmid. The general organization of the cloned S. typhi chromosomal fragment was similar to the fimbriae-encoding region of the S. typhimurium virulence plasmid. The deduced product of orf8 in the S. typhimurium virulence plasmid, as well as those of the corresponding ORFs in the homologous region of the S. typhi chromosome and in the S. enteritidis virulence plasmid (designated dlt and dlp, respectively), appeared to be related to the thioredoxin family of thiol:disulphide oxidoreductases. The dlp gene was able to complement the DTT-sensitive phenotype, the inability to metabolize glucose 1-phosphate and the low alkaline phosphatase activity of a dsbA mutant of Escherichia coli. The dlt gene partially complemented the lack of alkaline phosphatase activity, but not the other mutant phenotypes. The products of both genes could be detected using the T7 RNA polymerase promoter expression system. The estimated molecular masses of the products of the dlt and dlp genes by SDS-PAGE were 26 and 23 kDa, respectively, the first being in agreement with the deduced amino acid sequence and the latter, somewhat smaller. The processing of a possible leader peptide in the Dlp protein, but not in the Dlt protein, could be responsible for this difference. The Dlp protein appeared as a doublet band on SDS-PAGE, which is characteristic of the oxidized and reduced states of this kind of protein.
The EMBL accession numbers for the sequences of dlt and dlp reported in this paper are X94325 and X94326, respectively.
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Variation within serovars of Neisseria gonorrhoeae detected by structural analysis of outer-membrane protein PIB and by pulsed-field gel electrophoresis
More LessOuter-membrane protein PI is the antigen responsible for serovar specificity of Neisseria gonorrhoeae and is a potential vaccine target. In order to investigate possible hidden variation within a serovar, the sequence of the por genes encoding protein PIB have been obtained from a series of strains, including isolates known to be epidemiologically linked. The inferred amino acid sequences of the PIB molecules of isolates from known sexual contacts were identical, but non-related isolates showed significant heterogeneity in PIB sequence. These differences were not confined to the two variable regions (Var1 and Var2) which have previously been identified, but were largely, although not exclusively, located in regions predicted to form one of eight surface-exposed loops. The isolates were subjected to pulsed-field gel electrophoresis of restriction digests of chromosomal DNA, which also demonstrated identity between linked strains but revealed diversity within a serovar. The deduced amino acid sequences of PIB were also used to synthesize peptides for epitope-mapping experiments. These revealed that some mAbs, used to define serovar specificity, recognized linear epitopes located in loops 5 and 6, while others appeared to recognize conformational epitopes elsewhere in the molecule. The occurrence of the sequence differences within a serovar, which are not detected by the serotyping reagents, reveals that PIB represents a potential source of information which should permit considerably more detailed epidemiological studies than are currently possible and focuses attention on more conserved regions of the protein as potential targets for vaccination.
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Differences in genetic diversity of nonecapsulated Haemophilus influenzae from various diseases
More LessGenetic relationships among 80 isolates of nonencapsulated Haemophilus influenzae recovered from different disease types were determined by multilocus enzyme electrophoresis (MEE) at 13 enzyme loci in an attempt to assess the association between multilocus genotype and disease. The isolates were obtained from 15 patients with meningitis, 10 with otitis media, 19 with chronic bronchitis, 20 with cystic fibrosis, and 16 were obtained from healthy carriers. The 80 isolates were assigned to 69 electrophoretic types (ETs) falling into 5 groups. Isolates from each disease entity were represented by a variety of genotypes; however, cluster analysis from a matrix of genetic distances between ETs revealed that the ETs of the otitis media and meningitis isolates were all clustered within a genetic distance of 0∙55 (group 1). In addition, no genotypes were shared between H. influenzae carrier isolates and isolates from cases of disease. H. influenzae isolates from healthy individuals were distributed significantly differently from those from chronic bronchitis meningitis and otitis media patients. The genetic diversity (H) of carrier strains was greatest, although not statistically different from that of isolates from patients with disease. It was concluded that the genetic distribution of acute disease isolates is not random over the five ET groups, although the genetic diversity within the groups is not different. The effect of bacterial persistence in the host on the genetic diversity of H. influenzae is discussed.
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- Physiology And Growth
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Photoreactivation in an archaeon from geothermal environments
More LessUV-inactivated cells of Sulfolobus acidocaldarius rapidly regained viability when exposed to white light This recovery was strictly dependent upon illumination with visible light and was not attenuated by prior dark-incubation. The kinetics of photoreactivation were determined at several temperatures and at several wavelengths of light. The results obtained in vivo were consistent with a DNA photolyase having a broad action spectrum. Photoreactivation of S. acidocaldarius apparently represents the first DNA repair process to be measured in an archaeon which grows optimally near 80°C.
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Expression analysis of the ssgA gene product, associated with sporulation and cell division in Streptomyces griseus
More LessThe ssgA gene of Streptomyces griseus B2682, when present in high copy number, results in both suppression of sporulation and fragmented growth of mycelia. Western analysis with polyclonal antibodies against the gene product (SsgA) revealed a close correlation between SsgA accumulation and the onset of sporulation in wild-type cells. The protein was only detected in the cytoplasm. Certain developmental mutants of S. griseus (afs, relC and brgA) which are defective in aerial mycelium formation in solid culture and submerged spore formation in liquid culture failed to accumulate SsgA. The SsgA protein appeared shortly (1 h) after nutritional shift-down of strain B2682 cells, afs mutant cells sporulated and expressed SsgA only when A-factor was present both before and after nutritional shift-down. Introduction of the ssgA gene in a low-copy-number vector into strain B2682 resulted in fivefold overexpression of SsgA, and was accompanied by fragmented growth of mycelia and suppression of submerged spore formation (in liquid culture) and aerial mycelium formation (in solid culture). Streptomycin production was not inhibited. In a control experiment, a nonfunctional ssgA gene possessing a frameshift mutation near its N-terminus had no effect on either growth or sporulation. It is proposed that the ssgA gene product plays a role in promoting the developmental process of S. griseus.
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An interfacial uptake mechanism for the degradation of pyrene by a Rhodococcus strain
More LessThe mechanism of uptake of polycyclic aromatic hydrocarbons (PAHs) was studied using a kinetic approach by electrolytic respirometry. In the case of the degradation of pyrene dissolved in a non-water-soluble non-degradable solvent (2,2,4,4,6,8,8-heptamethylnonane), by a Rhodococcus sp., two successive phases of exponential growth, during which over 80% of substrate degradation took place, were clearly characterized. During the second phase of biodegradation, rates of pyrene uptake were higher than those determined in abiotic conditions for the physicochemical transfer of pyrene from the solvent to the aqueous phase and no evidence for the presence of glycolipidic biosurfactants was obtained. The value of the specific growth rate for the first phase (𝜇max) was independent of the volume of the solvent phase and of the concentration of pyrene and was, in all cases, higher than that for the second phase (𝜇i). The 𝜇i values increased with the volume of the solvent phase but were independent of pyrene concentration, a clear indication of an interfacial uptake mechanism. The experimental kinetic data fitted well with a mathematical model incorporating PAH uptake both from the interface and from the aqueous medium by a population consisting of adsorbed cells in dynamic equilibrium with the cells in the aqueous medium, interfacial uptake being predominant in these experiments. Similar results were obtained for the degradation of fluoranthene. This newly demonstrated mechanism of PAH uptake is of great significance for the degradation of higher PAHs.
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Pyruvate carboxylase as an anaplerotic enzyme in Corynebacterium glutamicum
More LessThe recent discovery that phosphoenolpyruvate carboxylase (PEPCx) is dispensable for growth and lysine production in Corynebacterium glutamicum implies that this organism possesses (an) alternative anaplerotic enzyme(s). In permeabilized cells of C. glutamicum, we detected pyruvate carboxylase (PCx) activity. This activity was effectively inhibited by low concentrations of ADP, AMP and acetyl-CoA. PCx activity was highest [45 ± 5 nmol min−1 (mg dry wt)−1] in cells grown on lactate or pyruvate, and was about two- to threefold lower when the cells were grown on glucose or acetate, suggesting that formation of PCx is regulated by the carbon source in the growth medium. In cells grown at low concentrations of biotin (< 5 μg I−1), PCx activity was drastically reduced, indicating that the enzyme is a biotin protein. Growth experiments with the wild-type and a defined PEPCx-negative mutant of C. glutamicum on glucose showed that the mutant has a significantly higher demand for biotin than the wild-type, whereas both strains have the same high biotin requirement for growth on lactate and the same low biotin requirement for growth on acetate. These results indicate that (i) PCx is an essential anaplerotic enzyme for growth on glucose in the absence of PEPCx, (ii) PCx is an essential anaplerotic enzyme for growth on lactate even in the presence of PEPCx, and (iii) PCx has no anaplerotic significance for growth on acetate as the carbon source. In support of these conclusions, screening for clones unable to grow on a minimal medium containing lactate, but able to grow on a medium containing glucose or acetate, led to the isolation of PCx-defective mutants of C. glutamicum.
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Effects of alternative methyl group acceptors on the growth energetics of the O-demethylating anaerobe Holophaga foetida
More LessThe anaerobic bacterium Holophaga foetida can metabolize the methyl groups of methoxylated aromatic compounds either to acetate or to dimethyl sulphide. The effects of this metabolic flexibility were investigated under conditions of excess; substrate (batch culture) and substrate limitation (chemostat culture). Growth yield data suggest that transfer of the methyl groups to sulphide, in contrast to the homoacetogenic transfer to CO2, was not coupled to energy conservation. Under conditions of excess substrate, methyl groups were quantitatively transferred to sulphide. Growth yields decreased but growth rates increased upon the addition of sulphide during exponential growth in pH- and sulphide-regulated batch cultures. From the measured growth yields, the Gibbs free energy dissipation of catabolism plus anabolism ( ) was calculated using stoichiometric equations incorporating biomass formation (macrochemical equations). The observed increase in growth rate correlated well with an increase in , suggesting a relationship between growth kinetics and growth energetics. During steady-state growth in pH- and sulphide-regulated chemostat culture, a considerable fraction of the methyl groups was converted to acetate, despite the presence of sulphide. This resulted in similar growth yields and correspondingly similar values in the presence and absence of sulphide. Apparently, H. foetida uncouples catabolism and anabolism in batch culture under conditions of excess substrate to a greater extent than in the chemostat under substrate limitation, by transferring the methyl groups quantitatively to sulphide and thereby dissipating the Gibbs free energy change of the methyl transfer. The physiological significance of these findings could be that H. foetida adjusts the energetics of its metabolism to the growth conditions (i) to maximize the growth rate if substrate is available in excess or, (ii) to maximize the growth yield if substrate is limiting.
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Periplasmic cyclic 1,2-β-glucan in Brucella spp. is not osmoregulated
More LessBiosynthesis of periplasmic cyclic 1,2-β-glucans in Brucella ovis strain REO198 and B. abortus strain S19 was found to be carried out by membrane-bound enzymes that use UDP-glucose (UDP-Glc) as donor substrate. Contrary to what happens in species of the genera Agrobacterium and Rhizobium, the accumulation of the reaction products in Brucella appeared not to be osmoticaliy regulated. Incubation of permeabilized cells with UDP-[14C]Glc led to the formation of soluble neutral cyclic 1,2-β-glucans and [14C]glucose-labelled glucoproteins. PAGE of pulse–chase experiments carried out with permeabilized cells showed that the molecular mass of the labelled protein was indistinguishable from Agrobacterium tumefaciens A348 and Rhizobium fredii USDA191 glucoproteins known to be intermediates in the synthesis of cyclic glucans. Brucella total membrane preparations were less efficient than permeabilized cells in the formation of cyclic glucan; this was attributed to defective cyclization. Accumulation of protein intermediates having oligosaccharides of high molecular mass that were not released from the protein was observed after chase with 2 mM UDP-Glc. This defect was not observed when permeabilized cells were used as enzyme preparation, thus suggesting that in Brucella a factor(s) that was lost or inactivated upon the preparation of membranes was required for the effective regulation between elongation and cyclization reactions.
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Comparative physiology of salt tolerance in Candida tropicalis and Saccharomyces cerevisiae
More LessThe salt tolerance of the respiratory yeast Candida tropicalis and the fermentative yeast Saccharomyces cerevisiae have been compared in glucose media. C. tropicalis showed a better adaptation to Na+ and Li+ and maintained higher intracellular K+:Na+ and K+:Li+ ratios than S. cerevisiae However, C. tropicalis showed a poorer adaptation to osmotic stress (produced by KCI and sorbitol) and exhibited reduced glycerol production as compared to S. cerevisiae In media with the non-repressing sugar galactose as carbon source, S. cerevisiae exhibited reduced glycerol production and increased sensitivity to osmotic stress. Under these conditions, S. cerevisiae, but not C. tropicalis, utilized trehalose as a more important osmolyte than glycerol. These results suggest that the relative tolerance of yeast to the osmotic and cation toxicities of NaCl, and the underlying relative capabilities for osmolyte synthesis and cation transport, are modulated by the general catabolite control exerted by glucose.
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Metabolic flux response to salt-induced stress in the halotoleirant yeast Debaryomyces hansenii
More LessThe toxic effect of NaCl and KCI on growth of the marine yeast Debaryomyces, hansenii on glucose or glycerol was studied. Above a threshold value, both salts reduced the specific growth rate, specific glucose and glycerol respiration rates and specific glucose fermentation rate, as well as biomass yields. The exponential inhibition constant, k, and minimum toxic concentration, c min, were similar for all physiological parameters assayed. The effect of either salt on the specific activity of several glycolytic enzymes showed a similar inhibition pattern, although at much lower salt concentrations compared with the physiological parameters. In agreement with published results on glycerol phosphate dehydrogenase stimulation by salt, we present evidence that a general glycolytic flux deviation could occur naturally during salt stress, due to the intrinsic sensitivity of the glycolytic enzymes to intracellular ion concentrations.
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- Plant-Microbe Interactions
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The soybean cultivar specificity gene noIX is present, expressed in a nodD-dependent manner, and of symbiotic significance in cultivar-nonspecific strains of Rhizobium (Sinorhizobium) fredii
More LessRhizobium (now Sinorhizobium) fredii is a symbiotic nitrogen-fixing bacterium that can nodulate soybean in a cultivar-specific manner. This process is governed by a set of negatively acting nodulation genes termed noIXWBTUV. These genes prevent R. fredii strain USDA257 from infecting soybean cultivars such as McCall, but they do not block nodulation of cultivar Peking. R. fredii strain USDA191 contains DNA sequences that hybridize to noIXWBTUV, yet it forms normal nitrogen-fixing nodules on both McCall and Peking soybean. These sequences were isolated and their structure and function examined in comparison to noIXWBTUV of strain USDA257. Restriction maps of the two loci are identical, as is a 2∙4 kb DNA sequence that corresponds to noIX and its promoter region. Expression of noIX by strain USDA191 is flavonoid-dependent in culture and readily detectable in nodules. The gene is not inducible in a mutant of strain USDA191 that lacks the regulatory nodD1 gene, and its expression is greatly attenuated in a nodD2 mutant. noIX is also present and flavonoid-inducible in HH103, a second R. fredii strain that nodulates McCall soybean normally. Inactivation of noIX in strain HH103, USDA191 or USDA257 leads to retardation of initial nodulation rates on soybean cultivars such as Peking and to acquisition of the capacity to form nitrogen-fixing nodules on two species of Erythrina. noIX is thus of symbiotic significance in all three strains, even though it regulates soybean cultivar specificity only in strain USDA257.
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Identification of genes in Rhizobium leguminosarum bv. trifolii whose products are homologues to a family of ATP-binding proteins
More LessThe specific interaction between rhizobia and their hosts requires many genes that influence both early and late steps in symbiosis. Three new genes, designated prsD, prsE (protein secretion) and orf3, were identified adjacent to the exo133 mutation in a cosmid carrying the genomic DNA of Rhizobium leguminosarum bv. trifolii TA1. The prsDE genes share significant homology to the genes encoding ABC transporter proteins PrtDE from Erwinia chrysanthemi and AprDE from Pseudomonas aeruginosa which export the proteases in these bacteria. PrsD shows at least five potential transmembrane hydrophobic regions and a large hydrophilic domain containing an ATP/GTP binding cassette. PrsE has only one potential transmembrane hydrophobic domain in the N-terminal part and is proposed to function as an accessory factor in the transport system. ORF3, like PrtF and AprF, has a typical N-terminal signal sequence but has no homology to these proteins. The insertion of a kanamycin resistance cassette into the prsD gene of the R. leguminosarum bv. trifolii TA1 wild-type strain created a mutant which produced a normal amount of exopolysaccharide but was not effective in the nodulation of clover plants.
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A secreted aspartic proteinase from Glomerella cingulata: purification of the enzyme and molecular cloning of the cDNA
More LessA secreted aspartic proteinase from Glomerella cingulata (GcSAP) as purified to homogeneity by ion exchange chromatography. The enzyme has an M r of 36000 as estimated by SDS-PAGE, optimal activity from pH 3∙5 to pH 4∙0 and is inhibited by pepstatin. The N-terminal sequence, 23 residues long, was used to design a gene-specific primer. This was used in 3ʹ RACE (rapid amplification of cDNA ends) PCR to amplify a 1∙2 kb fragment of the gcsap DNA. A second gene-specific primer was designed and used in 5ʹ RACE PCR to clone the 5՛ region. This yielded a 600 bp DNA fragment and completed the open reading frame. The gcsap open reading frame encodes a protein with a 78 residue prepro-sequence typical of other fungal secreted aspartic proteinases. Based on the deduced sequence, the mature enzyme contains 329 amino acids and shows approximately 40% identity to other fungal aspartic proteinases. Subsequent cloning and sequencing of gcsap fragments obtained from PCR with genomic DNA revealed a 73 bp intron beginning at nt 728. Southern nalyses at medium and high stringency indicated that G. cingulata possesses ne gene for the secreted aspartic proteinase, and Northern blots indicated that gene expression was induced by exogenous protein and repressed by ammonium salts. GcSAP s a putative pathogenicity factor of G. cingulata, and it will now be possible to create SAP- mutants and assess the role GcSAP lays in pathogenicity.
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- Systematics
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Homologous regions of the Salmonella enteritidis virulence plasmid and the chromosome of Salmonella typhi encode thiol: disulphide oxidoreductases belonging to the DsbA thioredoxin family
More LessDNA sequences of a fragment of nifH from diverse cyanobacteria were amplified, cloned and sequenced to determine the evolutionary relationship of nitrogenase within the cyanobacteria as a group, and to provide a basis for the identification of uncultivated strains of cyanobacteria in the environment. Analysis of 30 nitrogenase DNA and deduced amino acid sequences from cyanobacteria representing five major taxonomic subdivisions showed great variation in phylogenetic distances between the sequences. Sequences from heterocystous cyanobacteria formed a coherent cluster, in which branching forms did not form a clade distinct from the non-branching forms. Nitrogenase sequences from the unicellular cyanobacteria Gloeothece and Synechococcus sp. RF-1 formed a cluster, as did sequences from the genera Xenococcus and Myxosarcina. The nifH sequences of filamentous nonheterocystous cyanobacteria were not closely related to each other, forming deep branches with respect to the heterocystous cyanobacterial nifH sequences. The phylogeny of nifH based on amino acid sequences was consistent with taxonomic relationships among the strains; for example, a sequence obtained from a natural assemblage believed to be dominated by ‘Lyngbya’ clustered with nifH from Lyngbya lagerheimii. Results also indicate that the phylogeny of nifH among the cyanobacteria is largely consistent with the phylogeny of 16S rRNA, and furthermore that the nifH sequence can be used to identify uncultivated strains of nitrogen-fixing cyanobacteria.
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Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes
More LessMethanotrophic bacteria were enumerated and isolated from the chemocline and surface sediments of marine-salinity Antarctic meromictic lakes located in the Vestfold Hills, Antarctica (68° S 78° E). Most probable number (MPN) analysis indicated that at the chemocline of Ace Lake the methanotroph population made up only a small proportion of the total microbial population and was sharply stratified, with higher populations detected in the surface sediments collected at the edge of Ace Lake and Burton Lake. Methanotrophs were not detected in Pendant Lake. Only a single phenotypic group of methanotrophs was successfully enriched, enumerated and isolated into pure culture from the lake samples. Strains of this group were non-motile, coccoidal in morphology, did not form resting cells, reproduced by constriction, and required seawater for growth. The strains were also psychrophilic, with optimal growth occurring at 10–13°C and maximum growth temperatures of 16–21°C. The ribulose monophosphate pathway but not the serine pathway for incorporation of C1 compounds was detectable in the strains. The guanine plus cytosine (G+C) content of the genomic DNA was 43–46 mol%. Whole-cell fatty acid analysis indicated that 16:1ω8c (37–41%), 16:1ω6c (17–19%), 16:1ω7c (15–19%) and 16:0 (14–15%) were the major fatty acids in the strains. 16S rDNA sequence analysis revealed that the strains form a distinct line of descent in the family Methylococcaceae (group I methanotrophs), with the closest relative being the Louisiana Slope methanotrophic mytilid endosymbiont (91∙8–92∙3% sequence similarity). On the basis of polyphasic taxonomic characteristics the Antarctic lake isolates represent a novel group I methanotrophic genus with the proposed name Methylosphaera hansonii (type strain ACAM 549).
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Use of multilocus enzyme electrophoresis to examine genetic relationships amongst isolates of Mycobacterium intracellulare and related species
More LessAs part of a larger study investigating diversity and distribution of Mycobacterium spp. in Australia, multilocus enzyme electrophoresis was used to assess genetic relationships at 17 enzyme loci amongst a collection of reference strains and isolates initially identified on biochemical and other grounds as M. intracellulare (70), ‘X’ mycobacteria (10), M. scrofulaceum (7), M. avium (8) and M. avium subsp. paratuberculosis (2). Two of the isolates initially identified as M. intracellulare were shown to be quite distinct from the others. Both gave negative results in a species-specific DNA probe test, whilst one was positive by PCR. These results emphasize the uncertainties involved in identifying members of this group. The other M. intracellulare isolates formed a cohesive but diverse group, being divided into 48 electrophoretic types (ETs), with a mean genetic diversity of 0∙38. Forty-three of these ETs contained only single isolates. There was no clear relationship between the serovar and ET designation. The index of association calculated for M. intracellulare was significantly different from zero, suggesting that it is a clonal species. PFGE was also applied to selected isolates from the ETs containing multiple isolates, and some of these could be differentiated further. The strains of M. scrofulaceum and ‘X’ mycobacteria were distinct from M. intracellulare, but themselves were highly heterogeneous, with mean genetic diversities of 0∙66 and 0∙65, respectively. Each of these groups may represent more than one species. M. avium strains were distinct from the two M. avium subsp. paratuberculosis strains, as well as from the other mycobacteria studied.
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Genomic relationships between selected phage types of Salmonella enterica subsp. enterica serotype typhimurium defined by ribotyping, IS200 typing and PFGE
More LessThe genomic relationship between isolates representing 17 definitive phage types (DTs) of Salmonella enterica subsp. enterica serotype typhimurium (S. typhimurium) were analysed using three different typing methods: IS200 typing using the restriction enzymes EcoRI and Pvull, ribotyping using Smal and EcoRI, and PFGE using Xbal. These methods were used to study four DTs in greater detail; in all 18 (DT 49), 10 (DT 110), five (DT 120) and seven (DT 135) isolates were studied. The combined data generated two large clusters, which could be divided into five groups. Within the first cluster, a close similarity was indicated between isolates of the following phage types: group A – DTs 44, 49, 135 and 204c, with DT 9 distantly related; group B – DTs 95 and 99; and group C – DTs 104a, 110 and 120. The other large cluster contained group D – DTs 10, 20 and 146, with DT 12 distantly related, and group E – DTs 69, 103 and 153. The same grouping was observed by principal component analysis, but a minimum spanning tree linked DT 12 to group E and not group D in this analysis. Among the typing methods used, IS200 gave the best representation of the overall similarity between the S. typhimurium isolates. Five different IS200 profiles were obtained among isolates belonging to DT 49. Only one profile was observed within each of the phage types DT 110, 120 and 135. All isolates within each of these four phage types were of one ribotype. Isolates of DT 49 showed four PFGE patterns, while one pattern was present within isolates of the three other phage types. Members of these four phage types were found to be clonally related as they formed tight subclusters separated from isolates of other phage types.
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- Genome Analysis
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A 23.4 kb segment at the 69°-70° region of the Bacillus subtilis genome
More LessWithin the framework of the international project aimed at the sequencing of the Bacillus subtilis genome, a 23 911 bp chromosome segment has been cloned and sequenced. This region (23433 bp; 69°-70° of the genetic map) contains 17 complete ORFs and a partial one. A homology search for the products deduced from the 18 ORFs revealed that twelve of them had significant similarity to known proteins, including the quinolone-resistance protein, ABC transporter, aldehyde dehydrogenase, amino acid transporter, fosmidomycin-resistance protein, CDP-glucose 4,6-dehydratase, glucose-1-phosphate cytidyltransferase and cytochrome P450/NADPH-cytochrome P450 reductase.
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A 23 911 bp region of the Bacillus subtilis genome comprising genes located upstream and downstream of the Iev operon
Within the framework of the European project to sequence the whole Bacillus subtilis 168 genome, a 23 911 bp long chromosomal DNA fragment located around 233° on the B. subtilis genetic map was cloned and sequenced. From the generated sequencing data and the results of the homology search, the primary structure of this region was determined. In addition to the whole Iev operon, the region contains putative genes for an amino acid permease, two different alcohol dehydrogenases, a chitosanase, a protein belonging to the LysR family of transcriptional regulators, a protein related to the MerR transcriptional regulator, up to four proteins related to the product of the spoF gene, and genes coding for nine more inferred proteins of unknown function.
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The signal peptidase II (lsp) gene of Bacillus subtilis
More LessThe gene encoding the type II signal peptidase (SPase II) of Bacillus subtilis was isolated by screening a genomic DNA library of this bacterium for the ability to increase the levels of globomycin resistance in Escherichia coli, and to complement the growth deficiency at the non-permissive temperature of E. coli strain Y815 carrying a temperature-sensitive mutation in its lsp gene for SPase II. The deduced amino acid sequence of the B. subtilis SPase II showed significant similarity with those of other known SPase II enzymes. Activity of the B. subtilis SPase II was demonstrated by a pulse-labelling experiment in E. coli. In B. subtilis, the lsp gene is flanked by the isoleucyl-tRNA synthetase (ileS) gene and the pyrimicline biosynthetic (pyr) gene cluster, which is known to map at 139° of the chromosome. In the Gram-positive bacteria studied thus far, lsp appears to be the first gene in an operon. The promoter-distal gene (orf4) of this operon specifies a hypothetical protein in bacteria and yeast.
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Analysis of the genetic polymorphism between three Streptococcus thermophilus strains by comparing their physical and genetic organization
More LessThe physical maps of Streptococcus thermophilus CNRZ368 and NST2280 strain: were constructed by analysing PFGE patterns obtained with the low-frequency cutting enzymes SmaI, BssHU and SfiI. Their chromosomes are 1864 and 1840 kb circular molecules, respectively. Comparison of their physical maps with that of the reference A054 strain revealed a relatively conserved organization of the restriction sites. Three variable regions were detected with the map of CNRZ368 whereas 15 were found with the map of NST2280. To construct the genetic maps, probes corresponding to 10 single-copy genes, the rrn genes and the insertion sequences IS1191, IS981 and ISS1 were hybridized to Southern blots of chromosomal DNA digested with the different mapping enzymes. Comparison of the genetic maps of the three strains showed a conserved location of the mapped single-copy genes. However, six rrn loci were present in the chromosome of A054 and CNRZ368 whereas five were present in the NST2280 chromosome. A polymorphism was also found in the copy number of the insertion sequences between the three strains.
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Directed introduction of DNA cleavage sites to produce a high-resolution genetic and physical map of the Acinetobacter sp. strain ADP1 (BD413UE) chromosome
More LessThe natural transformability of the soil bacterium Acinetobacter sp. ADP1 (BD413UE), formerly classified as A. calcoaceticus, has facilitated previous physiological and biochemical investigations. In the present studies, the natural transformation system was exploited to generate a physical and genetic map of this strain's 3780·191 kbp circular chromosome. Previously isolated Acinetobacter genes were modified in vitro to incorporate a recognition sequence for the restriction endonuclease Not l. Following transformation of the wild-type strain by the modified DNA, homologous recombination placed each engineered Not l cleavage site at the chromosomal location of the corresponding gene. This allowed precise gene localization and orientation of more than 40 genes relative to a physical map which was constructed with transverse alternating field electrophoresis (TAFE) and Southern hybridization methods. The positions of Not l, Asc l and l-Ceu l recognition sites were determined, and the latter enzyme identified the presence of seven ribosomal RNA operons. Multiple chromosomal copies of insertion sequence IS 1236 were indicated by hybridization. Several of these copies were concentrated in one region of the chromosome in which a spontaneous deletion of approximately 100 kbp occurred. Moreover, contrary to previous reports, ColE1-based plasmids appeared to replicate autonomously in Acinetobacter sp. ADP1.
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Volumes and issues
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Volume 170 (2024)
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Volume 160 (2014)
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Volume 124 (1981)
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Volume 123 (1981)
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Volume 122 (1981)
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Volume 121 (1980)
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Volume 120 (1980)
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Volume 119 (1980)
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Volume 118 (1980)
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Volume 117 (1980)
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Volume 116 (1980)
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Volume 115 (1979)
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Volume 114 (1979)
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Volume 113 (1979)
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Volume 112 (1979)
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Volume 111 (1979)
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Volume 110 (1979)
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Volume 109 (1978)
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Volume 108 (1978)
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Volume 107 (1978)
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Volume 106 (1978)
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Volume 105 (1978)
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Volume 104 (1978)
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Volume 103 (1977)
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Volume 102 (1977)
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Volume 101 (1977)
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Volume 100 (1977)
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Volume 99 (1977)
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Volume 98 (1977)
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Volume 97 (1976)
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Volume 96 (1976)
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Volume 95 (1976)
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Volume 94 (1976)
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Volume 93 (1976)
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Volume 92 (1976)
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Volume 91 (1975)
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Volume 90 (1975)
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Volume 89 (1975)
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Volume 88 (1975)
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Volume 87 (1975)
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Volume 86 (1975)
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Volume 85 (1974)
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Volume 84 (1974)
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Volume 83 (1974)
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Volume 82 (1974)
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Volume 81 (1974)
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Volume 80 (1974)
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Volume 79 (1973)
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Volume 78 (1973)
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Volume 77 (1973)
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Volume 76 (1973)
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Volume 75 (1973)
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Volume 74 (1973)
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Volume 73 (1972)
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Volume 72 (1972)
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Volume 71 (1972)
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Volume 70 (1972)
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Volume 69 (1971)
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Volume 68 (1971)
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Volume 67 (1971)
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Volume 66 (1971)
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Volume 65 (1971)
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Volume 64 (1970)
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Volume 63 (1970)
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Volume 62 (1970)
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Volume 61 (1970)
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Volume 60 (1970)
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Volume 59 (1969)
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Volume 58 (1969)
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Volume 57 (1969)
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Volume 56 (1969)
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Volume 55 (1969)
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Volume 54 (1968)
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Volume 53 (1968)
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Volume 52 (1968)
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Volume 51 (1968)
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Volume 50 (1968)
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Volume 49 (1967)
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Volume 48 (1967)
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Volume 47 (1967)
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Volume 46 (1967)
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Volume 45 (1966)
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Volume 44 (1966)
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Volume 43 (1966)
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Volume 42 (1966)
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Volume 41 (1965)
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Volume 40 (1965)
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Volume 39 (1965)
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Volume 38 (1965)
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Volume 37 (1964)
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Volume 36 (1964)
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Volume 35 (1964)
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Volume 34 (1964)
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Volume 33 (1963)
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Volume 32 (1963)
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Volume 31 (1963)
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Volume 30 (1963)
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Volume 29 (1962)
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Volume 28 (1962)
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Volume 27 (1962)
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Volume 26 (1961)
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Volume 25 (1961)
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Volume 24 (1961)
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Volume 23 (1960)
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Volume 22 (1960)
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Volume 21 (1959)
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Volume 20 (1959)
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Volume 19 (1958)
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Volume 18 (1958)
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Volume 17 (1957)
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Volume 16 (1957)
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Volume 15 (1956)
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Volume 14 (1956)
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Volume 13 (1955)
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Volume 12 (1955)
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Volume 11 (1954)
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Volume 10 (1954)
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Volume 9 (1953)
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Volume 8 (1953)
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Volume 7 (1952)
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Volume 6 (1952)
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Volume 5 (1951)
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Volume 4 (1950)
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Volume 3 (1949)
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Volume 2 (1948)
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Volume 1 (1947)