- Volume 144, Issue 6, 1998

The hydrophobic probe N-phenyl-1-naphthylamine accumulated less in nonpathogenic Yersinia spp. and non-pathogenic and pathogenic Yersinia enterocolitica than in Yersinia pseudotuberculosis or Yersinia pestis. This was largely due to differences in the activity of efflux systems, but also to differences in outer membrane permeability because uptake of the probe in KCN/arsenate-poisoned cells was slower in the former group than in Y. pseudotuberculosis and Y. pestis. The probe accumulation rate was higher in Y. pseudotuberculosis and Y. pestis grown at 37 °C than at 26 °C and was always highest in Y. pestis. These yersiniae had LPSs with shorter polysaccharides than Y. enterocolitica, particularly when grown at 37 °C. Gel liquid-crystalline phase transitions (Tc 28–31 °C) were observed in LPS aggregates of Y. enterocolitica grown at 26 and 37 °C, with no differences between nonpathogenic and pathogenic strains. Y. pseudotuberculosis and Y. pestis LPSs showed no phase transitions and, although the fluidity of LPSs of Y. pseudotuberculosis and Y. enterocolitica grown at 26 °C were close below the Tc of the latter, they were always in a more fluid state than Y. enterocolitica LPS. Comparison with previous studies of Salmonella choleraesuis subsp. choleraesuis serotype minnesota rough LPS showed that the increased fluidity and absence of transition of Y. pseudotuberculosis and Y. pestis LPSs cannot be explained by their shorter polysaccharides and suggested differences at the lipid A/core level. It is proposed that differences in LPS-LPS interactions and efflux activity explain the above observations and reflect the adaptation of Yersinia spp. to different habitats.

LPSs play an important role in bacterial pathogenesis. In this study, the LPS expression of the seven known Bordetella species and its dependency on growth temperature was analysed by oxidative silver staining of proteinase-K-treated whole bacteria separated by Tricine-SDS-PAGE. The bordetellae were found to have extensively variable LPS in a species-specific way. In addition, the human and ovine Bordetella parapertussis strains exhibited host-specific LPS expression. LPSs from human B. parapertussis strains grown at 37 and 25 °C were distinct. Growth temperature also affected LPS production by several Bordetella bronchiseptica strains. In some of these cases, BvgAS, the global regulator of virulence factors, was involved in this regulation of LPS biosynthesis. In contrast, no evidence was found for the involvement of the Bordetella pertussis BvgAS system in regulation of LPS synthesis. The obligate human pathogens B. pertussis and Bordetella holmesii are closely related but were shown to produce immunologically distinct LPSs. These species are isolated from the upper respiratory tract and blood, respectively. This raises several interesting questions concerning the potential role of LPS as a virulence factor in the infection processes.

Analysis of the 16S rRNA genes retrieved directiy from different environments has proven to be a powerful tool that has greatly expanded our knowledge of microbial diversity and phylogeny. It is shown here that sequence similarity between 80 and 100% among 16S rDNAs can be estimated by the electrophoretic migration of their heteroduplexes. This was measured by hybridization and electrophoresis in polyacrylamide gels of the product obtained after PCR amplification of almost the entire 16S rRNA gene from different bacterial species. These heteroduplexes were also observed after amplification of samples containing DNA from two or more bacterial species and a procedure was applied to identify reliably heteroduplexes among the amplification products. The electrophoretic migration of the heteroduplexes observed after PCR was used to detect the presence of 16S rDNAs with different sequences in DNA extracted from both a mixture of two bacterial species and samples containing a natural bacterial community.

Bacterial PII proteins, encoded by glnB genes, are central signalling molecules in nitrogen regulatory pathways and are modulated by post-translational modification in response to the cellular nitrogen status. The glnB gene was cloned from the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme strain ATCC 29133 (PCC 73102) by heterologous hybridization to a Synechococcus sp. strain PCC 7942 gene fragment. Expression of the cloned gene was verified by hybridization to N. punctiforme total RNA and a single cross-reactive polypeptide was observed in immunoblots of N. punctiforme extracts probed with anti-Synechococcus 7942 PII antiserum. Modification of the purified N. punctiforme PII protein by a Synechococcus 7942 PII kinase was observed, but modified forms of PII were not detected in extracts of N. punctiforme from a variety of incubation conditions. The N. punctiforme glnB gene could not be disrupted by targeted gene replacement unless a second copy of glnB was provided in trans, suggesting that the gene or gene product is essential for growth under the conditions tested.

Proteins secreted by Mycobacterium tuberculosis may play a key role in virulence and may also constitute antigens that elicit the host immune response. However, the M. tuberculosis protein export machinery has not been characterized. A library of M. tuberculosis H37Rv genomic DNA fragments ligated into a signal sequence selection vector that contained a leaderless β-lactamase gene and an upstream Tac promoter was constructed. Transformation of Escherichia coli with the M. tuberculosis DNA library and selection on plates containing 50-100 μg ampicillin ml-1 resulted in the identification of 15 Ampr clones out of a total of 14000 transformants. Twelve of the β-lactamase gene fusions conferred high levels of Ampr (up to 1 mg ampicillin ml-1); insert sizes ranged from 350 to 3000 bp. Of ten inserts that were completely sequenced, two were identified as fragments of the genes for M. tuberculosis antigens 85A and 85C, which are the major secreted proteins of this pathogen. Seven of the remaining inserts were ≥97% identical to hypothetical ORFs in the M. tuberculosis genome, one of which encoded a protein with 35% identity to a low-affinity penicillin-binding protein (PBP) from Streptomyces clavuligerus. Four of the seven hypothetical ORFs encoded putative exported proteins with one or more membrane interaction elements, including lipoprotein attachment sites and type I and II transmembrane (TM) segments. All of the inserts encoded typical signal sequences, with the exception of a possible type II membrane protein. It is concluded that expression of β-lactamase gene fusions in E. coli provides a useful system for the identification and analysis of M. tuberculosis signal-sequence-encoding genes.

The enzymes for catabolism of the pentitols D-arabinitol (Dal) and ribitol (Rbt) and the corresponding genes from Klebsiella pneumoniae (dal and rbt) and Escherichia coli (atl and rtl) have been used intensively in experimental evolutionary studies. Four dal and four rbt genes from the chromosome of K. pneumoniae 1033-5P14 were cloned and sequenced. These genes are clustered in two adjacent but divergently transcribed operons and separated by two convergently transcribed repressor genes, daIR and rbtR. Each operon encodes an NAD-dependent pentose dehydrogenase (daID and rbtD), an ATP-dependent pentulose kinase (daIK and rbtK) and a pentose-specific ion symporter (dalT and rbtT). Although the biochemical reactions which they catalyse are highly similar, the enzymes showed interesting deviations. Thus, DalR (313 aa) and RbtR (270 aa) belong to different repressor families, and DalD (455 aa) and RbtD (248 aa), which are active as a monomer or as tetramers, respectively, belong to different dehydrogenase families. Of the two kinases (19.3% identity), DalK (487 aa) belongs to the subfamily of short D-xylulokinases and RbtK (D-ribulokinase; 535 aa) to the subfamily of long kinases. The repressor, dehydrogenase and kinase genes did not show extensive similarity beyond local motifs. This contrasts with the ion symporters (86.6% identity) and their genes (82.7% identity). Due to their unusually high similarity, parts of dalT and rbtT have previously been claimed erroneously to correspond to ‘inverted repeats’ and possible remnants of a ‘metabolic transposon’ comprising the dal and rbt genes. Other characteristic structures, e.g. a secondary attλ site and chi-like sites, as well as the conservation of this gene group in E. coli C are also discussed.

DNA gyrase, an essential type II topoisomerase, mediates negative supercoiling of the bacterial chromosome, thereby affecting the processes of DNA replication, transcription, recombination and repair. The gyrB gene from the Gram-negative soil bacterium Myxococcus xanthus was sequenced. The sequence predicts a protein of 815 amino acid residues displaying significant homology to all known GyrB proteins. A 6-His-GyrB fusion protein was overexpressed in Escherichia coli and purified to near homogeneity using affinity chromatography on Ni-nitrilotriacetic acid-agarose and novobiocin-Sepharose columns. The fusion protein bound novobiocin and cross-reacted with anti-E. coli GyrB antibodies, indicating structural and functional similarities to the E. coli DNA GyrB. The gene was mapped to the region of the origin of replication (oriC of M. xanthus.

Exchange and recombination of chromosomal markers is an intrinsic genetic property of the thermoacidophilic archaeon Sulfolobus acidocaldarius that has not been thoroughly characterized. To clarify the mechanism and experimental usefulness of this process, the frequency of S. acidocaldarius prototrophs produced from mixtures of two pyrimidine auxotrophs under a variety of conditions was determined. The apparent efficiency of genetic exchange was essentially independent of the density of cells deposited on the surface of solid media. Furthermore, recombinant formation could initiate in liquid suspensions, as indicated by high recombinant frequencies resulting from mixtures plated at low cell densities, and the formation of recombinants at equal or higher frequencies in liquid suspensions that were never plated. Apparent initiation of genetic exchange in liquid at 22 °C was not prevented by DNase, prior digestion of parental cells with protease from Streptomyces griseus, or any other non-lethal chemical agent tested. The results support prior indications that chromosomal marker exchange in S. acidocaldarius proceeds via conjugation, and further indicate that this conjugation can initiate quickly in dilute liquid suspension. The mating system of S. acidocaldarius thus appears physiologically distinct from that of Haloferax volcanii but perhaps similar to conjugational transfer of Sulfolobus plasmid pNOB8. The frequency of recombinants formed in these assays (10-4-10-5 per c.f.u.) greatly exceeds the number of spontaneous forward mutational events per generation for biosynthetic genes in S. acidocaldarius. This suggests that chromosomal exchange has the potential to influence the genetic dynamics of natural Sulfolobus populations.

Bacteroides fragilis Bf1 possesses two enzymes having glutamate dehydrogenase (GDH) activity. One is dual cofactor NAD(P)H-dependent, while the other has NADH-specific activity. The gene encoding the NADH-GDH (gdhB) was cloned by complementation of the glutamate auxotrophic mutant Escherichia coli MX3004 and the recombinant protein was characterized with respect to the GDH activities present in the parental organism grown under different nitrogen conditions. The NAD(P)H-dependent GDH of B. fragilis was confirmed to be most active under high ammonia conditions, but the NADH-specific GDH levels were increased by high peptide concentrations in the growth medium and not regulated by the levels of ammonia. Northern blotting analysis showed that gdhB regulation was at the transcription level, with a single transcript of ∼ 1.6 kb being produced. GDH activity was demonstrated by zymography of the parental and recombinant enzymes. The recombinant GDH was NADH-specific and co-migrated with the equivalent enzyme band from B. fragilis cell extracts. The gdhB structural gene comprises 1335 bp and encodes a protein of 445 aa (49 kDa). Comparisons of the derived protein sequence with that of GDH from other bacteria indicated that significant sequence homology and conservation of functional domains exists with enzymes of Family I-type hexameric GDH proteins.

Multiple molecular forms of glucose-6-phosphate dehydrogenase (G6PDH) were detected by activity staining in non-denaturing polyacrylamide gels of cell-free extracts from a range of cyanobacteria including Anabaena sp. PCC 7120, Synechococcus sp. PCC 7942, Plectonema boryanum PCC 73110, Synechocystis sp. PCC 6803, Nostoc sp. MAC PCC 8009 and the marine strain Synechococcus sp. WH7803. In most of the species tested, the profile of G6PDH activities was modulated by the growth of the cells in the presence of exogenous 10 mM glucose. Using an antiserum raised against a fragment of G6PDH from Anabaena sp. PCC 7120, it was shown that the different molecular forms of G6PDH all contained an antigenically related subunit, suggesting that the different forms arose from different quaternary structures involving the same monomer. An insertion mutant of Synechococcus sp. PCC 7942 was constructed in which the opcA gene, adjacent to zwf (encoding G6PDH), was disrupted. Although no reduction in the amount of G6PDH monomers (Zwf) was observed in the opcA mutant, activity staining of native gels indicated that most of this protein is not assembled into one of the active oligomeric forms. The oligomerization of G6PDH in extracts of the opcA mutant was stimulated in vitro by a factor present in crude extracts of the wild-type, suggesting that the product of the opcA gene is involved in the oligomerization and activation of G6PDH.

Omission of potassium from the growth medium caused multiple metabolic impairments and resulted in cessation of growth of the filamentous, heterocystous, nitrogen-fixing cyanobacterium Anahaena torulosa, during both diazotrophic and nitrogen-supplemented growth. Prominent defects observed during potassium deprivation were: (i) the loss of photosynthetic pigments, (ii) impairment of photosynthetic functions, (iii) reduced synthesis of dinitrogenase reductase (Fe-protein), (iv) inhibition of nitrogenase activity, and (v) specific qualitative modifications of protein synthesis leading to the repression of twelve polypeptides and synthesis and accumulation of nine novel polypeptides. The observed metabolic defects were reversible, and growth arrested under prolonged potassium deficiency was fully restored upon re-addition of potassium. Such pleiotropic effects of potassium deficiency demonstrate that apart from its well-known requirement for pH and turgor homeostasis, K+ plays other vital specific roles in cyanobacterial growth and metabolism.

Phytase catalyses the release of phosphate from phytate (myo-inositol hexakisphosphate), the predominant form of phosphorus in cereal grains, oilseeds and legumes. The presence of phytase activity was investigated in 334 strains of 22 species of obligately anaerobic ruminal bacteria. Measurable activities were demonstrated in strains of Selenomonas ruminantium, Megasphaera elsdenii, Prevotella ruminicola, Mitsuokella multiacidus and Treponema spp. Strains isolated from fermentations with cereal grains proved to have high activity, and activity was particularly prevalent in S. ruminantium, with over 96% of the tested strains being positive. The measured phytase activity was found exclusively associated with the bacterial cells and was produced in the presence of approximately 14 mM phosphate. The most highly active strains were all S. ruminantium, with the exception of the one Mitsuokella multiacidus strain examined. Phytase activity varied greatly among positive strains but activities as high as 703 nmol phosphate released (ml culture)-1 were measured for a S. ruminantium strain and 387 nmol phosphate released (ml culture)-1 for the Mitsuokella multiacidus strain.

Incubation of Aspergillus fumigatus NCPF 2140 in growth medium containing 1 % chitin as sole carbon source led to induction of specific extracellular chitinolytic activity of 1.5 μmol GlcNAc released min-1 (mg protein)-1. The effect was repressed by the inclusion of GlcNAc in the medium, indicating regulation by a negative feedback mechanism. Extracellular chitinase activity was inhibited by allosamidin (IC50 0.12 μM). Multiple chitinolytic enzymes were detected on zymograms of extracellular preparations; levels of individual enzymes induced were dependent upon whether cells were incubated with purified colloidal chitin or a crude preparation of crystalline chitin. A major, inducible, 45 kDa chitinase was purified using ammonium sulphate precipitation, chitin affinity chromatography and a novel procedure involving the electroelution of the enzyme from a substrate gel containing glycol chitin. The enzyme is a glycoprotein with endochitinase activity.

Porphyromonas gingivalis has been associated with the development of adult periodontitis and cysteine proteinases with Arg- and Lys-specific activity have been implicated as major virulence factors. In a cell sonicate of P. gingivalis W50, a complex of non-covalently associated proteins has been previously characterized. This complex is composed of a 45 kDa Arg-specific, calcium-stabilized cysteine proteinase (PrtR45), a 48 kDa Lys-specific cysteine proteinase (PrtK48) and seven sequence-related adhesins designated PrtR44, PrtR15, PrtR17, PrtR27, PrtK39, PrtK15 and PrtK44, with all proteins being encoded by the two genes prtR and prtK. It has been proposed that these non-covalently associated complexes form extracellularly after autolytic processing of the PrtR and PrtK polyproteins, with the adhesins binding to the proteinases (PrtR45 and PrtK48) and autoaggregating. Another form of the cell-associated, Arg-specific, calcium-stabilized cysteine proteinase is described here. Designated PrtRII50, it is a discrete 50 kDa protein with no adhesin-association and has enzymic characteristics and an inhibitor/activator profile almost identical to PrtR45. The PrtRII50 proteinase is encoded as a preproprotein by a second gene, prtRII, with high sequence similarity to PrtR except that it lacks the C-terminal adhesin domains. A comparison of the deduced amino acid sequence of PrtRII50 with that of the adhesin-associated proteinases PrtR45 and PrtK48 revealed that PrtRII50 does not contain a C-terminal motif that is conserved in PrtR45 and PrtK48. Related motifs are also found in the adhesin domains of PrtR and PrtK. It is proposed that this conserved motif is an adhesin-binding motif (ABM) involved in association of the PrtR and PrtK proteinases and adhesins into large complexes, as the PrtR-PrtK proteinase-adhesin complex inactivated by N-α-p-tosyl-L-lysine chloromethyl ketone (TLCK) was shown to bind specifically to a synthetic peptide corresponding to the conserved motif in a competitive binding assay.