bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of the Escherichia coli heat‐shock response
Authors: Bukau Bernd 
Published: October 2006

SummarySteady‐state‐ and stress‐induced expression of Escherichia coli heat‐shock genes is regulated at the transcriptional level through controls of concentration and activity of the positive regulator, the heat‐shock promoter‐specific subunit of RNA polymerase, σ;32. Central to these controls are functions of the DnaK, DnaJ, GrpE heat‐shock proteins as negative modulators that mediate degradation as well as repression of activity and, in some conditions, of synthesis of σ32. DnaJ has a key role in modulation since it binds σ32 and, jointly with DnaK and GrpE, represses its activity. Furthermore, DnaJ is capable of binding heat‐damaged proteins, targeting DnaK and GrpE to these substrates, and thereby mediating DnaK‐, DnaJ‐, GrpE‐dependent repair. It is proposed that one important signal transduction pathway that converts stress to a heat‐shock response relies on the sequestering of DnaJ through binding to damaged proteins which derepresses and stabilizes σ32. Damage repair ameliorates the inducing signal and frees DnaJ, DnaK, GrpE to shut off the heat‐shock response.
The interaction between coumarin drugs and DNA gyrase
Authors: Maxwell Anthony 
Published: October 2006

SummaryThe coumarin group of antibiotics have as their target the bacterial enzyme DNA gyrase. The drugs bind to the B subunit of gyrase and inhibit DNA supercoiling by blocking the ATPase activity. Recent data show that the binding site for the drugs lies within the N‐terminal part of the B protein, and individual amino acids involved in coumarin interaction are being identified. The mode of inhibition of the gyrase ATPase reaction by coumarins is unlikely to be simple competitive inhibition, and the drugs may act by stabilizing a conformation of the enzyme with low affinity for ATP.
Bacterial proteins binding to the mammalian extracellular matrix
Authors: Westerlund B. , Korhonen T. K. 
Published: October 2006

SummaryPathogenic bacteria frequently express surface proteins with affinity for components of the mammalian extracellular matrix, i.e. collagens, laminin, fibronectin or proteoglycans. This review summarizes our current knowledge on the mechanisms of bacterial adherence to extracellular matrices and on the biological significance of these interactions. The best‐characterized bacterial proteins active in these interactions are the mycobacterial fibronectin‐binding proteins, the fibronectin‐ and the collagen‐binding proteins of staphylococci and streptococci, specific enterobacterial fimbrial types, as well as the polymeric surface proteins YadA of yersinias and the A‐protein of Aeromonas. Some of these bacterial proteins are highly specific for an extracellular matrix protein, some are multifunctional and express binding activities towards a number of target proteins. The interactions can be based on a protein‐protein or on a protein‐carbohydrate interaction, or on a bridging mechanism mediated by a bivalent soluble target protein. Many of the interactions have also been demonstrated on tissue sections or in vivo, and adherence to the extracellular matrix has been shown to promote bacterial colonization of damaged tissues.
AmpG, a signal transducer in chromosomal β‐lactamase induction
Authors: Lindquist Susanne , Weston‐Hafer Kathleen , Schmidt Herbert , Pul Christian , Korfmann Gisela , Erickson Jay , Sanders Christine , Martin Hans H. , Normark Staffan 
Published: October 2006

SummaryThe chromosomal ampCβ‐lactamase in Citrobacter freundii and Enterobacter cloacae is inducible by β‐lactam antibiotics. When an inducible ampC gene is introduced on a plasmid into Escherichia coli together with its transcriptional regulator ampR, the plasmid‐borne β‐lactamase is still inducible. We have isolated mutants, containing alterations in a novel E. coli gene, ampG, in which a cloned C. freundii ampC gene is unable to respond to β‐lactam inducers. The ampG gene was cloned, sequenced and mapped to minute 9.6 on the E. coli chromosome. The deduced amino acid sequence predicted AmpG to be a 53kDa, trans‐membrane protein, which we propose acts as a signal transducer or permease in the β‐lactamase induction system. Immediately upstream of ampG there is another 579‐base‐pair‐long open reading frame (ORF) encoding a putative lipoprotein shown to be non‐essential for β‐lactamase induction. We have found that ampG and this ORF form an operon, whose promoter is located in front of the ORF. Located closely upstream of the putative promoter is the morphogene bolA, which is transcribed in the opposite orientation. However, using transcription fusions, we have found that the ampG transcription is not regulated by bolA. In addition, we show that transcription is probably not regulated by either the starvation specific sigma factor RpoS, which controls bolA, or by AmpD the negative regulator for ampC transcription.
Formation of several bacterial c‐type cytochromes requires a novel membrane‐anchored protein that faces the periplasm
Authors: Ritz D. , Bott M. , Hennecke H. 
Published: October 2006

SummaryWe report here the discovery of a novel bacterial gene (cycH) whose product is involved in the biogenesis of most of the cellular cytochromes c. The cycH gene was detected in the course of characterizing a cytochrome oxidase‐deficient Bradyrhizobium japonicum Tn5 mutant (strain CO×3) in which the transposon insertion disrupted cycH. Ali of the c‐type cytochromes detectable in aerobically grown B. Japonicum wild‐type cells were absent in the C0X3 mutant, with the exception of cytochrome c1. A secondary phenotypic effect was the spectroscopic absence of the aa3‐type cytochrome c oxidase. The nucleotide sequence of the cloned wild‐type cycH gene predicted a membrane‐bound 369‐amino‐acid protein with an Mr of 39727. Results from studies on its membrane topology suggested that approximately 110 N‐terminal amino acids are involved in anchoring the protein in the membrane, whereas the remaining two‐thirds of the protein are exposed to the periplasm. We postulate that the CycH protein plays an essential role in an as yet unidentified periplasmic step in the biogenesis of holocytochromes c, except that of cytochrome c1.
Phosphorylation of Spo0A activates its stimulation of in vitro transcription from the Bacillus subtilis spollG operon
Authors: Bird T. H. , Grimsiey J. K. , Hoch J. A. , Spiegelman G. B. 
Published: October 2006

SummaryThe spollG operon of Bacillus subtilis codes for a sporulation‐specjfic sigma factor, σ;E, In vivo expression of the spollG promoter is activated shortly after the onset of sporulation and is dependent on kinA, spo0F, spo0B and spo0A genes. The products of these genes have been shown to participate in a phosphorelay reaction in vitro, culminating in phosphorylation of the transcription factor, Spo0A. The effect of Spo0A phosphorylation on in vitro transcription from the spollG promoter was determined. Aliquots from phos‐phorelay reactions enhanced spollG promoter activity 10‐fold in transcription assays and stimulation of transcription was dependent on Spo0A phosphorylation. Our results provide biochemical evidence that Spo0A and the phosphoreiay form a signal transduction pathway which activates spoil gene expression in development.
SyrD is required for syringomycin production by Pseudomonas syringae pathovar syringae and is related to a family of ATP‐binding secretion proteins
Authors: Quigley Neil B. , Mo Yin‐Yuan , Gross Dennis C. 
Published: October 2006

SummaryThe syrD gene of Pseudomonas syringae pathovar syringae strain B301D‐R was characterized and sequenced. The syrD open reading frame is 1695bp long and encodes a predicted protein, SyrD, of =63kDa. Database searches revealed that SyrD shares a high degree of similarity with the ATP‐binding cassette (ABC) superfamily of transporter proteins which are responsible for specific nutrient uptake and for secretion of certain cellular products in prokaryotes, and for multiple drug resistance in mammals. The amino acid sequence homology between SyrD and the ABC proteins was greatest at the conserved residues which constitute the ATP‐binding cassette of these proteins; these residues lie in the hydrophilic C‐terminal half of SyrD. The N‐terminus of SyrD is predicted to be hydrophobic and to contain six membrane‐spanning α‐helices. syrD mutants of strain B301D‐R were significantly less virulent than other syr mutants, were deficient in four large polypeptides thought to be components of a syringomycin synthetase complex, and showed reduced expression of a syrB‐lacZ reporter gene fusion in trans. It is proposed that SyrD is a cyto‐plasmic membrane protein that functions as an ATP‐driven efflux pump for the secretion of syringomycin.
The virD4 gene is required for virulence while virD3 and orf5 are not required for virulence of Agrobacterium tumefaciens
Authors: Lin Tzu‐Se , Kado Clarence I. 
Published: October 2006

SummaryThe virD operon of the resident Ti plasmid of Agrobacterium tumefaciens contains loci involved in T‐DNA processing and undefined virulence functions. Nucleotide sequence of the entire virD operon of pTiC58 revealed similarities to the virD operon of the root‐inducing plasmid pRiA4b and to that of the octopine‐type plasmid pTiA6NC. However, comparative sequence data show that virD of pTiC58 is more akin to that of the pRiA4b than to that of the pTiA6NC. T7f10::virD gene fusions were used to generate polypeptides that confirm the presence of four open reading frames virD1, virD2, virD3, and virD4 within virD which have a coding capacity for proteins of 16.1, 49.5, 72.6, and 73.5 kDa, respectively. virD3 therefore encodes a polypeptide 3.4 times larger (72.6 versus 21.3 kDa) than that encoded by virD3 of octopine Ti plasmids. Non‐polar virD4 mutants could not be complemented by a distant homologue, TraG protein of plasmid RP4. An independently regulated fifth ORF (orf5) is located immediately downstream of 3′ end of virD4 and encodes a polypeptide of 97.4 kDa. The expression of orf5 is dependent on its own promoter and is independent of acetosyringone induction in A. tumefaciens. Recently, it has been shown that virD3 of octopine Ri or Ti plasmids is not required for virulence. In this report, we confirm and extend these findings on a nopaline Ti plasmid by using several virD non‐polar mutants that were tested for virulence. virD3 and orf5 non‐polar mutants showed no effect on tumorigenicity on 14 different plant species, while virD4 mutants lost their tumorigenicity completely on all these test plants. These data suggest that virD3 and orfS are not essential for virulence whereas virD4 is absolutely required on a wide range of host plants.
An outer membrane protein (OmpA) of Escherichia coli can be translocated across the cytoplasmic membrane of Bacillus subtllis
Authors: Meens Jochen , Frings EIke , Klose Michael , Freudl Roland 
Published: October 2006

SummaryThe translocation of secretory proteins derived from a Gram‐positive (Staphylococcus hyicus prolipase) or a Gram‐negative (Escherichia coli pre‐OmpA protein) bacterium across the cytoplasmic membrane was studied in E. coli and Bacillus subtilis. in both microorganisms, the prolipase was found to be secreted across the plasma membrane when either the pre‐prolipase signal peptide (38 amino acids in length) or the pre‐OmpA signal peptide (21 amino acids in length) was used. Expression of the gene encoding the authentic pre‐OmpA protein in B. subtilis resulted in the translocation of mature OmpA protein across the plasma membrane. Processing of the OmpA precursor in B. subtilis required the electrochemical potential and was sensitive to sodium azide, suggesting that the B. subtilis SecA homologue was involved in the translocation process. The mature OmpA protein, which was most likely present in an aggregated state, was fully accessible to proteases in protoplasted cells. Therefore, our results clearly demonstrate that an outer membrane protein can be secreted by B. subtilis, supporting the notion that the basic mechanism of protein translocation is highly conserved in Gram‐positive and Gram‐negative bacteria.
The maturation pathway of microcin B17, a peptide inhibitor of DNA gyrase
Authors: Yorgey Peter , Davagnino Juan , Kolter Roberto 
Published: October 2006

SummaryThe maturation pathway of microcin B17 (MccB17), a ribosomally synthesized peptide antibiotic which inhibits DNA gyrase, has been characterized. Synthesis of MccB17 involves several steps beginning with the translation of the MccB17 structural gene, mcbA, to yield a 69 amino acid precursor, preMccB17. PreMccB17 is then modified and folded by the action of three gene products, McbBCD, to yield proMccB17. Mutations in mcbA were isolated that permit modifications of the resulting mutant peptides, but prevent folding, suggesting that modification and folding are sequential steps. ProMccB17 is subsequently converted to MccB17 by removal of the W‐terminal 26‐amino‐acid leader by a chromosomally encoded protease. Removal of the leader resulted in aggregation of the peptide, suggesting that the leader may function to maintain peptide solubility during synthesis in the cell. Finally, polyclonal antibodies raised against MccB17 recognize both MccB17 and proMccB17, but do not recognize preMccB17. This demonstrates the dramatic structural changes that result from the modifications and has been used to distinguish intermediates in the steps of maturation.
Osmostress response of the yeast Saccharomyces
Authors: Mager Willem H. , Varela João C. S. 
Published: October 2006

SummaryExposure of yeast cells to high osmolarities leads to dehydration, collapse of ion gradients over the plasma membrane and decrease in cell viability. The response of yeast cells to high external osmolarities is designated osmostress response. It is likely that both osmoregulatory and general stress reactions are involved in this so far poorly understood process. Part of the response aims at raising the internal osmotic potential, i.e. the production of osmolytes such as glycerol, and exclusion of toxic solutes. In addition, heat‐shock proteins and trehalose are synthesized, probably to protect cellular components and to facilitate repair and recovery. Recent analyses of osmosensitive yeast mutants strongly suggest the involvement of protein kinase‐mediated signal‐transduction pathways in the maintenance of the osmotic integrity of the cell. This has stimulated interesting hypotheses as to the actual osmosensing mechanism.
Expression of the gene encoding the major bacterial nucleoid protein H‐NS is subject to transcriptional auto‐repression
Authors: Falconi Maurizio , Higgins N. Patrick , Spurio Roberto , Pon Cynthia L. , Gualerzi Claudio O. 
Published: October 2006

SummaryExpression of a promoterless cat gene fused to a DNA fragment of approximately 400 bp, beginning at –313 of Escherichia coli hns, was significantly repressed in E. coli and Salmonella typhimurium strains with wild‐type hns but not in mutants carrying hns alleles. CAT expression from fusions containing a shorter (110 bp) segment of hns was essentially unaffected in the same genetic backgrounds. The stage of growth was found to influence the extent of repression which was maximum (approximately 75%) in mid‐log cultures and negligible in cells entering the stationary phase. The level of repression in early‐log phase was lower than in mid‐log phase cultures, probably because of the presence of high levels of Fis protein, which counteracts the H‐NS inhibition by stimulating hns transcription. The effects observed in vivo were mirrored by similar results obtained in vitro upon addition of purified H‐NS and Fis protein to transcriptional systems programmed with the same hns caf fusions. Electrophoretic gel shift assays, DNase I footprinting and cyclic permutation get analyses revealed that H‐NS binds preferentially to the upstream region of its own gene recognizing two rather extended segments of DNA on both sides of a bend centred around –150. When these sites are filled by H‐NS, an additional site between approximately –20 and –65, which partly overlaps the promoter, is also occupied. Binding of H‐NS to this site is probably the ultimate cause of transcriptional auto‐repression.
Inhibition of bacteriophage Mu transposition by Mu repressor and Fis
Authors: van Drunen C. M. , van Zuylen C. , Mientjes E. J. , Goosen N. , van de Putte P. 
Published: October 2006

SummaryIn this paper we show that the Escherichia coli protein Fis has a regulatory function in Mu transposition in the presence of Mu repressor. Fis can lower the transposition frequency of a mini‐Mu 3–80‐fold, but only if the Mu repressor is expressed simultaneously. In this novel type of regulation of transposition by the concerted action of Fis and repressor, the IAS, the internal activating sequence, is also involved as deletion of this site leads to the loss of the Fis effect. As the IAS contains strong repressor binding sites these are probably the target for the repressor in the observed negative regulation by Fis and repressor. However, the role of Fis and repressor is not only to inactivate the IAS, since a 4bp insertion in the IAS, which changes the spacing of the repressor‐binding site, abolishes the enhancing function of the IAS but leaves the repressor‐Fis effect intact. A likely target for Fis in this regulation is a strong Fis‐binding site, which is located adjacent to the L2 transposase‐binding site. However, when this Fis‐binding sequence was substituted by a random sequence and Fis no longer showed specific binding to this site, the Fis effect was still observed. Although it is still possible that Fis can function by binding to this non‐specific site in a particular complex, it seems more likely that Fis is directly or indirectly involved in determining the level of the repressor.
Deletions of Tn916‐like transposons are implicated in tetM‐mediated resistance in pathogenic Neisseria
Authors: Swartley J. S. , McAllister C. F. , Hajjeh R. A. , Heinrich D. W. , Stephens D. S. 
Published: October 2006

SummaryUsing the tetM‐containing conjugative transposon Tn916 as a mutagenesis tool, we identified two distinct classes of transposon insertions in the meningococcal chromosome. Class I Insertions have an intact copy of Tn916 that appears to have transposed by a novel recombinational mechanism, similar to the transposition of conjugative transposons in Gram‐positive bacteria. Class II insertions were characterized by deletions of Tn916 but preservation of the tetM determinant. In addition, we identified Class II Tn916‐like insertions in the naturally occurring 25.2 MDa tetM‐containing plasmids of both Neisseria meningitidis and Neisseria gonorrhoeae. The truncated Tn916 like insertions appeared to be present in the same site in these two plasmids; however, the deletions of the transposon were different. Plasmid sequence adjacent to the truncated transposon in the 25.2 MDa plasmids was found in a tetracycline‐sensitive N. gonorrhoeae 24.5 MDa conjugative plasmid. These data suggest that the 25.2 MDa plasmids are the result of one or a series of Class II Tn916‐like insertions into 24.5 MDa conjugative plasmids. Class II insertions of Tn916‐like transposons are implicated in the dissemination of tetM resistance in pathogenic Neisseria.
Theta replication of the lactococcal plasmid pWVO2
Authors: Kiewiet Rense , Bron Sierd , de Jonge Karel , Venema Gerard , Seegers Jos F. M. L. 
Published: October 2006

SummarypWVO2 is a 3.8 kb narrow‐host‐range plasmid from Lactococcus lactis ssp. cremoris Wg2, which does not replicate in Bacillus subtilis or Escherichia coli. Single‐stranded pWVO2 DNA was not observed in lactococcal cells, indicating that this plasmid does not replicate via a rolling‐circle mechanism. The sequence of pWVO2 neither showed the structural organization typical for rolling‐circle plasmids, nor were sequence similarities with known rolling‐circle plasmids present. By 2‐D agarose gel electrophoresis of replication intermediates, it was shown that pWVO2 replicates via a theta mechanism. This is the first proof for the existence of theta‐replicating plasmids in lactococci. The pWVO2 minimal replicon is strongly related to that of several other lactococcal plasmid replicons. It contains one open reading frame encoding the replication protein, which is preceded by a 22 bp sequence tandemly repeated three and a half times. Further upstream is another 10bp direct repeat present in an A/T‐rich sequence. This structural organization resembles that of several iteroncontaining theta‐type plasmids from E. coli. Derivatives of pWVO2 were stably maintained in L. lactis and are good candidates for the development of stable food‐grade cloning vectors for this organism.
Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325° to 333deg;
Authors: Glaser P. , Kunst F. , Arnaud M. , Coudart M.‐P. , Gonzales W. , Hullo M.‐F. , Ionescu M. , Lubochinsicy B. , Marcelino L. , Moszer I. , Presecan E. , Santana M. , Schneider E. , Schwelzer J. , Vertes A. , Rapoport G. , Danchin A. 
Published: October 2006

SummaryIn the framework of the European project aimed at the sequencing of the Bacillus subtilis genome the DNA region located between gerB (314°) and sacXV (333°) was assigned to the Institut Pasteur. In this paper we describe the cloning and sequencing of a segment of 97 kb of contiguous DNA. Ninety‐two open reading frames were predicted to encode putative proteins among which only forty‐two were found to display significant similarities to known proteins present in databanks, e.g. amino acid permeases, proteins involved in cell wall or antibiotic biosynthesis, various regulatory proteins, proteins of several dehydrogenase families and enzymes II of the phosphotransferase system involved in sugar transport. Additional experiments led to the identification of the products of new B. subtilis genes, e.g. galactokinase and an operon involved in thiamine biosynthesis.
Homologous pairing proteins encoded by the Escherichia coii recE and recT genes
Authors: Kolodner Richard , Hall Sharynn D. , Luisi‐DeLuca Cynthia 
Published: October 2006

SummaryEarly genetic analysis of alternate recombination pathways in Escherichia coli identified the RecE recombination pathway and the required exonuclease VIII encoded by the recE gene. Observations that not ail recombination events promoted by the RecE pathway require recA suggest the existence of an additional homologous pairing protein besides RecA in E. coli. Genetic and biochemical analysis of the recE gene region indicates there are two partially overlapping genes, recE and recT, encoding at least two proteins: exoVIII and the RecT protein. Biochemical analysis has shown that the RecT protein, in combination with exoVIII, promotes homologous pairing and strand exchange in reactions containing linear duplex DNA and homologous, circular, single‐stranded DNA as substrates. This reaction occurs in the absence of any high‐energy cofactor. These two proteins, RecT and exoVIII, appear to be members of a second class of homologous pairing proteins that are required in genetic recombination and differ from the class of homologous pairing proteins that includes RecA. Members of this second class of proteins appear to include both bacteriophage‐encoded proteins and proteins from eukaryotes and their viruses.