bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Menkes X‐chromosome disease and the staphylococcal cadmium‐resistance ATPase: a remarkable similarity in protein sequences
Authors: Silver Simon , Nucifora Giuseppina , Phung Le T. 
Published: October 2006

SummaryA search with the proposed amino acid translation product from the new ‘candidate gene’ for human Menkes disease against protein sequence libraries showed a remarkable similarity to that for the cadmium efflux ATPase from Staphylococcus aureus resistance plasmids. The Menkes sequence appears closer to the CadA Cd2+ sequence than to P‐type ATPases from animal sources. Menkes syndrome is an X‐chromosome invariably fatal disease that results from abberant copper metabolism. The gene that is defective in Menkes patients, i.e. the Menkes candidate gene, encodes a P‐type ATPase, whose properties satisfactorily explain the phenotype of the disease. P‐type ATPases are all cation pumps, either for uptake (e.g. the bacterial Kdp K+ ATPase), for efflux (e.g. the muscle sarcoplasmic reticulum Ca2+ ATPase), or for cation exchange (e.g. the animal cell Na+/K+ ATPase). These enzymes have a conserved aspartate residue that is transiently phosphorylated from ATP during the transport cycle, hence the name ‘P‐type’ ATPase. The Menkes sequence shares with the staphylococcal CadA ATPase those regions common to all P‐type ATPases and also an N‐terminal dithiol region that was proposed to be a ‘metal‐binding motif’. There are one or two copies of this motif in the available CadA sequences and six copies in the Menkes sequence.
Analysis in Neisseria meningitidis and other Neisseria species of genes homologous to the FKBP immunophilin family
Authors: McAllister Carl F. , Stephens David S. 
Published: October 2006

SummaryThe immunophilin family of FK506‐binding proteins (FKBPs), involved in eukaryotic protein folding and cell regulation, have recently been found to have prokaryotic homologues. Genes with sequences homologous to those encoding human FKBPs were examined in Neisseria species. An FKBP DNA sequence was present, as shown by the polymerase chain reaction and Southern blotting experiments, in the chromosome of Neisseria meningitidis (14 strains) and in all 11 different commensal Neisseria spp. studied, but was not found in Neisseria gonorrhoeae (11 strains tested) or in Moraxella catarrhalis. The nucleotide and predicted protein sequences of the FKBP‐encoding domain from five of the meningococcal strains were highly conserved (e.g. ≥97% homologous). The meningococcal nucleotide sequence was ≥93% homologous and the consensus meningococcal protein sequence was ≥97% homologous to FKBP sequences found in seven different commensal Neisseria spp. The meningococcal nucleotide and predicted protein sequences were ≥59% homologous to the conserved C‐terminus of the human FKBP gene family.The FKBP nucleotide sequence was present as a single copy in the chromosome of commensal Neisseria spp. and in most strains of N. meningitidis. The FKBP gene was linked to the silent pilin locus, pilS, in class II‐piliated meningococcal strains. In meningococcal strains expressing class I pili, the FKBP gene was linked to one of several pilS loci but not the pilE locus present in these strains. FKBP genes found in commensal Neisseria spp. were not linked to known pilin loci.
Clustering and co‐ordinated activation of carotenoid genes in Myxococcus xanthus by blue light
Authors: Ruiz‐Vázquez Rosa , Fontes Marta , Murillo Francisco J. 
Published: October 2006

SummaryBlue light activates carotenoid production in the non‐photosynthetic, Gram‐negative bacterium Myxococcus xanthus. Light is known to stimulate the expression of two unlinked genes for carotenoid synthesis, carB and carC, through a mechanism in which the regulatory genes carA, carQ and carR take part. Genes carQ and carR are linked together at a separate locus, whereas carA is linked to carB. We have introduced Tn5 at various sites between carA and carB. Chemical analyses of the mutant strains demonstrate the presence in this region of a cluster of genes for carotenoid synthesis. Gene expression analysis strongly argues for most (or all) of the genes in the cluster being transcribed from a single, light‐inducible promoter under the control of genes carA, carQ and carR.
Transcriptional regulation of Salmonella enterica virulence plasmid genes in cultured macrophages
Authors: Rhen Mikael , Riikonen Petri , Taira Suvi 
Published: October 2006

SummaryThe plasmid‐carried spv genes promote virulence of salmonellae in mice by allowing bacterial growth in the reticuloendothelial tissue. When the bacteria are cultivated under normal laboratory conditions the spv genes appear dormant. This communication explores the transcriptional regulation of spv genes within murine macrophage‐like J774‐A.1 cells utilizing a new reporter system. Transcriptional fusions were constructed between promoter elements of the Salmonella enterica var. Typhimurium spv genes and the KS71A fimbrial gene cluster. The expression of KS71A fimbriae In fusion‐carrying Escherichia coli strains was found to be under the control of the transcriptional activator gene spvR. In strains overproducing SpvR, KS71A fimbriae were assembled on the bacterial cell surface and could be detected by bacterial agglutination or immunofluorescence of intact bacteria; the reporter activity was quantified by estimating the percentage of fluorescent bacteria and by immunoblotting of cell lysates. The activity of the reporters, when transformed into the parent Typhimurium TML R66, was low and revealed less than 0.3% fimbriated cells under in vitro culture conditions. A 15–30‐fold increase in fimbriation was observed when the bacteria were cultivated within J774‐A.1 cells. No such increase occurred when the reporter fusions were transformed into TML R66 cured of the virulence plasmid. Insertional inactivation of the spvR gene of the virulence plasmid in Typhimurium TML R66 also abolished induction, whereas corresponding inactivation of spvA or spvB did not reduce induction. No increase in reporter activity was obtained in Typhimurium of line Q1, which is naturally avirulent for mice, although the strain was provided with virulence plasmid pEX102 of line TML R66. We conclude that the intracellular environment of J774‐A.1 cells induces the spv genes and that this induction requires gene functions of both the bacterial chromosome and the virulence plasmid.
Retrotransfer of IncP piasmid R751 from Escherichia coli maxicells: evidence for the genetic sufficiency of self‐transferable plasmids for bacterial conjugation
Authors: Heinemann Jack A. , Ankenbauer Robert G. 
Published: October 2006

SummaryGene transfer between organisms is a prime contributor to evolution. Bacterial conjugation is probably the most important mechanism by which genes are spread among prokaryotes and perhaps also contributes to eukaryotic evolution. Conjugation is mediated by plasmids. The mechanism of conjugation remains ill‐understood despite progress in the identification, mapping and sequencing of genes required for plasmid transmission. All conjugation‐specific genes (those required only for DNA transfer and establishment) identified to date map to plasmids. We found that IncP plasmids could enter and subsequently convert maxicells, which are trapped in a metabolic state that prevents de novo expression of chromosomal genes, into conjugative donors. This suggests that IncP plasmids encode not only necessary functions but indeed all functions specific to DNA transmission. Thus, like viruses, plasmids can convert non‐viable cells into gene vectors.
Identification and characterization of a siderophore regulatory gene (pfrA) of Pseudomonas putida WCS358: homology to the alginate regulatory gene aigQ of Pseudomonas aeruginosa
Authors: Venturi Vittorio , Ottevanger Clemens , Leong John , Weisbeek Peter J. 
Published: October 2006

SummaryGenes encoding biosynthesis of pseudobactin 358 (a microbial iron transport agent) and its cognate outer membrane receptor protein. PupA, are transcribed only under iron limitation in plant growth‐promoting Pseudomonas putida WCS358. Two cosmid clones were identified from a gene bank of WCS358 DNA which could independently and in an iron‐dependent manner activate transcription from a WCS358 siderophore gene promoter in heterologous Pseudomonas strain A225. The functional region of one of the clones was localized by subcloning, transposon Tn3Gus mutagenesis, and DNA sequencing. Genomic transposon insertion mutants in the functional region lost the capacity to activate a siderophore gene promoter fusion transcriptionally; furthermore, these mutants no longer produced pseudobactin 358. The activating region consisted of a single gene designated pfrA (Pseudomonasferric regulator). The pfrA gene codes for a single polypeptide, PfrA, of approximately 18kDa, which has 58% identity to AlgQ (also known as AlgR2), a positive regulator involved in transcriptionally regulating alginate biosynthesis in Pseudomonas aeruginosa. Cross‐complementation studies between the pfrA gene of P. putida and the algQ gene of P. aeruginosa revealed that pfrA can restore mucoidy (alginate production) in an algQ mutant and that algQ could poorly complement a pfrA genomic mutant. It is concluded that PfrA is involved in the positive regulation of siderophore biosynthetic genes in response to iron limitation; furthermore, pfrA and algQ appeared to be interchangeable between P. putida and P. aeruginosa.
The influence of DNA topology on the environmental regulation of a pH‐regulated locus in Salmonella typhimurium
Authors: Karem Kevin , Foster John W. 
Published: October 2006

Summary Salmonella typhimurium is exposed to major shifts in H+ concentration both in its natural and pathogenic environments. The organism undergoes extensive changes in gene expression in response to these pH fluctuations. A current question of regulatory biology is how a change in external pH selectively modulates transcription. We have analysed the expression of one such pH‐regulated locus, aniG, and found it is controlled by several additional environmental conditions including osmolarity and oxygen. For factors such as osmolarity and anaerobiosis, an environmentally triggered change in DNA supercoiling has been suggested as a means for controlling gene expression. Thus, environmentally induced changes in DNA topology were explored as a possible common means for establishing the multiple controls on aniG. The involvement of DNA supercoiling in the genetic response of S. typhimurium to external pH has not previously been defined. This report establishes that alkaline environments lower the linking number of reporter plasmids when compared to acidic environments. A consistent pattern was then established whereby conditions or mutations leading to either increased or decreased negative supercoiling were associated with altered expression of aniG. A similar relationship was observed for another environmentally regulated locus, proU. The DNA topology effects on aniG expression were dependent on the presence of EarA, the negative regulator of aniG. These data can be explained by a model in which repressor‐operator interactions are very sensitive to changes in operator conformation. These environmentally induced topological influences on operator DNA structure contribute to the magnitude of pH control exerted upon aniG.
The major heat‐modifiable outer membrane protein CD is highly conserved among strains of Branhamella catarrhalis
Authors: Murphy Timothy F. , Kirkham Charmaine , Lesse Alan J. 
Published: October 2006

SummaryThe outer membrane of Branhamella catarrhalis contains a major, heat‐modifiable outer membrane protein called CD which has epitopes on the surface of the intact bacterium. The gene encoding CD was cloned and expressed in Escherichia coli. The protein migrates in gels as a doublet, indicating that CD is encoded by single gene whose gene product has two stable conformations. The nucleotide sequence of the gene encoding CD was determined and shows homology with the OprF outer membrane protein of Pseudomonas species. The CD protein contains a proline‐rich region, which appears to account for its aberrant migration in gels. Restriction fragment‐length analysis of 30 isolates of B. catarrhalis with oligonucleotide probes corresponding to sequences in the CD gene produced identical patterns in Southern blot assays. The major heat‐modifiable outer membrane protein CD shares homology with the OprF protein and is highly conserved among strains of B. catarrhalis.
Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA
Authors: Hahn Jeanette , Inamine Gordon , Kozlov Yura , Dubnau David 
Published: October 2006

SummaryThe binding and transport of DNA by competent Bacillus subtilis requires the assembly of a specialized apparatus. We present here the characterization of comE, an operon under competence control that is required for both DNA binding to the competent ceil surface, and for uptake. comE contains three open reading frames (0RF1‐3) read in the forward direction, preceded by a long untranslated leader sequence and an apparent EσA promoter. A minor promoter also is responsible for transcription of ORF2 and ‐3. A transcript containing a single ORF is produced in the reverse direction. The reverse ORF overlaps ORF1 and the untranslated comE leader. The comE transcript is present at a very low level during growth and at an elevated level in stationary‐phase cells. Converseiy, the reverse transcript is present during exponential growth and disappears during stationary phase. The reverse ORF resembles prokaryotic and eukaryotic pyrroiine‐5‐carboxylate reductases, while ORF2 is similar to several dCMP deaminases. 0RF1 and 0RF3 are predicted to be integral membrane proteins. The latter is specifically required for DNA uptake but not for binding.
Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli
Authors: Oppenheim Amos B. , Rudd Kenneth E. , Mendelson Itai , Teff Dinah 
Published: October 2006

SummaryInterspersed repeated DNA sequences are characteristic features of both prokaryotic and eukaryotic genomes. REP sequences are defined as conserved repetitive extragenic palindromic sequences and are found in Escherichia coli, Salmonella typhimurium and other closely related enteric bacteria. These REP sequences may participate in the folding of the bacterial chromosome. In this work we describe a unique class of 28 conserved complex REP clusters, about 100bp long, in which two inverted REPs are separated by a singular integration host factor (IHF) recognition sequence. We term these sequences RIP (for repetitive IHF‐binding palindromic) elements and demonstrate that IHF binds to them specifically. It is estimated that there are about 70 RIP elements in E. coli. Our analysis shows that the RIP elements are evenly distributed around the bacterial chromosome. The possible function of the RIP element is discussed.
nif gene expression studies in Rhodobacter capsulatus: nfrC‐independent repression by high ammonium concentrations
Authors: Hübner Philipp , Masepohl Bernd , Klipp Werner , Bickle Thomas A. 
Published: October 2006

SummaryThe expression of nif genes in Rhodobacter capsulatus depends on the two regulatory genes, rpoN and nifA, encoding a nif‐specific alternative sigma factor of RNA polymerase and a nif‐specific transcriptional activator, respectively. The expression of the rpoN gene itself is also RPON/NIFA dependent. In order to better characterize the regulation of nif gene induction, chromosomal nifH‐, rpoN‐, nifAl‐ and nifA2‐ lacZ fusions were constructed and the expression of these different nif‐lacZ fusions was determined under photoheterotrophic conditions at different starting ammonium concentrations. The two nifA genes were found to be induced first, followed by nifH and finally by rpoN upon weak, medium and strong nitrogen starvation, respectively. This induction profile and the correlation between the expression of the different nif genes suggested that nifAl expression is the limiting factor for nif gene induction. This hypothesis was tested by construction of different nifA1 overexpressing mutants. Contrary to the current model of n/Y gene expression in R. capsulatus, which predicted constitutive nif gene expression in such mutants, a strong repression of nifH and rpoW was found at high ammonium concentration. The low nifH expression under these conditions is unaffected by nifA2 and is not increased in a ntrC mutant, ruling out any role of NTRC as a mediator of this repression. This finding implies an additional, so far unidentified, regulation by fixed nitrogen in R capsulatus. Changing the expression level of rpoN indicated that low levels of RPON are already sufficient for full nifH induction. The nifA1 and rpoN expression mutants were also tested for diazotrophic growth. Similar generation times were determined for the mutants and for the wild type, but diazotrophic growth of the nifA1 overexpressing ntrC mutant RCM14 did not start until after a prolonged lag phase of two to three days.
Isogenic P‐fimbrial deletion mutants of pyelonephritogenic Escherichia coli: the role of α Gal(1–4)β Gal binding in virulence of a wild‐type strain
Authors: Mobley Harry L.T. , Jarvis Karen G. , Elwood John P. , Whittle Donna I. , Lockatell C. Virginia , Russell Robert G. , Johnson David E. , Donnenberg Michael S. , Warren John W. 
Published: October 2006

Summary Escherichia coli strains causing acute pyelonephritis often express multiple fimbrial types and haemolysin, which may contribute to their ability to adhere to, and interact with, kidney epithelial cells. Strain CFT073, a pap+, sfa+, pil+, hly+ pyelonephritis strain, previously established as virulent in the CBA mouse model of ascending urinary tract infection and cytotoxic for cultured human renal epithelial cells, was selected for construction of isogenic strains. From a gene bank of this strain, two distinct copies of the pap operon were isolated. The two P‐fimbrial determinants were sub‐cloned into pCVD442, a positive selection suicide vector containing the sacB gene of Bacillus subtilis. Deletion mutations were introduced into each of the two constructs, within papEFG of one operon and papDEFG of the other. Suicide vectors carrying pap deletions were mobilized from E. coli SM10 lambda pir into CFT073 (NalR) and cointegrates were passaged on non‐selective medium. The first pap mutation was identified by screening a Southern blot of DNA from sucrose‐resistant colonies using a papEFG probe. This mutant retained the MRHA+ phenotype since a second functional copy of pap was still present. A double pap‐deletion mutant, UPEC76, confirmed by Southern blotting, was unable to agglutinate human type O erythrocytes or α Gal(1–4)β Gal‐coated latex beads.CBA mice (N =100) were challenged transurethrally with 105, 106, 107, or 109 cfu of strains CFT073 or UPEC76. After one week, quantitative cultures of urine, bladder, and kidney were done and histologic changes were examined. No substantive differences in organism concentration or histological findings between parent and mutant were detected in urine, bladder, or kidney at any challenge concentration. We conclude that adherence by P fimbriae of uro‐pathogenic E. coli strain CFT073 plays only a subtle role in the development of acute pyelonephritis in the CBA mouse model.
Proteolytic cleavage at arginine residues within the hydrophilic disulphide loop of the Escherichia coli Shiga‐like toxin I A subunit is not essential for cytotoxicity
Authors: Burgess Beverley J. , Roberts Lynne M. 
Published: October 2006

Summary Bschehchia coli Shiga‐like toxin I is a type II ribosome‐inactivating protein composed of an A subunit with RNA‐specific N‐glycosidase activity, non‐covalently associated with a pentamer of B subunits possessing affinity for galabiose‐containing glycolipids. The A subunit contains a single intrachain disulphide bond encompassing a hydrophilic sequence containing two trypsin‐sensitive arginine residues. By analogy with other bacterial toxins it has been proposed that proteolytic nicking, deemed essential for a cytotoxic effect, occurs within this disulphide‐bonded loop to generate the A1 and A2 fragments. Reduced A1 is then believed to translocate an internal membrane to inactivate protein synthesis in the cytosol. In this report, the disulphide‐loop arginines of the SLT I A subunit were mutated to block the specific proteolysis presumed to occur. However, the mutant generated remained an effective toxin having similar catalytic activity to wild‐type toxin and only a marginally reduced cytotoxicity towards cultured cells. We conclude that the disulphide‐loop arginine residues are not the unique and essential processing sites previously assumed, but that processing may occur at alterNatlve accessible sites to compensate for loss of target sites within the loop.
The response of the picoplanktonic marine cyanobacterium Synechococcus species WH7803 to phosphate starvation involves a protein homologous to the periplasmic phosphate‐binding protein of Escherichia coli
Authors: Scanlan David J. , Mann Nicholas H. , Carr Noel G. 
Published: October 2006

SummaryDuring phosphate‐limited growth the marine phycoerythrin‐containing picoplanktonic cyanobacterium Synechococcus sp. WH7803 synthesizes novel polypeptides, including two abundant species of 100 kDa and 32kDa. The 32kDa polypeptide was localized to the cell wall, although in a related strain, Synechococcus sp. WH8103, it could be detected in both the cell wall fraction and the periplasm. The gene (designated pstS) encoding this polypeptide was cloned and shown to be present in a single copy. The deduced amino acid sequence indicated a polypeptide consisting of 326 amino acids with a calculated Mr of 33763. Comparison of this sequence with that obtained by microsequencing the N‐terminus of the 32kDa polypeptide showed that the mature protein was synthesized as a precursor, the first 24 amino acid residues being cleaved between two alanine residues at positions 24 and 25. The amino acid sequence of the mature polypeptide showed 35% identity and 52% similarity to the periplasmic phosphate‐binding protein (PstS) from Escherichia coli, including three regions of much stronger homology which, by comparison with E. coli PstS, are directly involved in phosphate binding. Northern blot analysis revealed a pstS transcript of 1.2 kb in RNA extracted from cells grown in Pi‐replete conditions and one of 1.4 kb in considerably increased abundance under Pi‐depleted conditions. Homologues of the pstS gene were detected in other marine phycoerythrin‐containing Synechococcus strains, but not in freshwater or halotolerant species.
Bacillus subtilis CtaA and CtaB function in haem A biosynthesis
Authors: Svensson Birgitta , Lübben Mathias , Hederstedt Lars 
Published: October 2006

SummaryHaem A, a prosthetic group of many respiratory oxidases, is probably synthesized from haem B (protohaem IX) in a pathway in which haem O is an intermediate. Possible roles of the Bacillus subtilis ctaA and CtaB gene products in haem O and haem A synthesis were studied. Escherichia coli does not contain haem A. The CtaA gene on plasmids in E. coli resulted in haem A accumulation in membranes. The presence of CtaB together with ctaA increased the amount of haem A found in E. coli. Haem O was not detected in wild‐type B. subtilis strains. A previously isolated B. subtilis CtaA deletion mutant was found to contain haem B and haem O, but not haem A. B. subtilis ctaB deletion mutants were constructed and found to tack both haem A and haem O. The results with E. coli and B. subtilis strongly suggest that the B. subtilis CtaA protein functions in haem A synthesis. It is tentatively suggested that it functions in the oxygeNatlon/oxidation of the methyl side group of carbon 8 of haem O. B. subtilis CtaB, which is homologous to Saccharomyces cerevisiae COX10 and E. coli CyoE, also has a role in haem A synthesis and seems to be required for both cytochrome a and cytochrome o synthesis.