bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tandem DNA‐bound cAMP‐CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli
Authors: Sogaard‐Andersen L. , Mellegaard N. E. , Douthwaite S. R. , Valentin‐Hansen P. 
Published: October 2006

SummaryWe have studied the deoP2 promoter in Escherichia coli to define features important for its interaction with the CytR repressor. As is characteristic for CytR‐regulated promoters, deoP2 encodes tandem binding sites for the activating complex cAMP‐CRP. One of these sites, CRP‐1, overlaps the ‐ 35 region, and is sufficient for activation; the second site, CRP‐2, centred around‐93, is indispensable for repression. Here we demonstrate, by means of in vivo titration, that CytR interaction with deoP2 depends not only on CRP‐2, but also on CRP‐1 and the length and possibly the sequence separating these two sites. Also, point mutations in either CRP site reduce or abolish CytR titration; however, no co‐operativity is observed in the interaction of CytR with the two CRP binding sites. Furthermore, the reduction in CytR titration parallels the reduction in binding of cAMP‐CRP to the mutated CRP sites in vitro. These observations are not easily explained by current models for the action of prokaryotic repressors; instead we favour a model in which the interaction of CytR with deoP2 depends on the presence of tandem DNA‐bound cAMP–CRP complexes.
Conservation of a hexapeptide sequence in the anchor region of surface proteins from Gram‐positive cocci
Authors: Fischetti V.A , Pancholi V. , Schneewind O. 
Published: October 2006

summaryA highly conserved hexapeptide sequence (both at the protein‐and DNA level) has been identified within the C‐terminal end of all 11 known surface proteins from Gram‐positive cocci. The hexapeptide, with the consensus sequence LPXTGE, is located about 9 amino acids N‐terminal from the C‐terminal hydrophobic domain which is found in all these surface molecules. The conservation of the hexapeptide, despite sequence variation within the regions flanking it, suggests that it is important for the attachment of these proteins within the cell.
Selenocysteine: the 21st amino acid
Authors: Böck A. , Forchhammer K. , Heider J. , Leinfelder W. , Sawers G. , Veprek B. , Zinoni F. 
Published: October 2006

SummaryGreat excitement was elicited in the field of selenium biochemistry in 1986 by the parallel discoveries that the genes encoding the selenoproteins glutathione peroxidase and bacterial formate dehydrogenase each contain an in‐frame TGA codon within their coding sequence. We now know that this codon directs the incorporation of selenium, in the form of selenocysteine, into these proteins. Working with the bacterial system has led to a rapid increase in our knowledge of selenocysteine biosynthesis and to the exciting discovery that this system can now be regarded as an expansion of the genetic code. The prerequisites for such a definition are co‐translational insertion into the polypeptide chain and the occurrence of a tRNA molecule which carries selenocysteine. Both of these criteria are fulfilled and, moreover, tRNASec even has its own special translation factor which delivers it to the translating ribosome. It is the aim of this article to review the events leading to the elucidation of selenocysteine as being the 21st amino acid.
Physiological roles of the DnaK and GroE stress proteins: catalysts of protein folding or macromolecular sponges?
Authors: LaRossa R. A. , Van Dyk T. K. 
Published: October 2006

SummaryWhen organisms ranging from microbes to man are subjected to certain environmental stresses a characteristic heat shock’ response is observed. In Escherichia coli this response is characterized by the induction of several proteins, three of which are the 70 kilodalton product of the dnaK gene, the 60 kilodalton product of the groEL (mopA) gene and the 15 kilodalton product of the groES (mopB) gene. In this review, utilizing enteric bacteria as model organisms, we focus on the role of these proteins within the context provided by well‐established functions of other heat shock products. These facts serve as a starting point from which to speculate upon the in vivo role of these proteins during steady‐state growth.
Physiology and molecular genetics of poly(β‐hydroxyalkanoic acid) synthesis in Alcaligenes eutrophus
Authors: Steinbüchel A. , Schlegel H. G. 
Published: October 2006

SummaryThe Alcaligenes eutrophus genes for β‐ketothiolase, NADPH‐dependent acetoacetyl‐CoA reductase and poly(β‐hydroxybutyric acid) synthase (PHB synthase) which comprise the three‐step PHB‐biosynthetic pathway, were cloned. Molecular studies revealed that these genes are organized in a single operon. The A. eutrophus PHB‐biosynthetic genes are readily expressed in other bacteria, and DNA fragments harbouring the operon can be used as a cartridge to confer to other bacteria the ability to synthesize PHB from acetyl‐CoA. The biochemical and physiological capabilities of A. eutrophus for the synthesis of a wide variety of polyhydroxyalkanoates are discussed.
Error‐prone EF‐Tu reduces in vivo enzyme activity and cellular growth rate
Authors: Hughes D. 
Published: October 2006

SummaryMutations in Salmonella typhimurium encoding error‐prone EF‐Tu (tufA8, tufB103) enhance translational error levels and also cause a reduced growth rate. The relative changes in error level and growth rate are inversely related and dependent on the status of the two tuf genes. Possible causes of the reduced growth rate were investigated. Several important parameters with the potential to alter growth rate (the EF‐Tu‐ribo‐some interaction, the in vivo elongation rate and the processivity of translation), are all relatively unaffected by the tuf mutations. The small reduction in processivity observed in some strains is not quantitatively related to the growth rate reduction. Instead, the error‐enhancing mutations are associated with a large reduction in the specific activity of a test protein, β‐galactosidase, suggesting by inference that the reduced growth rate is a consequence of the synthesis of error‐containing proteins.
A copy‐number mutant of plasmid pSC101
Authors: Xia G.‐X. , Manen D. , Goebel T. , Linder P. , Churchward G. , Caro L. 
Published: October 2006

SummaryCopy‐number mutants of plasmid pSC101 were isolated by u.v. mutagenesis and selection for elevated expression of ampicillin resistance. Three independent mutations were identical and mapped in codon 93 of the initiation protein RepA. The mutated plasmids were maintained at a level four to five times higher than that of the wild type. For one of them, it was determined that: (i) the mRNA of the autoregulated repA gene, cloned onto a pUC19 plasmid under the control of its own promoter, was expressed at a level 1.7 times higher than that of the wild type; (ii) the RepA protein, under the same conditions, was expressed at a similarly higher level; (iii) the affinity of the mutated protein for three repeated sequences in the origin region of the plasmid was, on average, 3.4 times higher than that of the wild‐type protein. We postulate that the copy‐number effect is due to a combination of these two effects, i.e. higher protein concentration and increased affinity of the protein for the repeated sequences.
Gas vesicle synthesis in the cyanobacterium Pseudanabaena sp.: occurrence of a single photoregulated gene
Authors: Damerval T. , Castets A.‐M. , Houmard J. , de Marsac N. Tandeau 
Published: October 2006

SummaryGas vesicles are subcellular inclusions found in a large number of aquatic prokaryotes. The gvpA gene, which frequently occurs as a multigene family, encodes the major gas vesicle structural protein. In several cyanobacteria, another gene, gvpC, encodes a different protein which might be a dispensable element for gas vesicle formation. We report here the molecular characterization of a gvpA gene in Pseudanabaena sp. PCC 6901. In this planktonic cyanobacterium, it is the only gvp gene which could be detected, and electrophoretic analysis of isolated gas vesicles revealed the presence of a single protein. A monocistronic mRNA species corresponds to the transcription of the gvpA gene and the abundance of the gvpA mRNA is inversely correlated with photosynthetic photon flux density, indicating that a light‐dependent transcriptional regulation is likely to be involved in the control of gas vacuolation in this strain.
Osmotic induction of the periplasmic trehalase in Escherichia coli K12: characterization of the treA gene promoter
Authors: Repoila F. , Gutierrez C. 
Published: October 2006

SummaryThe Escherichia coli treA gene encodes an osmotically inducible periplasmic trehalase. A strain carrying a treA–lacZ transcriptional fusion was constructed. The β‐galactosidase activity produced in this strain growing exponentially in a medium of high osmotic pressure was 10‐fold higher than that produced in a medium of low osmotic pressure, demonstrating that treA transcription is osmotically inducible. treA transcriptional induction depends neither on the presence of trehalase itself nor on the synthesis of cytoplasmic trehalose which occurs in response to osmotic stress in wild‐type E. coli strains. The treA promoter was identified by S1 nuclease protection. Deletion analysis demonstrated that sequences sufficient for the osmotic induction lie downstream from nucleotide –40 with respect to the transcription start. Transcription initiation at treAp required the presence of a functional σ70 subunit of RNA polymerase. treA expression was increased in the presence of a mutation in osmZ, which was previously identified as leading to a partially constitutive expression of the osmotically inducible proU operon.
The Escherichia coli cell cycle: one cycle or multiple independent processes that are co‐ordinated?
Authors: Nordstrom K. , Bernander R. , Dasgupta S. 
Published: October 2006

SummaryIn the life cycle of a bacterium there are several key processes: cellular growth, chromosome replication and decatenation, nucleoid partition, septum formation, and cell division. These processes have to be carefully controlled and co‐ordinated both with respect to each other and to the growth of the cell, and could be viewed as parts of a single cycle in which each step is dependent upon the previous one. Alternatively, they could be independently controlled and carefully tuned to each other without actually constituting a true cycle. In this review, using Escherichia coli as model system, we discuss these two ways of describing the bacterial life cycle. The evidence supporting independent control of the processes is presented, and some of the key questions in the elucidation of the regulation of the bacterial life cycle are discussed.
Cell division and peptidoglycan assembly in Eschenchia coli
Authors: Nanninga N. 
Published: October 2006

SummaryResearch on bacterial cell division has recently gained renewed impetus because of new information about peptidoglycan assembly and about specific cell‐division genes and their products. This paper concerns aspects of cell division that specifically concern the peptidoglycan. It is shown that upon division, peptidoglycan assembly switches from lateral wall location to the cell centre, that assembly takes place at the leading edge of the invaginating constriction, that the mode of glycan strand insertion changes from a single‐stranded mode to a multi‐stranded mode, and that the initiation of division (in contrast to its continuation) requires penicillin‐insensitive peptidoglycan synthesis (PIPS). A membrane component X (possibly FtsQ) is proposed to coordinate PIPS with the cell division‐initiating protein FtsZ. It is suggested that a largely proteinaceous macromolecular complex (divisome) at the leading edge of constriction encompasses three compartments (cytoplasm, membrane and periplasm). The composition of this complex is proposed to vary depending on whether division is being initiated or completed.
A suppressor of yeast spp81/ded1 mutations encodes a very similar putative ATP‐dependent RNA helicase
Authors: Jamieson D. J. , Beggs J. D. 
Published: October 2006

SummaryThe spp81/ded1 mutations were isolated as suppressors of a Saccharomyces cerevisiae pre‐mRNA splicing mutation, prp8‐1, The SPP81/DED1 gene encodes a isolated plasmids which were able to suppress the cold‐sensitive growth defect of SPP81 mutants. These plasmids encoded a gene (named DBP1) which mapped to chromosome XVI and not to the SPP81/DED1 locus on chromosome XV. The cloned gene suppressed the defect of SPP81/ded1 mutants when present on both high and low copy‐number plasmids but complemented SPP81/ded1 null mutants only when present on high copy‐number plasmids. In contrast to the SPP81/DED1 gene the DBP1 gene was not essential for cell viability. The nucleotide sequence of the DBP1 gene revealed that it also encoded a putative ATP‐dependent RNA helicase which showed considerable similarity at the amino acid level to the SPP81/DED1 protein.
Structure and function of peripiasmic chaperone‐like proteins involved in the biosynthesis of K88 and K99 fimbriae in enterotoxigenic Escherichia coli
Authors: Bakker D. , Vader C. E. M. , Roosendaal B. , Mooi F. R. , Oudega B. , de Graaf F. K. 
Published: October 2006

SummaryThe nucleotide sequence of faeE and fanE, two genes involved in the biosynthesis of K88 and K99 fimbriae, respectively, was determined and the amino acid sequence of the FaeE and FanE proteins was deduced. Immunobiotting of subcellular fractions with an anti‐serum raised against purified FaeE confirmed that FaeE is located in the periplasm. Indications were obtained that FaeE functions as a chaperone‐like protein, Its interaction with the fimbrial subunit (FaeG) in the periplasm stabilizes this polypeptide and prevents its degradation by the ceil‐envelope protease DegP. Furthermore, FaeE prevents the formation of FaeG multimers which cannot be incorporated into fimbriae. The reactions of the FaeE/FaeG dimers with a set of monoclonal antibodies directed against the various epitopes present on K88 fimbriae revealed that the fimbrial subunits associated with FaeE were present in a conformation resembling their native configuration. Indications about the domains in FaeG involved in the interaction with FaeE are discussed.
Temperature‐regulated expression of invasion genes in Shigella flexneri is controlled through the transcriptional activation of the virB gene on the large plasmid
Authors: Tobe T. , Nagai S. , Okada N. , Adter B. , Yoshikawa M. , Sasakawa C. 
Published: October 2006

SummaryThe invasion phenotype of shigellae is subject to thermoregulation that is known to be expressed through activation of some invasion (inv) genes such as ipaB, ipaC, and ipaD encoded by the large virulence plasmid of Shigeila flexneri. The expression of ipa genes is regulated positively by virF through the activation of virB on the plasmid. To identify the mediator for the thermoregulation of the large plasmid, we have studied the effect of temperature on the transcription of virF and virB genes and ipa and the other two inv operons. The results showed that transcription of VirB was affected by temperature more strictly than that of virF. Analysis of the mRNA level of virB at different levels of virF transcription indicated that virB transcription depended upon both temperature and virF. On the other hand, transcriptions of ipa and the other two inv operons depended on the activation of virB transcription but not on temperature. By inducing wr8 transcription from a tac promoter fused with the virB region, invasion ability was restored to a WrF‐deletion mutant at 30°C as well as at 37°C. By using conditions in which the temperature‐dependent expression of the invasion phenotype was circumvented by the induction of virB transcription, intercellular spreading ability in a virF+, virB::Tn5 strain was shown to be expressed even at 30°C. These results suggest that the virB transcription stage is the main target for the thermoregulation.
Regulation of the chlA locus of Escherichia coli K12; involvement of molybdenum cofactor
Authors: Baker K. P. , Boxer D. H. 
Published: October 2006

SummaryThe chlA encodes functions required for the biosynthesis of the molybdopterin part of the molybdenum cofactor. Mutants, carrying gene fusions at the chlA locus, which place β‐galactosidase expression under the control of the chlA promoter, have been isolated employing λ plac Mui as the mutagen. The mutants exhibited β‐galactosidase expression which was greatly enhanced when grown anaerobically. Secondary mutations at the chlB, D, E or G loci did not affect the high level of expression. The fnr gene product was not required for the anaerobic expression. Bacteriophage λ transducing phages were isolated which carried the φ (chlA‐lac) mutations and were used to construct chlA/φ (chlA‐lac) merodiploids. The merodiploids exhibited a much lower level of expression but showed the same characteristics as strains carrying lac fusions to the single chromosomal chlA locus. Genetic evidence is presented which strongly suggests that the molybdenum cofactor is a repressor of chlA expression. The anerobic enhancement of chlA expression is mediated via a mechanism that is distinct from the molybdenum cofactor effect.
L‐pilin variants of Neisseria gonorrhoeae MS11
Authors: Manning P. A. , Kaufmann A. , Roll U. , Pohlner J. , Meyer T. F. , Haas R. 
Published: October 2006

SummaryPhase‐ and antigenic variation of pilin expression in Neisseria gonorrhoeae is based on the genetic exchange between silent pilin genes (pilS)and the pilin expression locus (pilE). Similarly, the non‐piliated L‐variants of strain MS11, which show an increased resistance to certain antibiotics, are the result of recombination with the pilElocus. However, this recombination is atypical in that pilE(L) carries a tandem arrangement of a complete pilin gene and additional partial pilin genes under the control of the same pilE promoter. Since the two pilin gene copies are tandemly arranged and are often in the same translational frame, oversized pilin molecules are produced, which do not assemble into pili. The tandem gene copies introduced in a piiE(L)locus originate from silent loci where they are already joint. Upon reversion to the P+ phenotype the L‐variants lose one pilin gene copy from the pilE(L) in a process reminiscent of the deletion events that otherwise lead to the formation of the non‐revertible and non‐piliated Pn mutants of MS11 gonococci. Thus deletion of pilin genes from pHE can be regarded as a third mechanism of pilin variation in gonococci.
Insertional inactivation of the Staphylococcus aureusβ‐toxin by bacteriophage φ13 occurs by site‐and orientation‐specific integration of the φ 13 genome
Authors: Coleman D. , Knights J. , Russell R. , Shanley D. , Birkbeck T. H. , Dougan G. , Charles I. 
Published: October 2006

SummaryLysogenization of Staphylococcus aureus by the sero‐type F converting bacteriophage φ13 results in loss of β‐toxin expression. Sequence analysis of the S. aureusβ‐toxin gene (hlb), the attachment site (aftP)‐containing region of φ 13 DNA and the chromosome/bacteriophage DNA junctions of a φ13 lysogen, revealed that the molecular mechanism of loss of βtoxin expression was due to insertion of the φ13 genome into the 5′ end of hlb. The insertion site (attB) within hlb contained a 14 base pair core sequence in common with attP and both ends of the integrated linear prophage genome of a φ 13 lysogen. These findings indicate that integration of the φ13 genome into hlb is site‐and orientation‐specific.
Modular structure of Fix J: homology of the transcriptional activator domain with the ‐35 binding domain of sigma factors
Authors: Kahn D. , Ditta G. 
Published: October 2006

SummaryThe FixL/Fix J two‐component system is a global regulator of nitrogen‐fixation genes in Rhizobium meliloti. The transcriptional activator FixJ contains two modules: its N‐terminal module is homologous with other two‐component regulators; its C‐terminal module shows homology with various transcriptional activators, and with the C‐terminal region of σ factors, which is involved in the discrimination of the ‐35 region of bacterial promoters. We show that C‐terminal module of Fix J contains the entire transcription activation function, and that the N‐terminal module regulates this activity negatively. Oligonucleotide directed mutagenesis of the transcriptional activator module demonstrated the importance of a potential helix‐turn‐helix structure.
Fermentable sugars and intracellular acidification as specific activators of the RAS‐adenylate cyclase signalling pathway in yeast: the relationship to nutrient‐induced cell cycle control
Authors: Thevelein J. M. 
Published: October 2006

SummaryThe RAS proteins of the yeast Saccharomyces cerevisiae fulfil a similar control function on yeast adenylate cyclase as the mammalian Gs proteins on mammalian adenylate cyclase. The discovery that glucose and other fermentable sugars act as specific activators of the RAS‐adenylate cyclase pathway in yeast appeared to offer a mechanism for the way in which at least one nutrient would control progression over the start point in the G1 phase of the yeast cell cycle by means of this pathway. Recently, however, evidence has been obtained to show that the glucose‐activation pathway of adenylate cyclase is a glucose‐repressible pathway and therefore not operative during growth on glucose. In addition, mutant strains were obtained which lack the glucose‐activation pathway and show normal exponential growth on glucose. This appears to confine the physiological role of this pathway to control of the transition from the derepressed state (growth on respirative carbon sources) to the repressed state (growth on fermentative carbon sources) by means of an already well‐documented cAMP‐triggered protein phosphorylation cascade. Intracellular acidification also stimulates the RAS‐adenylate cyclase pathway, which might constitute a rescue mechanism for cells suffering from stress conditions. The presence of a nitrogen source does not stimulate the RAS‐adenylate cyclase pathway. Although other nutrient signals for the pathway might still be discovered, it appears more and more likely that the well‐known requirement of cAMP for progression over the start point of the yeast cell cycle is limited to providing a basal cAMP level rather than acting as a second messenger for an extracellular signal. A model In which a nitrogen‐source‐induced pathway leads to activation of cAMP‐dependent protein kinase synergistically with cAMP, or alternatively causes activation only of the free catalytic subunits, would provide an elegant explanation for the apparent contradiction that nitrogen‐source induced progression over the start point of the yeast cell cycle does not seem to be mediated by cAMP but on the other hand seems to depend on cAMP and cAMP‐dependent protein kinase.