bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular aspects of phosphate transport in Escherichia coli
Authors: Rao N. N. , Torriani A. 
Published: October 2006

Summary Escherichia coli transports inorganic phosphate (Pi) by the low‐affinity transport system, Pit. When the level of the external Pi is lower than 20μM, another transport system, Pst, is induced with a Kt of 0.25μM. An outer‐membrane porin, PhoE, with a Km of about 1μM is also induced. The outer membrane allows the intake of organic phosphates which are degraded to Pi by phosphatases in the periplasm. The Pi‐binding protein will capture the free Pi produced in the periplasm and direct it to the transmembrane channel of the cytoplasmic membrane. The channel consists of two proteins, PstA and PstC, which have six and five transmembrane helices, respectively. On the cytoplasmic side of the membrane the channel is linked to the PstB protein, which carries a nucleotide (probably ATP)‐binding site. PstB probably provides the energy required by the channel to free Pi. The Pst system has two functions in E. coli: (i) the transport of Pi, and (ii) the negative regulation of the phosphate regulon (a complex of 20 proteins mostly related to organic phosphate transport). It is remarkable that these two functions are not related, since the repressibility of the regulon depends on the integral structure of Pst (PiBP + PstA + PstC + PstB) and not on the Pi transported. Another gene of the pst operon, phoU, produces a protein involved in the negative regulation of the Pho regulon, but the mechanism of this function has not been explained. Thus the regulatory function of the Pst system remains obscure. Its basal level, present when Pi is abundant, is sufficient to repress the Pho regulon but the negative regulatory function is lost upon Pi starvation.
Construction and characterization of a protective antigen‐deficient Bacillus anthracis strain
Authors: Cataldi A. , Labruyère E. , Mock M. 
Published: October 2006

SummaryThe pag gene coding for protective antigen (PA), one of the three toxin components of Bacillus anthracis, has been cloned into the mobilizable shuttle vector pAT187 and transferred by conjugation from Escherichia coli to B. anthracis. Using this strategy, an insertionally mutated pag gene constructed and characterized in E. coli, was introduced into B. anthracis Sterne strain. This transconjugant was used to select a recombinant clone (RP8) carrying the inactivated pag gene on the toxin‐encoding piasmid, pXO1. Strain RP8 was deficient for PA while still producing the two other toxin components, i.e. lethal factor (LF) and edema factor (EF). In contrast to spores from the wild‐type Sterne strain, spores prepared from RP8 were totally non‐lethal in mice. These results clearly establish the central role played by PA in B. anthracis pathogenicity.
Sequence, localization and function of the invasin protein of Yersinia enterocoiitica
Authors: Young V. B. , Miller V. L. , Falkow S. , Schoolnik G. K. 
Published: October 2006

SummaryThe inv locus of Yersinia enterocolitica is sufficient to convert a non‐invasive Escherichia coli K12 strain into a microorganism that is able to penetrate cultured mammalian cells. The nucleotide sequence of inv reveals an open reading frame corresponding to an 835‐amino‐acid protein that is homologous to the invasin protein from Yersinia pseudotuberculosis. A polyclonal antiserum elicited by a synthetic peptide corresponding to the C‐terminal 88 amino acids of this open reading frame detected a unique 100kD protein in cell lysates of Y. enterocolitica strain 8081c and in an E. coli strain harbouring the cloned inv gene. This protein localized to the outer membranes of both microorganisms and was cleaved by low concentrations of extracellular trypsin. HEp‐2 cells were shown to attach to surfaces coated with bacterial outer membranes containing invasin and this attachment was destroyed by treatment of the membranes with trypsin. Thus it appears that the invasin protein from Y. enterocolitica is able to mediate both attachment to and entry of cultured epithelial cells.
Protein transfer into the recipient cell during bacterial conjugation: studies with F and RP4
Authors: Rees C. E. D. , Wilkins B. M. 
Published: October 2006

SummaryTransfer of donor cell proteins to the recipient bacterium was examined in F‐ and RP4‐mediated conjugation. Transfer of a 120kD polypeptide, identified as the larger product of the plasmid DNA primase gene, was readily detected during RP4‐promoted conjugation. The protein was transmitted to the cytoplasm of the recipient, presumably complexed to the transferred ssDNA. F DNA was transferred without detectable association with any cytoplasmic tra protein or with the ssDNA‐binding protein encoded by the plasmid. However, a 92kD protein, possibly F TraD product, was transmitted to the membrane fraction of the recipient cell.
On the evolutionary origins of the bacterial phosphoenolpyruvate:sugar phosphotransferase system
Authors: Wu L.‐F. , Saier M. H. 
Published: October 2006

SummaryThe genes encoding the proteins of the fructose‐specific phosphotransferase system (PTS) of Rhodobacter capsulatus were sequenced, and the deduced amino acyl sequences of the energy‐coupling protein, Enzyme I, and the transport protein, Enzyme IItru, were compared with published sequences. Enzyme I was found to be homologous to pyruvate: phosphate dikinase of plants, while Enzyme IIfru was found to be homologous to the insulin‐responsive glucose facilitator of mammals. The evolutionary and functional implications of these findings are discussed.
What are antibiotics? Archaic functions for modern activities
Authors: Davies J. 
Published: October 2006

SummarySecondary metabolites are proposed to have played important roles in the evolution of the reactions of living forms on earth, in effecting and modulating reactions during biochemical evolution by chemical and structural interaction with ‘receptor’ sites in primitive macromolecular templates. For example, in the evolution of the translation system, as the polymerizing reactions became more complex and proteins became involved, the low molecular‐weight effectors were functionally replaced by polypeptides, but retained their ability to interact with receptor sites in nucleic acids and proteins. Many of these low molecular‐weight effectors now play a different role, that of antagonists, by interacting with the original receptor sites in contemporary activity as antibiotics.
Characterization of divergent NtrA‐dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli
Authors: Lutz S. , Böhm R. , Beier A. , Böck A. 
Published: October 2006

SummaryThe regulatory region of two divergently oriented transcriptional units involved in the formation of the gas‐evolving hydrogenase (isoenzyme 3) of Escherichia coli was investigated. DNA sequence analysis revealed the existence of a 210bp non‐coding region containing two sequences showing homology to ‐24/‐12 NtrA‐dependent promoters. These sequences were arranged in a divergent orientation entirety consistent with their being involved in transcribing the divergent operons. Through S1 protection experiments it could be shown that transcription of both promoters was NtrA‐dependent and that it was regulated in an identical manner: oxygen repressed expression, as did anaerobic growth in the presence of nitrate; transcription was induced in cells grown anaerobically in the absence of exogenous electron acceptors and formate was found to be obligately required for this anaerobic induction. Lying at an approximately equal distance between both promoters was a short stretch of DNA which showed similarity to the sequence previously identified (Birkmann and Böck, 1989a) as being necessary for formate induction of the fdhF gene.
Characterization of the traT gene and mutants that increase outer membrane permeability from the Salmonella typhimurium virulence plasmid
Authors: Sukupolvi S. , Vuorio R. , Qi S.‐Y. , O'Connor D. , Rhen M. 
Published: October 2006

SummaryThe nucieotide sequence of the traT gene present in the virulence‐associated pfasmid of Salmonella typhimurium was determined. The predicted TraT protein encoded by this gene was found to consist of 243 amino acids and to resemble the known TraT proteins of the plasmids of the F incompatibility group. Thus it contains a signal sequence of 20 amino acids, an amino‐terminal lipid attachment site, and two strongly hydrophobic regions close to each other in the mature protein. A mutation leading to increased permeability of the outer membrane to hydrophobic agents, previousfy focalrzed to the traT gene, was shown to change a glycine residue to arginine within one of these hydrophobic regions. The same principle was found to apply to TraT of R6‐5: the introduction, by site‐directed mutagenesis, of either positively or negatively charged amino acids or the helix‐disrupting proline in the corresponding hydrophobic region led to increased hydrophobic permeability of the outer membrane.
Duplication and variation of the thermostable direct haemolysin (tdh) gene in Vibrio parahaemolyticus
Authors: Nishibuchi M. , Kaper J. B. 
Published: October 2006

SummaryThe relationship between phenotypic variation and nucleotide sequence variation of the gene encoding Vibrio parahaemolyticus thermostable direct haemolysin (tdh gene) was examined. Strains showing a typical haemolysin‐positive phenotype carried two chromosomal gene copies (designated tdh1 and tdh2) while fdh‐gene‐positive strains showing a weakly positive or negative haemolysin phenotype possessed only a single chromosomal gene copy. Both gene copies from a typical haemolysin‐positive strain were cloned and sequenced and possessed 97.2% homo‐logy. Comparison of the amino acid sequence predicted from the nucleotide sequence with the protein sequence determined by Edman degradation as well as construction of a tdh1‐deficient yet haemolytic strain of V. parahaemolyticus suggest that the tdh2 locus is primarily responsible for the haemolytic phenotype. Two other tdh gene copies were cloned from a phenotypically negative strain which was unusual in that it contained one gene copy on a plasmid (designated tdh4) in addition to a single copy on the chromosome (tdhS). Both tdh3 and tdh4 were expressed in Escherichia coli and TDHs with haemolytic activity were produced. These gene copies were sequenced and shared 96.7% homology with the tdh1 gene. The V. parahaemolyticus strain carrying tdh3 and tdh4 gene copies did not produce detectable amounts of tdh‐specific RNA transcript. It seems, therefore, that differences in the transcriptional control are primarily responsible for the differences seen in haemolytic phenotype.
Functional analysis of the fsoC gene product of the F71 (fso) fimbrial gene cluster
Authors: Riegman N. , Acton D. , Sakkers R. , van Die I. , Hoekstra W. , Bergmans H. 
Published: October 2006

SummaryContrary to what would be expected from data in the literature, mutations in the fsoC gene of the F71 (fso) P‐fimbrial gene cluster do not completely block fimbrial biogenesis. fsoC mutants still express small amounts of fimbriae of normal length, which carry the non‐adhesive minor subunit protein, FsoE, but lack the adhesin, FsoG. The FsoC protein operates at the same stage in fimbrial biogenesis as the FsoF and FsoG proteins. The data suggest that FsoC, FsoF and FsoG interact to form an initiation complex for fimbrial biogenesis.
Isolation of the Actinobacillus pleuropneumoniae haemolysin gene and the activation and secretion of the prohaemolysin by the HlyC, HlyB and HlyD proteins of Escherichia coli
Authors: Gygi D. , Nicolet J. , Frey J. , Cross M. , Koronakis V. , Hughes C. 
Published: October 2006

SummaryThe gene encoding the c. 105 kD secreted haemolysin protein of the porcine pathogen Actinobacillus pleuropneumoniae serotype 1 has been isolated by screening a lambda gt11 expression library in Escherichia coli with antiserum raised against the wild‐type protein. A derivative recombinant DNA pJFF702 expressed the hlylA haemolysin gene from the pUC19 lac promoter but the resulting haemolysin I protein remained within the E. coli cell and was haemolytically inactive. Export of the intracellular A. pleuropneumoniae prohaemolysin out into the medium was achieved by the presence in trans of the E. coli haemolysin secretion genes hlyB and hlyD, and high levels of intracellular haemotytic activity were attained similarly by the E. coli post‐translational haemolysin activator gene, hlyC. Southern hybridization of A. pleuropneumoniae parental DNA nevertheless indicated only a low degree of nucleotide sequence identity to the haemolysin structural and secretion genes hlyA and hlyB of E. coli. The data show that despite substantial nucleotide sequence divergence the A. pleuropneumoniae serotype 1 haemolysin determinant is closely related to that which is dispersed throughout other Gram‐negative human and animal pathogens.
Mechanism of post‐segregational killing by the hoklsok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid‐free cells
Authors: Gerdes K. , Thisted T. , Martinussen J. 
Published: October 2006

SummaryThe hok/sok system of plasmid R1, which mediates plasmid stabilization via killing of plasmid‐free segregants, encodes two genes: hok and sok. The hok gene product is a potent cell‐killing protein. The expression of hok is regulated post‐transcriptionally by the sok gene‐encoded repressor, an antisense RNA complementary to the hok mRNA leader region. We show here that the hok mRNA is very stable, while the sok RNA decays rapidly. We also observe a new hok mRNA species which is 70 nucleotides shorter in the 3′‐end than the full‐length hok transcript. The appearance of the truncated hok mRNA was found to be regulated by the sok antisense RNA. Furthermore, the presence of the truncated hok mRNA was found to be correlated with efficient expression of the Hok protein. On the basis of these findings, we propose an extended model in order to explain the killing of plasmid‐free segregants by the hok/sok system.
Interconversion of the DNA‐binding specificities of two related transcription regulators, CRP and FNR
Authors: Spiro S. , Gaston K. L. , Bell A. I. , Roberts R. E. , Busby S. J. W. , Guest J. R. 
Published: October 2006

SummaryIn Escherichia coli, FNR and CRP are homologous transcriptional regulators which recognize similar nucleotide sequences via DNA‐binding domains containing analogous helix‐turn‐helix motifs. The molecular basis for recognition and discrimination of their target sites has been investigated by directed amino acid substitutions in the corresponding DNA‐recognition helices. In FNR, Glu‐209 and Ser‐212 are essential residues for the recognition of FNR sites. A V208R substitution confers CRP‐site specificity without loss of FNR specificity, but this has adverse effects on anaerobic growth. In contrast, changes at two (V206R and E209D) or three (V208R, S212G and G216K) positions in FNR endow a single CRP‐site binding specificity. In reciprocal experiments, two substitutions (R180V and G184S) were required to convert the binding specificity of CRP to that of FNR. Altering Asp‐199 in FNR failed to produce a positive control phenotype, unlike substitutions at the comparable site in CRP. Implications for the mechanism of sequence discrimination by FNR and CRP are discussed.
The bex locus in encapsulated Haemophilus influenzae: a chromosomal region involved in capsule polysaccharide export
Authors: Kroll J. S. , Loynds B. , Brophy L. N. , Moxon E. R. 
Published: October 2006

SummaryThe nucleotide sequence of a 5.1 kb region in the Haemophiius influenzae type b capsulation locus has been determined and found to contain four open reading frames: bexD, bexC, bexB, and bexA. Comparison of the deduced products of bexC, bexB, and bexA to known proteins, and TnphoA mutagenesis, suggests that they form components of an ATP‐driven polysaccharide export apparatus. Furthermore, close sequence similarity between BexA and BexB and products of the kpsT and kpsM genes at the Escherichia coli K5 capsulation locus (Smith et al., 1990 — accompanying paper) suggests that capsulation genes in these organisms may have a common ancestry.
Molecular analysis of the Escherichia coli K5 kps locus: identification and characterization of an inner‐membrane capsular polysaccharide transport system
Authors: Smith A. N. , Boulnois G. J. , Roberts I. S. 
Published: October 2006

SummaryThe complete nucleotide sequence has been determined of a region of the Escherichia coli K5 antigen gene cluster postulated to encode functions for the translocation of capsular polysaccharide across the inner membrane. This revealed two genes, designated kpsM and kpsT, organized in a single transcriptional unit. Analysis of the predicted amino acid sequence of the KpsM and KpsT proteins indicates that they may function as dual components in a polysaccharide export system analogous to the periplasmic binding protein‐dependent transport systems of Gram‐negative bacteria. We propose that the KpsT protein acts as an energizer, coupling ATP hydrolysis to the transport process mediated by the KpsM protein. Extensive sequence homology between the KpsM and KpsT proteins and the products of the bexB and bexA genes present in the capsulation (cap) locus of Haemophilus influenzae, indicates that a common mechanism for the export of polysaccharide across the inner membrane may exist in these two microorganisms.
Exopolysaccharide production in Rhizobium and its role in invasion
Authors: Gray J. X. , Rolfe B. G. 
Published: October 2006

SummaryA complex interaction between rhizobia and specific legume plants results in the formation of nitrogen‐fixing root nodules. The necessity for signal exchange and a chemically based recognition system between the symbiotic partners has been appreciated for some time, but the details are only gradually being elucidated. The two basic nodule ontogenies exhibit different requirements for Rhizobium exopolysaccharides. These surface exopolysaccharide molecules of Rhizobium are synthesized at a membrane complex, which is regulated by both transcriptional and post‐trans‐lational controls. The acidic exopolysaccharide probably plays both a passive and an active role during the invasion process.
Proteinase inhibition, immunoglobulin‐binding proteins and a novel antimicrobial principle
Authors: Björck L. 
Published: October 2006

SummaryRecent work has demonstrated that a tripeptide derivative mimicking the active proteinase‐binding site of cystatin C, a human cysteine proteinase inhibitor, can block growth of group A streptococci and replication of herpes simplex virus (HSV). In the case of HSV, intact cystatin C was also found to inhibit replication of the virus. Many streptococcal strains and HSV‐infected cells produce immunoglobulin (Ig)‐binding proteins, and a possible connection between such proteins and proteolytic activity was indicated by the finding that bacterial Ig‐binding proteins also show affinity for proteinase inhibitors. The significance of these various observations is not clear, but available data suggest that proteinases play a role in vital microbial functions (e.g. viral replication) and may be utilized as targets for antimicrobial agents. The results discussed here also indicate that peptide derivatives based on the structure of proteinase inhibitors occurring in nature could be used as such agents.
A family of ATPases involved in active partitioning of diverse bacterial plasmids
Authors: Motallebi‐Veshareh M. , Rouch D. A. , Thomas C. M. 
Published: October 2006

SummaryLow copy‐number bacterial plasmids F (the classical Escherichia coli sex factor) and prophage P1 encode partitioning functions which may provide fundamental insights into the active processes which ensure that bacterial genomes are segregated to both daughter cells prior to cell division. These partitioning systems involve two proteins: ParA and ParB. We report that IncC from the broad host‐range plasmid RK2 is a member of the family of ParA partitioning proteins and that these proteins (as well as related proteins encoded by plasmids from Agrobacterium tume‐faciens and Chlamydia trachomatis) contain type I nucleotide‐binding motifs. Also, we show that the cell division inhibitor MinD is homologous to members of the ParA family. Sequence comparisons of ParB proteins suggest that they may contain sites for phosphorylation. We propose that ATP hydrolysis by the ParA protein may result in phosphorylation of the ParB protein, thereby causing a conformational shift necessary to separate paired plasmid molecules at the cell division plane.
Cloning and physical mapping of the sor genes for L‐sorbose transport and metabolism from Klebsiella pneumoniae
Authors: Wöhrl B. M. , Lengeler J. W. 
Published: October 2006

SummaryThe sor genes of Klebsiella pneumoniae KAY2026, which enable the bacterium to metabolize the ketose L‐sorbose, have been cloned on an 8.3kb DNA fragment into the multicopy plasmid, pACYC184. The genes were mapped by restriction analysis, by deletion mapping and by insertion mutagenesis with Tn1725. The corresponding gene products were identified by the maxicell technique. The structural genes sorD, sorA and sorE code for a D‐glucitol‐6‐P dehydrogenase (27 kilodalton (kD)), an Enzymell (EIISor) activity specific for L‐sorbose and an L‐sorbose‐1‐P reductase (45kD). Besides these genes for known functions, three additional genes were discovered: sorC, coding for a transcriptional 40kD regulatory protein, and sorF and sorB, coding for two proteins of 14kD and 19kD, respectively, involved in transport. The genes form an operon (gene order sorCpCDFBAE) and are inducible by L‐sorbose.
Studies on Clostridium acetobutylicum ginA promoters and antisense RNA
Authors: Janssen P. J. , Jones D. T. , Woods D. R. 
Published: October 2006

SummaryThe Clostridium acetobutylicum glnA gene has two transcript start sites under the control of promoters P1 and p2. Initiation of transcription was regulated by nitrogen and a downstream region was implicated in the regulation of transcript initiation by nitrogen in Escherichia coli. Putative antisense RNA was produced from a single downstream transcript start site under the control of P3. An up‐promoter mutation in P3 resulted in lower levels of glutamine synthetase (GS) activity. Putative antisense RNA had a role in down‐regulating GS expression but was not involved in regulation by nitrogen. Deletion of downstream inverted repeat sequences resulted in very low levels of GS activity.
The pYV plasmid of Yersinia encodes a lipoprotein, YlpA, related to TraT
Authors: China B. , Michiels T. , Cornelis G. R. 
Published: October 2006

SummaryA series of lipoproteins was detected in the membrane fraction of Yersinia enterocolitica W227, a typical strain from serotype O:9. At least two of them, YlpA and YlpB, are encoded by the pYV plasmid. The sequence of ylpA reveals the presence of a typical lipoprotein signal peptide. The mature YlpA protein would be 223 residues long with a calculated molecular weight of 23798 for the proteic moiety of the molecule. YlpA shares 88% identical residues with the TraT protein encoded by plasmid pED208, 80% identity with TraT proteins encoded by plasmids R100 and F, and 77% identity with the TraT protein encoded by the virulence plasmid of Salmonella typhimurium. The ylpA gene hybridized with the pYV plasmid of Yersinia pseudotuberculosis, suggesting that this gene is conserved among Yersinia spp. The production of YlpA is controlled by virF and only occurs at 37°C in the absence of Ca2+ ions. This co‐regulation with the yop genes suggests that ylpA is a virulence determinant. However, mutations in ylpA clearly affect neither the resistance to human serum nor the virulence for intravenously inoculated mice.