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Volume 146,
Issue 6,
2000
Volume 146, Issue 6, 2000
- Microbiology Comment
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PCR-based detection of mobile genetic elements in total community DNA
Kornelia Smalla, Ellen Krögerrecklenfort, Holger Heuer, Winnie Dejonghe, Eva Top, Mark Osborn, Jessica Niewint, Christoph Tebbe, Michelle Barr, Mark Bailey, Alicia Greated, Christopher Thomas, Sarah Turner, Peter Young, Dora Nikolakopoulou, Amalia Karagouni, Anneke Wolters, Jan Dirk van Elsas, Karine Drønen, Ruth Sandaa, Sara Borin, Julia Brabhu, Elisabeth Grohmann and Patricia Sobecky
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- Biochemistry
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Three multidomain esterases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that carry divergent dockerin sequences
The GenBank accession numbers for the sequences reported in this paper are AJ238716 (cesA) and AJ272430 (xynE).
Three enzymes carrying esterase domains have been identified in the rumen cellulolytic anaerobe Ruminococcus flavefaciens 17. The newly characterized CesA gene product (768 amino acids) includes an N-terminal acetylesterase domain and an unidentified C-terminal domain, while the previously characterized XynB enzyme (781 amino acids) includes an internal acetylesterase domain in addition to its N-terminal xylanase catalytic domain. A third gene, xynE, is predicted to encode a multidomain enzyme of 792 amino acids including a family 11 xylanase domain and a C-terminal esterase domain. The esterase domains from CesA and XynB share significant sequence identity (44%) and belong to carbohydrate esterase family 3; both domains are shown here to be capable of deacetylating acetylated xylans, but no evidence was found for ferulic acid esterase activity. The esterase domain of XynE, however, shares 42% amino acid identity with a family 1 phenolic acid esterase domain identified from Clostridum thermocellum XynZ. XynB, XynE and CesA all contain dockerin-like regions in addition to their catalytic domains, suggesting that these enzymes form part of a cellulosome-like multienzyme complex. The dockerin sequences of CesA and XynE differ significantly from those previously described in R. flavefaciens polysaccharidases, including XynB, suggesting that they might represent distinct dockerin specificities.
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- Bioenergetics And Transport
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Cyanide inhibits respiration yet stimulates aerobic growth of Zymomonas mobilis
More LessPotassium cyanide at submillimolar concentrations (20–500 μM) inhibited the high respiration rates of aerobic cultures of Zymomonas mobilis but, remarkably, stimulated culture growth. In batch culture, after an extended lag phase, exponential growth persisted longer, resulting in higher biomass densities. In aerobic chemostat cultures, elevated biomass concentration was observed in the presence of cyanide. This growth stimulation effect is attributed to decreased production of the inhibitory metabolite acetaldehyde at lowered respiration rates, when more reducing equivalents are channelled to alcohol dehydrogenase. Growth in the presence of cyanide did not alter the membrane cytochrome content. In non-growing cyanide-preincubated cells, with ethanol as the respiratory substrate, cyanide increased ATP levels; in such cells, a large part of the cyanide-sensitive respiration was inhibited within a few seconds after ethanol addition, while inhibition of the rest of respiration took several minutes. The more cyanide-sensitive respiration was apparently energy-nongenerating, and was absent in membrane preparations. Pelleting of membranes from cell-free extracts produced ‘soluble’ fractions in which a b-type haem was detectable by reduced minus oxidized difference spectroscopy. The function of the Z. mobilis respiratory chain in cell growth and respiratory protection, and the possible physiological role of aerobic generation of inhibitory metabolites, are discussed.
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- Development And Structure
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Gliding mutants of Mycoplasma mobile: relationships between motility and cell morphology, cell adhesion and microcolony formation
The present study characterizes gliding motility mutants of Mycoplasma mobile which were obtained by UV irradiation. They were identified by their abnormal colony shapes in 0·1% agar medium, showing a reduced number of satellite colonies compared to the wild-type. A total of ten mutants were isolated based on their colony phenotype. Using dark-field and electron microscopy, two classes of mutants, group I and group II, were defined. Cells of group I mutants had irregular, flexible and sometimes elongated head-like structures and showed a tendency to aggregate. Neither binding to glass nor gliding motility was observed in these mutants. Cells of group II mutants were rather spherical in shape, with the long axis reduced to 80% and the short axis enlarged to 120% of that of wild-type cells, respectively. Their gliding speed was 20% faster than that of wild-type cells. Three of the ten mutants remained unclassified. Mutant m6 had a reduced binding activity to glass and a reduced gliding motility with 50% of the speed of the wild-type strain. The ability of wild-type and mutant colonies to adsorb erythrocytes was found to correlate with the binding activity required for gliding, indicating that mycoplasma gliding depends on cytadherence-associated components. Finally, the ability to form microcolonies on surfaces was shown to correlate with the gliding activity, suggesting a certain role of gliding motility in the parasitic life-cycle of mycoplasmas.
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Identification of a novel gene, fimV, involved in twitching motility in Pseudomonas aeruginosa
More LessThe GenBank accession number for the sequence determined in this work is U93274.
Transposon mutagenesis was used to identify a new locus required for twitching motility in Pseudomonas aeruginosa. Four Tn5-B21 mutants which lacked twitching motility and a fifth which exhibited impaired motility were found to map to the same KpnI restriction fragment at approximately 40 min on the P. aeruginosa genome. Cloning and sequencing studies showed that all five transposon insertions occurred within the same 2·8 kb ORF, which was termed fimV. The product of this gene has a putative peptidoglycan-binding domain, predicted transmembrane domains, a highly acidic C terminus and anomalous electrophoretic migration, indicating unusual primary or secondary structure. The P. aeruginosa genome also possesses a paralogue of fimV. Homologues of fimV were also found in the sequenced genomes of the other type-IV-fimbriated bacteria Neisseria gonorrhoeae, Neisseria meningitidis, Legionella pneumophila and Vibrio cholerae, but not in those of other bacteria which lack type IV fimbriae. A fimV homologue was also found in the genome sequence of Shewanella putrefaciens, along with many other homologues of type IV fimbrial genes, indicating that this bacterium is also likely to produce type IV fimbriae. Wild-type twitching motility was restored to fimV mutants by complementation in a dosage-dependent manner. Overexpression of fimV resulted in an unusual phenotype where the cells were massively elongated and migrated in large convoys at the periphery of the colony. It is suggested that FimV may be involved in remodelling of the peptidoglycan layer to enable assembly of the type IV fimbrial structure and machinery.
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- Environmental Microbiology
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Relative abundance of Archaea and Bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization
More LessSlot-blot hybridization of rRNA with domain-specific oligonucleotide probes targeting the 16S rRNA of Archaea and Bacteria was utilized to assess the relative abundance of these domains along a thermal gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). The highest prokaryotic rRNA concentrations (defined as the sum of bacterial and archaeal rRNA) were found in the uppermost sediment surface (0–20 mm), decreasing strongly with depth. This indicates that the microbial activity was mainly occurring in the surface layer of this hydrothermal vent. Furthermore, rRNA concentrations were higher in regions closer to the vent, suggesting that the hydrothermal activity stimulated microbial activity. Archaea seemed to be a minor component of the microbial community at this vent site, even in the zones with higher temperatures. Bacteria made up at least 78% (mean 95%) of the prokaryotic rRNA. However, along the steepest temperature gradient, the proportion of archaeal rRNA increased. Nevertheless, even in the hottest sediment layer where a quantification was possible (in situ temperature 82 °C) archaeal rRNA made up only 11·9% of the prokaryotic rRNA. This suggests that Archaea were generally of minor importance at this vent site and were probably restricted to a narrow niche. The factors that allow Bacteria to dominate in a high temperature environment that was once believed to be the realm of Archaea remain elusive.
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Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments
More LessThe GenBank accession numbers for the sequences determined in this study are given in Methods.
Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy’s Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter. The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria. Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter.
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- Genetics And Molecular Biology
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Quantitative detection of Streptococcus pneumoniae cells harbouring single or multiple copies of the gene encoding the green fluorescent protein
More LessA modified gfp gene from Aequorea victoria, encoding a variant of the green fluorescent protein (GFP), was subcloned into the mobilizable plasmid pMV158. gfp was placed under the control of the inducible P M promoter of the Streptococcus pneumoniae gene malM, cloned in plasmid pLS70. The P M promoter is regulated by the product of the pneumococcal malR gene, which is inactivated by growing the cells in maltose-containing media. By homologous recombination, the P M–gfp construction was integrated into the host chromosome in a single copy. In both conditions (single and multiple copies), the pneumococcal cells were able to express GFP in an inducible or constitutive form, depending on whether the S. pneumoniae strain harboured a wild-type or a mutant malR gene. Quantification of the levels of GFP expressed by cultures supplemented with sucrose or maltose as carbon sources was feasible by fluorescence spectroscopy. Phase-contrast and fluorescence microscopy allowed pneumococcal cells expressing GFP in mixed cultures to be distinguished from those not carrying the gfp gene.
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Restriction fragment differential display of pediocin-resistant Listeria monocytogenes 412 mutants shows consistent overexpression of a putative β-glucoside-specific PTS system
More LessThe EMBL accession numbers for the sequences reported in this paper are AJ251202, AJ251203 and AJ251204.
Pediocin PA-1, which is a bacteriocin produced by lactic acid bacteria, has potential as a biopreservative of food. However, such use may lead to the development of resistance in the target organism. Gene expression in two independent pediocin-resistant mutants of Listeria monocytogenes 412 was compared to the original isolate by restriction fragment differential display PCR (RFDD-PCR). This method amplifies cDNA restriction fragments under stringent PCR conditions, enabled by the use of specific primers complementary to ligated adaptor sequences. RFDD-PCR was very well suited for analysis of listerial gene expression, giving reproducible PCR product profiles. Three gene fragments having increased expression in both resistant mutants were identified. All three had homology to components of β-glucoside-specific phosphoenolpyruvate-dependent phosphotransferase systems (PTS), one fragment having homology to enzyme II permeases, and the two others to phospho-β-glucosidases. Overexpression of the putative PTS system was consistently observed in 10 additional pediocin-resistant mutants, isolated at different pH, salt content and temperature. The results suggest that RFDD-PCR is a strong approach for the analysis of prokaryotic gene expression and that the putative β-glucoside-specific PTS system is involved in mediating pediocin resistance.
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Structure–function analysis of NADPH:nitrate reductase from Aspergillus nidulans: analysis of altered pyridine nucleotide specificity in vivo
More LessNitrate reductase (NaR) catalyses the reduction of nitrate to nitrite via a two-electron transfer. In fungi, the electron donor for NaR is NADPH whereas plants can have two enzymes, NADH:NaR and a bispecific NAD(P)H:NaR. PCR mutagenesis was employed to introduce mutations into the niaD gene of Aspergillus nidulans in order to identify residues involved in co-enzyme specificity. The niaD3000 mutation (NiaD T813D, K814Q) altered co-enzyme specificity: the new enzyme had high levels of NADH:NaR activity in vitro, whilst all NADPH-associated activity was lost. However, strains carrying this mutation did not grow on nitrate. Enzyme assays suggested that this was not due to inhibition of the mutant enzyme by NADPH. All revertants of the niaD3000 mutants had restored NADPH activity and lost NADH activity. Sequence analysis of these revertants showed that they all contained a single amino acid change at Asp-813, suggesting that this position is crucial to co-enzyme specificity. Further studies have shown that the mutant enzyme was not protected from deactivation by either co-factor in cell-free extracts (unlike the wild-type), and that induction of the glucose-6-phosphate dehydrogenase occurred independently of NADPH levels. These data highlight the importance of functional tests in vivo under physiological conditions.
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Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element
More LessThe nifA promoter of Herbaspirillum seropedicae contains potential NtrC, NifA and IHF binding sites together with a −12/−24 σN-dependent promoter. This region has now been investigated by deletion mutagenesis for the effect of NtrC and NifA on the expression of a nifA::lacZ fusion. A 5’ end to the RNA was identified at position 641, 12 bp downstream from the −12/−24 promoter. Footprinting experiments showed that the G residues at positions −26 and −9 are hypermethylated, and that the region from −10 to +10 is partially melted under nitrogen-fixing conditions, confirming that this is the active nifA promoter. In H. seropedicae nifA expression from the σN-dependent promoter is repressed by fixed nitrogen but not by oxygen and is probably activated by the NtrC protein. NifA protein is apparently not essential for nifA expression but it can still bind the NifA upstream activating sequence.
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Identification of a second lipase gene, gehD, in Staphylococcus epidermidis: comparison of sequence with those of other staphylococcal lipases
More LessThe GenBank accession number for the nucleotide sequence determined in this work is AF090142.
The identification and molecular characterization of a previously unidentified lipase, gehD, from the human cutaneous commensal Staphylococcus epidermidis is reported. A lipase-GehC-deficient but otherwise isogenic mutant of S. epidermidis 9 was constructed by allele replacement. However, the mutant was found to retain 50% of the wild-type lipase activity in liquid culture. Rescreening of a genomic library revealed the presence of a second lipase gene, gehD, which was subsequently mapped and sequenced. In common with other staphylococcal lipases, GehD appeared to be translated as a 650–700 amino acid precursor which is processed post-translationally to an extracellular mature lipase of 360 amino acids with a size of approximately 45 kDa. Comparison of the amino acid sequence of GehD with those of other staphylococcal lipases revealed a high level of conservation between the mature lipase domains of different species. By hybridization studies, both gehC and gehD genes were found to be present in S. epidermidis isolates from both clinical and non-clinical backgrounds, but neither hybridized to DNA isolated from other staphylococcal strains. Construction of a phylogenetic tree and calculation of amino acid sequence homologies between mature lipases, however, suggested that the lipases of S. epidermidis may be more closely related to those of Staphylococcus aureus than to each other.
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The Pseudomonas aeruginosa hscA gene encodes Hsc66, a DnaK homologue
More LessThe GenBank accession number for the sequence of the W51D chromosomal region including the hscB, hscA and fdxA genes is AF096864.
Under heat-stress conditions bacteria induce, among other heat-shock proteins, the Hsp70 molecular chaperone (DnaK), which is involved in protein stabilization. It has been shown in Escherichia coli that an Hsp70 homologue called Hsc66, which is widespread in bacteria, functions as a chaperone in vitro. This paper reports the isolation of a Pseudomonas aeruginosa W51D mutant (W51M22) by insertion of the mini-Tn5-Hg transposon, which was unable to grow on ethanol and other short-chain alcohols as sole source of carbon. The transposon insertion in this mutant was shown to be located in the hscA gene encoding Hsc66. The inability of mutant W51M22 to use ethanol was complemented by the E. coli hscBA–fdx operon. The authors characterized the transcriptional arrangement of hscA, showing that it forms part of an operon with the upstream hscB gene, and that it is also expressed from its own promoter. These results are compatible with the P. aeruginosa Hsc66 protein being a functional molecular chaperone involved in the stabilization, in the presence of ethanol, of some proteins required for bacterial growth on short-chain alcohols.
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The Fusobacterium nucleatum porin FomA possesses the general topology of the non-specific porins
More LessFomA is a major non-specific porin of Fusobacterium nucleatum with no sequence similarity to other known porins. According to the topology model, the protein consists of 16 transmembrane β-strands, connected by eight surface-exposed loops and seven periplasmic turns. In this study, the insertion mutagenesis approach was applied to probe the topology model. A Semliki Forest Virus (SFV) epitope was successfully inserted at 11 different sites of the FomA protein and a 6-aa insertion was successfully inserted at two different sites. Correct folding of the mutant proteins and proper incorporation into the outer membrane were assessed by heat modifiability and by an in vivo porin activity assay. Immunofluorescence microscopy analysis of intact cells, using mAbs directed against the inserted SFV epitope, revealed that three of the eight putative extracellular loops are indeed surface-exposed. Trypsin accessibility experiments confirmed the cell surface exposure of two additional loops. The results support the proposed topology model, showing that FomA possesses the general β-barrel topology of the non-specific porins, with the interesting exception that the third loop does not seem to fulfil the role of a constriction loop.
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ctsR of Lactococcus lactis encodes a negative regulator of clp gene expression
More LessThe GenBank accession numbers for the nucleotide sequences of ctsR and ORF555 and their flanking regions are AJ249133 and AJ249134, respectively.
Bacteria undergo a complex programme of differential gene expression in response to stress. In Bacillus subtilis, it was recently shown that CtsR, a negative transcriptional regulator, mediates stress-induced expression of components of the Clp protease complex. In this study, a gene was identified in the Gram-positive bacterium Lactococcus lactis that encodes a 17 kDa product with 38% identity to the CtsR protein of B. subtilis. By Northern analyses it was found that in a L. lactis strain carrying a large internal deletion of ctsR, including the region encoding a putative helix–turn–helix motif, the amounts of clpC, clpP, clpB and clpE mRNAs were increased 3–8-fold compared to those present in wild-type L. lactis MG1363. In another ctsR mutant strain in which only one-third of CtsR was deleted, leaving the putative DNA-binding domain and the C-terminal 29 amino acids intact, only minor derepression of clp gene expression was observed and, furthermore, all the clp genes were still induced by heat. These results indicate that the amino acids of CtsR involved in temperature sensing are located either close to the DNA-binding domain or in the C-terminal part of the protein. Thus, in L. lactis in addition to B. subtilis, CtsR is a key regulator of heat-shock-induced gene expression, suggesting that the presence of CtsR-homologous DNA-binding sites observed in many Gram-positive bacteria reflects functional heat-shock regulatory systems.
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The dnrO gene encodes a DNA-binding protein that regulates daunorubicin production in Streptomyces peucetius by controlling expression of the dnrN pseudo response regulator gene
More LessThe dnrO gene is located adjacent to and divergently transcribed from the response regulator gene, dnrN, that activates the transcription of the dnrI gene, which in turn activates transcription of the daunorubicin biosynthesis genes in Streptomyces peucetius. Gene disruption and replacement of dnrO produced the dnrO::aphII mutant strain and resulted in the complete loss of daunorubicin biosynthesis. Suppression of the dnrO::aphII mutation by the introduction of dnrN or dnrI on a plasmid suggested that DnrO is required for the transcription of dnrN, whose product is known to be required for dnrI expression. These conclusions were supported by the effects of the dnrO mutation on expression of dnrO, dnrN and dnrI, as viewed by melC fusions to each of these regulatory genes. DnrO was overexpressed in Escherichia coli and the cell-free extract was used to conduct mobility shift DNA-binding assays. The results showed that DnrO binds specifically to the overlapping dnrN/dnrO p1 promoter region. Thus, DnrO may regulate the expression of both the dnrN and dnrO genes.
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Genetic linkage of the vanB2 gene cluster to Tn5382 in vancomycin-resistant enterococci and characterization of two novel insertion sequences
More LessGenBank and GenPept accession numbers are given in Table 3 T3 .
VanB-type vancomycin resistance is encoded by the vanB gene cluster, which disseminates by horizontal gene transfer and clonal spread of vancomycin-resistant enterococci (VRE). Genetic linkage of the vanB gene cluster to transposon Tn5382 and the insertion sequences IS16 and IS256-like has previously been shown. In this study linkage of defined vanB gene cluster subtypes to these elements was examined. All the vanB2 subtype strains studied (n=14) revealed co-hybridization of vanB and Tn5382, whereas the strains of vanB1 (n=8) and vanB3 (n=1) subtypes were Tn5382 negative. Conjugative cotransfer of the vanB2 gene cluster and Tn5382 was demonstrated for two strains. DNA sequencing of the vanX B–ORFC region in vanB2 strains confirmed that the vanB2 gene cluster is an integral part of Tn5382. No general pattern of linkage was observed with regard to IS16 and IS256-like. Two novel insertion sequences were identified in specific vanB2 subtype strains. (i) A 1611 bp element (ISEnfa110) was detected in the left flank of Tn5382. Its insertion site, lack of terminal inverted and direct repeats, and two conserved motifs in its putative transposase all conform to the conventions of the IS110 family. (ii) A 787 bp element (ISEnfa200) was detected in the vanS B–vanY B intergenic region. Its ORF encoded a putative protein with 60–70% identity to transposases of the IS200 family. No further copies of ISEnfa110 were found by colony hybridization of 181 enterococcal isolates, whereas ISEnfa200 was found in four additional vanB2 strains from the USA. The five strains had identical ISEnfa200 element insertion sites, and Tn5382 was located downstream from a pbp5 gene conferring high-level ampicillin resistance. These isolates showed related PFGE patterns, suggesting possible clonal spread of a VRE strain harbouring a Tn5382–vanB2–ISEnfa200 element linked to a pbp5 gene conferring ampicillin resistance.
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