bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic diversity and organization of virulence genes in the pathogenic anaerobe Clostridium perfringens
Authors: Canard B. , Saint‐Joanis B. , Cole S. T. 
Published: October 2006

SummaryPulsed‐field gel electrophoresis has been used to assess genomic diversity and to identify virulence regions in 10 strains, representing all five serotypes, of the anaerobic pathogen Clostridium perfringens. Detailed physical and gene maps of the 3.6 Mb circular chromosomes have been established in eight cases and used to deduce a consensus map. With one exception the chromosomal arrangement was relatively constant and map comparison allowed three hypervariable regions to be identified. One of these was associated with the enterotoxin gene, cpe, which is an important cause of human diarrhoea following the ingestion of food contaminated with C. perfringens. Another variable region spanning the major virulence gene plc, which encodes the cytolytic toxin, α, was located near oriC in all cases whereas the gene for another lethal typing toxin, ɛ, was borne by an episome. It now seems likely that the serological variations, and the changes in the pathogenic spectrum which constitute the C. perfringens typing system, may be due entirely to the loss, or acquisition, of extrachromosomal genetic elements.
Transcriptional regulation of the plastocyanin and cytochrome C553 genes from the cyanobacterium Anabaena species PCC 7937
Authors: Bovy Arnaud , de Vrieze Geert , Borrias Miles , Weisbeek Peter 
Published: October 2006

SummaryThe effect of copper on the levels of plastocyanin (PC) and cytochrome c553 (cyt‐c)‐specific transcripts from Anabaena sp. PCC 7937 was investigated. The addition of copper resulted in a marked increase in PC mRNA levels, and a decrease in cyt c mRNA levels. Thus the functional exchange between PC and cyt c seems to be regulated at the mRNA level. The copper‐dependent increase in PC and decrease in cyt c mRNA levels was abolished when chloramphenicol was added to the cells. This suggests that de novo synthesis of at least one trans‐acting element is required to regulate PC and cyt c mRNA levels. Both PC and cyt c mRNA stability was found to be unaltered under varying Cu2+ regimes. This leads to the conclusion that expression of both genes is regulated at the level of initiation of transcription.
Cloning of genes affecting capsule expression in Staphylococcus aureus strain M
Authors: Lee Chia Y. 
Published: October 2006

Summary Staphylococcus aureus strain M produces large amounts of capsular polysaccharide. It produces a non‐encapsulated variant at a frequency of 0.01% at 37° C. At high temperature (43° C), the frequency of capsule loss was shown to be 1–38%. A 19kb plasmid and a prophage were found to be carried by the M strain, but curing of these elements did not affect capsular production. To clone the capsular (cap) genes, a plasmid library of S. aureus M was constructed directly in S. aureus RN4200. The library was then infected with phage 80α. After transduction of the phage lysates to a Cap‐ mutant derived from M strain, a recombinant plasmid was obtained which complemented the mutant to a Cap+ phenotype. Chromosomal walking experiments were used to clone additional nearby cap genes. Complementation tests using a collection of Cap‐ mutants showed that most of the mutants were complemented by a 19.4 kb DNA fragment, suggesting that the majority of the cap genes affecting capsule production are clustered together.
Co‐ordinate expression of virulence genes during swarm‐cell differentiation and population migration of Proteus mirabilis
Authors: Ariison Clive , Lai Hsin‐Chih , Hughes Colin 
Published: October 2006

SummaryThe uropathogenic Gram‐negative bacterium Proteus mirabilis exhibits a form of multicellular behaviour termed swarming, which involves cyclical differentiation of typical vegetative cells into filamentous, multi‐nucleate, hyperflagellate swarm cells capable of rapid and co‐ordinated population migration across surfaces. We observed that differentiation into swarm cells was accompanied by substantial increases in the activities of intracellular urease and extracellular haemolysjn and metalloprotease, which are believed to be central to the pathogenicity of P. mirabills. In addition, the ability of P. mirabilis to invade human urothelial cells in vitro was primarily a characteristic of differentiated swarm cells, not vegetative cells. These virulence factor activities fell back as the cells underwent cyclical reversion to the vegetative form (consolidation), in parallel with the diagnostic modulation of flagellin levels on the cell surface. Control cellular alkaline phosphatase activities did not increase during differentiation or consolidation. Non‐flagellated, non‐motile transposon insertion mutants were unable to invade urothelial cells and they generated only low‐level activities of haemolysin, urease and protease (0–10% of wild type). Motile mutants unable to differentiate into swarm cells were comparably reduced in their haemolytic, ureolytic and invasive phenotypes and generated threefold less protease activity. Mutants that were able to form swarm cells but exhibited various aberrant patterns of swarming migration produced wild‐type activities of haemotysin, urease and protease, but their ability to enter urothelial cells was three‐ to 10‐fold lower. Analysis of haemolysin (hpmA) transcripts showed that during swarm cell differentiation there was a c. 50‐fold increase in the level of the predicted major 5.2 kb and minor 6.9 kb mRNAs transcribed from the hpm operon, and assay of mRNA complimentary to urease (ureC) and flagellin (fliC) gene sequences confirmed that modulation of virulence factor activity during the swarming cycle resulted from differential expression of virulence genes in parallel with fliC gene expression. Hybridization of stage‐specific mRNA with 30 random, non‐overlapping chromosomal gene probes provided no evidence for universal changes in the expression of the P. mirabiis genome, suggesting that differential virulence gene expression may be a specific strategy.
gyrB mutations which confer coumarin resistance also affect DNA supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase
Authors: Confreres Asunción , Maxwell Anthony 
Published: October 2006

SummaryCoumarins are inhibitors of the ATP hydrolsis and DNA supercoiling reactions catalysed by DNA gyrase. Their target is the B subunit of gyrase (GyrB), encoded by the gyrB gene. The exact mode and site of action of the drugs is unknown. We have identified four mutations conferring coumarin resistance to Escherichia coli: Arg‐136 to Cys, His or Ser and Gly‐164 to Val. In vitro, the ATPase and supercoiling activities of the mutant GyrB proteins are reduced relative to the wild‐type enzyme and show resistance to the coumarin antibiotics. Significant differences in the susceptibility of mutant GyrB proteins to inhibition by either chlorobiocin and novobiocin or coumermycin have been found, suggesting wider contacts between coumermycin and GyrB. We discuss the significance of Arg‐136 and Gly‐164 in relation to the notion that coumarin drugs act as competitive inhibitors of the ATPase reaction.
A Salmonella dublin virulence plasmid locus that affects bacterial growth under nutrient‐limited conditions
Authors: Pullinger Gillian D. , Lax Alistair J. 
Published: October 2006

SummaryThis paper reports the characterization of a new locus, vagC/vagD, on the virulence plasmid of Salmonella dublin. Strain G19, harbouring a TnA insertion in vagC, exhibited reduced virulence although vagC was outside the 8 kb essential virulence region. G19 was also unable to grow on minimal‐medium containing various sole carbon/energy sources, unlike the wild‐type and plasmid‐cured strains. Sequencing of the locus revealed the presence of two ORFs (vagC and vagD) which overlapped by one nucleotide. The VagC polypeptide (12 kDa) was observed using minicell expression. Results indicated that vagD was responsible for the pheno‐typic differences observed between the wild type and G19, and that vagC modulated the activity of vagD. Furthermore, microscopic analysis of G19 cells harvested from minimal‐medium plates showed that a high proportion of cells were elongated, which suggested that vagC and vagD might be involved in coordination of plasmid replication with cell division. We propose that vagD, under certain environmental conditions, acts to prevent cell division until plasmid replication is complete, thus aiding plasmid maintenance. vagC and vagD are absent from the related virulence plasmid of Salmonella typhimurium.
petR, located upstream of the fbcFBC operon encoding the cytochrome bc1 complex, is homologous to bacterial response regulators and necessary for photosynthetic and respiratory growth of Rhodobacter capsulatus
Authors: Tokito Mariko K. , Daldal Fevzi 
Published: October 2006

SummaryInterposon mutagenesis of a region upstream of the petABC(fbcFBC) operon, encoding the ubiquinol: cytochrome c2 oxidoreductase (bc1 complex) of the photosynthetic bacterium Rhodobacter capsulatus revealed the presence of two genes, petP and petR. DNA nucleotide sequence determination of this region indicated that petP and petR are transcribed In the same direction as the petABC(fbcFBC) operon, and are translationally coupled. A silent insertion located In the interoperonal region separating petPR and the petABC(fbcFBC) genes indicated that these clusters have separate promoters. The deduced amino acid sequence of the putative petR gene product is homologous to various bacterial response regulators, especially to those of the OmpR subgroup. Moreover, it was found that PetR‐ mutants are unable to grow on rich or minimal media by either photosynthesis or respiration, demonstrating that these gene products are essential for growth of R. capsulatus.
Escherichia coli integration host factor stabilizes bacteriophage Mu repressor interactions with operator DNA in vitro
Authors: Alazard R. , Bétermier M. , Chandler M. 
Published: October 2006

SummaryUsing gel retardation and DNase I protection techniques, we have demonstrated that the Escherichia coli integration host factor (IHF) stabilizes the interaction between Mu repressor and its cognate operator‐binding sites in vitro. These results are discussed in terms of a model in which IHF may commit the phage to the lytic or lysogenic pathway depending on the occupancy of the operator sites by the repressor.
Stabilization of bacteriophage Mu repressor‐operator complexes by the Escherichia coli integration host factor protein
Authors: Gama Maria‐José , Toussaint Ariane , Higgins N. Patrick 
Published: October 2006

SummaryAll of the previously described effects of integration host factor (IHF) on bacteriophage Mu development have supported the view that IHF favours transposition‐replication over the alternative state of lysogenic phage growth. In this report we show that, consistent with a model in which Mu repressor binding to its operators requires a particular topology of the operator DNA, IHF stimulates repressor binding to the Ol and O2 operators and enhances Mu repression. IHF would thus be one of the keys, besides supercoiling and the H‐NS protein, that lock the operator region into the appropriate topological conformation for high‐affinity binding not only of the phage transposase but also of the phage repressor.
Isolation and molecular characterization of a novel broad‐host‐range plasmid from Bordetella bronchiseptica with sequence similarities to plasmids from Gram‐positive organisms
Authors: Antoine Rudy , Locht Camille 
Published: October 2006

SummaryA 2.6kb plasmid, named pBBR1, was isolated from Bordetella bronchiseptica S87. After insertion of an antibiotic resistance marker, this plasmid could be transferred into Escherichia coli, Bordetella pertussis, B. bronchiseptica, Vibrio cholerae, Rhizobium meliloti, and Pseudomonas putida by transformation or conjugation. Conjugation was possible only when the IncP group transfer functions were provided in trans. As shown by incompatibility testing, pBBR1 does not belong to the broad‐host‐range IncP, IncQ or IncW groups. DNA sequence analysis revealed two open reading frames: one was called Rep, involved in replication of the plasmid, and the other, called Mob, was involved in mobilization. Both the amino‐termtnal region of Mob and its promoter region show sequence similarities to Mob/Pre proteins from plasmids of Gram‐positive bacteria. In spite of these sequence similarities, pBBR1 does not replicate via the rolling‐circle mechanism commonly used by small Gram‐positive plasmids. We therefore speculate that pBBR1 may combine a mobilization mechanism of Gram‐positive organisms with a replication mechanism of Gram‐negative organisms. Determination of the plasmid copy number in E. coli and B. pertussis indicated that pBBR1 has a rather high copy number, which, in conjunction with its small size and broad host range, renders it paricularly interesting for studies of broad‐host‐range replicons and for the development of new cloning vectors for a wide range of Gram‐negative bacteria.
Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis, and other alpha‐proteobacteria
Authors: Relman David A. , Lepp Paul W. , Sadler Kay N. , Schmidt Thomas M. 
Published: October 2006

SummaryBacillary angiomatosis (BA) and chronic bartonellosis are bacterial infections of humans which result in an unusual vascular proliferative tissue response. In order to determine their phylogenetic relationships, we have determined greater than 95% of the 16S rRNA sequences for these two organisms by amplification directly from infected BA tissue and from a Bartonella bacilliformis lyophilized culture. The BA agent and B. bacilliformis are closely related alpha‐proteobacteria (98.5%), although the BA agent is more closely related to Rochalimaea quintana (99.1%). Contrary to previous belief, the BA agent is distinct from, and less closely related to, the cat scratch bacillus (Afipia fells) (90.7%). We propose a novel secondary structure in a hypervariable region of the 16S rRNA which is useful for alignment of primary sequences and which may be useful for design of nucleic acid probes.
Expression of the Escherichia coli dam gene
Authors: Løbner‐Olesen Anders , Boye Erik , Marinus M. G. 
Published: October 2006

SummaryThe Escherichia coli dam gene and upstream sequences were cloned from the Kohara phage 4D4. Five promoters were found to contribute to dam gene transcription. PI and P2 (the major promoter) were situated approximately 3.5 kb upstream of the structural gene, P3 was within the aroB gene, P4 was within the urf74.3 gene, and P5 was in the urf74.3‐dam intergenic region. The nucleotide sequence of 2280 bp of DNA containing P1 and P2, was determined and shown to have the potential to encode a protein of approximately 16 kDa between P1, P2, and the aroB gene. This 16 kDa open reading frame has been Identified as aroK, the gene for shikimic acid kinase I. Thus the dam gene is part of an operon containing aroK, aroB, urf74.3, and dam. The transcriptional start points of the promoters were determined. A comparison of their nucleotide sequences suggested that P1‐P4 were all recognized by the σ70 subunit of the RNA polymerase.
DNA twist as a transcriptional sensor for environmental changes
Authors: Wang Jian‐Ying , Syvanen Michael 
Published: October 2006

SummaryA variety of reports describe shifts in the environment which cause a corresponding change in the measured linking number of plasmid DNA isolated from bacterial cells. This change in linking number is often attributed to a change in superhelical density. This, coupled with the observation that transcription is often dependent upon the superhelical density of the DNA template seen in vitro, has led to the suggestion that superhelical density may control expression of certain genes. However, since many environmental changes could, in principle, influence DNA twist itself, then the measured differences in linking number, δLk, may simply be a consequence of variation in twist according to the relationship δLk=δTw+δWr, where δTw and δWr are changes in twist and writhe, respectively. In fact, we show that when an environmental change causes a change in the helical pitch of the DNA, and if the superhelical density of DNA is regulated to remain constant according to the homeostatic model of Menzel and Gellert, then δLkδTw. We have found that there are a number of published reports describing variation in promoter activity as a function of linking number that can be explained by considering twist. We suggest that there are classes of σ70 promoters whose ability to be recognized by RNA polymerase is exquisitely sensitive to the relative orientation of the ‐35 and ‐10 regions, and environmental conditions can control this relative orientation by changing DNA twist. The recA and proU promoters which are activated by cold shock and osmotic shock, respectively, behave as if they are twist‐sensitive promoters. Consideration of DNA twist can also account for the change in activity of a number of other promoters when they are placed in bacterial strains defective in either DNA gyrase or topoisomerase.
A developmentally regulated cysteine proteinase gene of Leishmania mexicana
Authors: Mottram Jeremy C. , Robertson Colin D. , Coombs Graham H. , Barry J. David 
Published: October 2006

SummaryWe have isolated a gene encoding a previously unreported class of trypanosomatid cysteine proteinase (CP) from the protozoan parasite Leishmania mexicana. The single‐copy gene (Imcpa) has several unusual features that distinguish it from CP genes cloned from the related species Trypanosoma brucei and Trypanosoma cruzi. These include a shorter C‐terminal extension of only 10 amino acids and a three‐amino‐acid insertion, GlyValMet, close to the predicted N‐terminus of the mature protein. Northern blot analysis showed that the gene is expressed in all life‐cycle stages but at higher levels in the amastigote stage in the mammal and in stationary phase promastigote cultures which contain the infective meta‐cyclic form of the parasite. A precursor protein of 38 kDa was detected in amastigotes and stationary phase promastigotes with antisera specific to the LmCPa pro‐region, but was barely detectable in early log‐phase promastigotes. Anti‐central domain antisera recognized the 38 kDa precursor and 24 and 27 kDa proteins. The major CPs of L. mexicana amastigotes, previously designated types A, B and C, were not detected with the antisera, suggesting that the gene codes for a previously uncharacterized CP in L. mexicana. The 24 kDa protein detected by the antiserum has no activity towards gelatin but apparently hydrolyses the peptide substrate BzPhe‐ValArgAMC. The relative levels of the 24 and 27 kDa proteins vary between the different life‐cycle stages. The results indicate that expression of this CP is regulated at both the RNA and protein level.
Evasion of type I and type II DNA restriction systems by Incl1 plasmid Collb‐P9 during transfer by bacterial conjugation
Authors: Read Timothy D. , Thomas Angela T. , Wilkins Brian M. 
Published: October 2006

SummaryTransmission of unmodified plasmid Collb‐P9 by bacterial conjugation is markedly resistant to restriction compared with transfer by transformation. One process allowing evasion of type I and II restriction systems involves conjugative transfer of multiple copies of the plasmid. A more specialized evasion mechanism requires the Ard (alleviation of restriction of DNA) system encoded by Collb. The ard gene is transferred early in conjugation and specifically alleviates DNA restriction by all known families of type I enzyme, including Eco K. Collb has no effect on EcoK modification but this activity is impaired by multicopy recombinant plasmids supporting overexpression of ard. Genetic evidence shows that Ard protects Collb from Eco K restriction following conjugative transfer and that this protection requires expression of the gene on the immigrant plasmid. It is proposed that carriage of ard facilitates transfer of Collb between its natural enterobacterial hosts and that the route of DNA entry is important to the restriction‐evasion mechanism.
Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin
Authors: Gilbert H. J. , Hazlewood G. P. , Laurie J. I. , Orpin C. G. , Xue G. P. 
Published: October 2006

SummaryA cDNA (xynA), encoding xylanase A (XYLA), was isolated from a cDNA library, derived from mRNA extracted from the rumen anaerobic fungus, Neocallimastix patriciarum. Recombinant XYLA, purified from Escherichia coli harbouring xynA, had a Mr, of 53000 and hydrolysed oat‐spelt xylan to xylobiose and xylose. The enzyme did not hydrolyse any cellulosic substrates. The nucleotide sequence of xynA revealed a single open reading frame of 1821 bp coding for a protein of Mr, 66192. The predicted primary structure of XYLA comprised an N‐terminal signal peptide followed by a 225‐amino‐acid repeated sequence, which was separated from a tandem 40‐residue C‐terminal repeat by a threonine/proline linker sequence. The large N‐terminal reiterated regions consisted of distinct catalytic domains which displayed similar substrate specificities to the full‐length enzyme. The reiterated structure of XYLA suggests that the enzyme was derived from an ancestral gene which underwent two discrete duplications. Sequence comparison analysis revealed significant homology between XYLA and bacterial xylanases belonging to cellulase/xylanase family G. One of these homologous enzymes is derived from the rumen bacterium Ruminococcus flavefaciens. The homology observed between XYLA and a rumen prokaryote xylanase could be a consequence of the horizontal transfer of genes between rumen prokaryotes and lower eukaryotes, either when the organisms were resident in the rumen, or prior to their colonization of the ruminant. It should also be noted that Neocallimastix XYLA is the first example of a xylanase which consists of reiterated sequences. It remains to be established whether this is a common phenomenon in other rumen fungal plant cell wall hydrolases.
Cell division in Escherichia coli minB mutants
Authors: Akerlund Thomas , Bernander Rolf , Nordström Kurt 
Published: October 2006

SummaryIn Escherichia coli minB mutants, cell division can take place at the cell poles as well as non‐polarly in the cell. We have examined growth, division patterns, and nucleoid distribution in individual cells of a minC point mutant and a minB deletion mutant, and compared them to the corresponding wild‐type strain and an intR1 strain in which the chromosome is overreplicated. The main findings were as follows. In the minB mutants, polar and non‐polar divisions appeared to occur independently of each other. Furthermore, the timing of cell division in the cell cycle was found to be severely affected. In addition, nucleoid conformation and distribution were considerably disturbed. The results obtained call for a re‐evaluation of the role of the MinB system in the E coli cell cycle, and of the concept that limiting quanta of cell division factors are regularly produced during the cell cycle.