bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post‐transcriptional control of a sporulation regulatory gene encoding transcription factor σH in Bacillus subtilis
Authors: Healy J. , Weir J. , Smith I. , Losick R. 
Published: October 2006

SummaryThe transcriptional regulatory gene spo0H encodes an RNA polymerase sigma factor called σH that directs gene expression at an early stage of sporulation in the Gram‐positive bacterium Bacillus subtilis. We now report that conditions that induce sporulation cause a rapid increase In the cellular concentration of σH. This increase could account for the stimulated transcription of certain σH‐controlled genes at the onset of sporulation. Experiments in which the expression of spo0H was monitored by use of a spo0H‐lacZ fusion and in which expression of spo0H was artificially manipulated by use of an isopropyl‐β‐D‐thiogalacto‐side‐inducible promoter indicate that sporulation‐induced increases in the amount of σH are not controlled at the level of the transcription of its structural gene. Rather, we infer the existence of post‐transcriptional control mechanisms that govern σH levels, and we present evidence suggesting that increases in the amount of σH at the start of sporulation are due to increased translation or stability of the spo0H mRNA and, to a lesser extent, decreased turnover of spo0H protein.
Variable antigen genes of the relapsing fever agent Borrelia hermsii are activated by promoter addition
Authors: Barbour A. G. , Burman N. , Carter C. J. , Kitten T. , Bergström S. 
Published: October 2006

Summary Borrelia hermsii, an agent of replapsing fever, avoids the host's immune response by means of multiphasic antigenic variation. Serotype specificity is determined by variable antigens called the Vmp lipoproteins. Through recombination between linear plasmids a formerly silent vmp gene replaces another vmp gene at a telomeric expression locus. We examined strain HS1 borreliae before and after a switch from serotype 7 to serotype 21. The nucleotide sequences of 5 regions of silent and expressed vmp7 and vmp 21 were determined. Silent and active vmp 7 and vmp 21 genes shared a block of homologous sequences surrounding their 5′ ends. Sequences upstream of silent vmp 7 and vmp 21 genes lacked the promoter and substantially differed from each other. In this antigenic switch a vmp gene was activated by a recombination that placed it downstream of a promoter.
The bacterial porin superfamily: sequence alignment and structure prediction
Authors: Jeanteur D. , Lakey J. H. , Pattus F. 
Published: October 2006

SummaryThe porins of Gram‐negative bacteria are responsible for the ‘molecular sieve’ properties of the outer membrane. They form large water‐filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Owing to the strong hydrophilicity of their amino acid sequence and the nature of their secondary structure (beta strands), conventional hydropathy methods for predicting membrane topology are useless for this class of protein. The large number of available porin amino acid sequences was exploited to improve the accuracy of the prediction In combination with tools detecting amphipathicity of secondary structure. Using the constraints of β‐sheet structure these porins are predicted to contain 16 membrane‐spanning strands, 14 of which are common to the two (enteric and the neisserial) porin subfamilies.
Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation
Authors: Condemine G. , Robert‐Baudouy J. 
Published: October 2006

SummaryA group of four genes of Erwinia chrysanthemi involved in pectin degradation has been characterized. These four genes form independent transcription units and are regulated by the negative regulatory gene, kdgR. The functions of two of these genes are known: kduD codes for the 2‐keto‐3‐deoxygluconate oxydoreductase and kdul for the 5‐keto‐4‐deoxyuronate isomerase, two enzymes of the pectin degradation pathway. kdgC has 36% homology with pectate lyase genes of the periplasmic family but its product does not seem to have pectinolytic activity. The fourth gene, kdgF, could have a role in the pathogenicity of E. chrysanthemi. A comparison of the regulatory regions of all the genes controlled by kdgR allowed better definition of the KdgR‐binding‐site consensus.
Molecular cloning and expression in Escherichia coli K‐12 of the rfb gene cluster determining the O antigen of an E. coli O111 strain
Authors: Bastin D. A. , Romana L. K. , Reeves P. R. 
Published: October 2006

SummaryThe O antigen of Escherichia coli O111 is identical in structure to that of Salmonella enterics serovar adelaide. Another O‐antigen structure, similar to that of E. coli O111 and S. enterica serovar adelaide is found in both E. coli O55 and S. enterica serovar greenside. Both O‐antigen structures contain colitose, a 3,6 dideoxyhexose found only rarely in the Enterobacteriaceae. The O‐antigen structure is determined by genes generally located in the rfb gene cluster. We cloned the rfb gene cluster from an E. coli O111 strain (M92), and the clone expressed O antigen in both E. coli K‐12 and a K‐12 strain deleted for rfb. Lipopoly‐saccharide analysis showed that the O antigen produced by strains containing the cloned DNA is polymerized. The chain length of O antigen was affected by a region outside of rfb but linked to it and present on some of the plasmids containing rfb. The rfb region of M92 was analysed and compared, by DNA hybridization, with that of strains with related O antigens. The possible evolution of the rfb genes in these O antigen groups is discussed.
The sugar‐specific outer membrane channel ScrY contains functional characteristics of general diffusion pores and substrate‐specific porins
Authors: Schülein K. , Schmid K. , Benzl R. 
Published: October 2006

SummaryEscherichia coli K–12 strain PS1–28–37 carries the multicopy plasmid pPSO28–37 containing a DNA fragment coding for two of the proteins that enable bacteria to utilize sucrose as sole carbon source. One of the different gene products of the plasmid is the outer membrane protein, ScrY. This protein was isolated and purified by chromatography across a gel filtration column. Reconstitution experiments with lipid by layer membrane demonstrated that ScrY formed ion‐permeable channels with properties very similar to those of general diffusion pores of enteric bacteria. The presence of sugars in the aqueous phase led to a dose‐dependent block of ion transport through the channel, like the situation found with LamB (maltoporin) of Escherichia coli and Salmonella typhimurium. The binding constants of a variety of different sugars were determined. The stability constant for malto‐oligosaccharide binding increased with increasing numbers of glucose residues. Disaccharides generally had a larger binding constant than monosaccharides. The binding of different sugars to ScrY and LamB of E. coli discussed with respect to the kinetics of sugar movement through the channel.
IS901, a new member of a widespread class of atypical insertion sequences, is associated with pathogenicity in Mycobacterium avium
Authors: Kunze Z. M. , Wall S. , Appelberg R. , Silva M. T. , Portaels F. , McFadden J. J. 
Published: October 2006

SummaryAn insertion sequence (IS901), found in pathogenic strains of Mycobacterium avium, but absent in M. avium complex isolates from patients with acquired immune deficiency syndrome (AIDS), has been isolated and sequenced. This insertion element has a nucleotide sequence of 1472 bp, with one open reading frame (0RF1), which codes for a protein of 401 amino acids. The amino acid sequence, terminal ends and target site of IS901 are similar to those of IS900, present in Mycobacterium paratuberculosis. However, the DNA sequences of these two IS elements exhibit only 60% homology, compared to a DNA homology of 98% between their respective hosts. IS901, like IS900, appears to belong to a family of related insertion elements present in actinomycetes and other bacteria. M. avium strains containing IS900 were found to be more virulent in mice than closely related strains lacking IS901. IS901 may be a useful tool for the study of the genetics of virulence in the M. avium complex and for obtaining stable integration of foreign genes into mycobacteria.
Escherichia coli DNA helicases: mechanisms of DNA unwinding
Authors: Lohman T. M. 
Published: October 2006

SummaryDNA helicases are ubiquitous enzymes that catalyse the unwinding of duplex DNA during replication, recombination and repair. These enzymes have been studied extensively; however, the specific details of how any helicase unwinds duplex DNA are unknown. Although it is clear that not all helicases unwind duplex DNA in an identical way, many helicases possess similar properties, which are thus likely to be of general importance to their mechanism of action. For example, since helicases appear generally to be oligomeric enzymes, the hypothesis is presented in this review that the functionally active forms of DNA helicases are oligomeric. The oligomeric nature of helicases provides them with multiple DNA‐binding sites, allowing the transient formation of ternary structures, such that at an unwinding fork, the helicase can bind either single‐stranded and duplex DNA simultaneously or two strands of single‐stranded DNA. Modulation of the relative affinities of these binding sites for single‐stranded versus duplex DNA through ATP binding and hydrolysis would then provide the basis for a cycling mechanism for processive unwinding of DNA by helicases. The properties of the Escherichia coli DNA helicases are reviewed and possible mechanisms by which helicases might unwind duplex DNA are discussed in view of their oligomeric structures, with emphasis on the E. coli Rep, RecBCD and phage T7 gene 4 helicases.
Bacillus subtilis chemotaxis: a deviation from the Escherichia coli paradigm
Authors: Bischoff D. S. , Ordal G. W. 
Published: October 2006

SummaryIn Escherichia coli, chemotactic sensory transduction is believed to involve phosphoryl transfer for excitation, and changes in receptor methylation for adaptation. In Bacillus subtilis, changes in degree of receptor methylation do not bring about adaptation. Novel methylation reactions are believed to be involved in excitation in B. subtillis. The main chemotaxis proteins of E. coli—CheA, CheB, CheR, CheW and CheY—are present in B. subtilis but play somewhat different roles in the two organisms. Several unique chemotaxis proteins are also present in B. subtilis. Some of the properties of B. subtilis chemotaxis are also seen in Halobacterium halobium, suggesting that there may be a similar underlying mechanism that predates the evolutionary separation of the bacteria from the archaea and eucarya.
Pseudomonas aeruginosa AlgB, which modulates the expression of alginate, is a member of the NtrC subclass of prokaryotic regulators
Authors: Goldberg J. B. , Dahnke T. 
Published: October 2006

SummaryThe Pseudomonas aeruginosa exopolysaccharide alginate is an important virulence factor in chronic pulmonary infections of cystic fibrosis patients. We determined the nucleotide sequence of the gene, algB, which regulates the level of exopolysaccharide produced by mucoid P. aeruginosa. The predicted amino acid sequence of AlgB revealed a high degree of similarity to the regulatory proteins in the NtrC subclass of ‘two‐component regulatory systems’. AlgB expression in Escherichia coli minicells showed a molecular weight of ˜ 50 000 Da, comparable to that of the inferred amino acid sequence (49 318 Da). We show that algB is transcriptionally active in mucoid strains of P. aeruginosa and regulates the expression of the alginate biosynthetic gene, algD, thereby resulting in increased expression of alginate in mucoid P. aeruginosa.
Molecular characterization of mutations of nlt‐4, the pathway‐specific regulatory gene which controls nitrate assimilation in Neurospora crassa
Authors: Yuan G.‐F. , Marzluf G. A. 
Published: October 2006

SummaryThe nit‐4 genes of three conventional Neurospora crassa mutations and of the closely related species, Neurospora intermedia, have been isolated by amplifying the genomic DNA with the polymerase chain reaction. Nucleotide sequencing has revealed that the three nit‐4 mutants, alleles 15,1214, and 2994, are the result of a missense mutation, a nonsense mutation and a frameshift mutation, respectively. The nucleotide sequence of the NIT4 protein coding region of a nit‐4 mutant (allele 2994) and of N. intermedia have been determined and compared with that of wild‐type N. crassa. The molecular characteristics confirm that the mutated gene of 2994 originated from N. intermedia and was introgressed into N. crassa. The polyglutamine domains of the N. crassa wild type, the 2994 mutant, or N. intermedia cannot replace an upstream glutamine‐rich domain which is essential for nit‐4 function.
Iron regulates growth of Trichomonas vaginalis and the expression of immunogenic trichomonad proteins
Authors: Lehker M. W. , Alderete J. F. 
Published: October 2006

SummaryIron is an essential nutrient for Trichomonas vaginalis and is acquired via highly specific receptor‐mediated mechanisms from the host. Responses of T. vaginalis to conditions of iron limitation or iron excess were analysed in order to determine whether iron levels in the growth medium regulate certain properties of the parasite. When compared with organisms grown in excess iron, iron limitation resulted in ≥80% lower rates of protein synthesis and ≥3‐fold decreases in cell densities. These parasites also exhibited generation times of 10 hours, 2.5‐fold longer than organisms grown in the usual complex medium. Iron‐restricted growth also resulted in increased binding of lactoferrin by trichomonads, which paralleled elevated expression of the lactoferrin‐binding receptor protein having a relative molecular mass of 136000 daltons (136 kDa). A Mr 126kDa protein was concomitantly repressed in low‐iron‐grown parasites. The greater amounts of lactoferrin bound by iron‐depleted T. vaginalis organisms corresponded with both the expression of additional receptors onto trichomonal surfaces and increased affinity of the receptor for the lactoferrin molecule. Finally, immunoblot analysis of parasites grown under high‐ and low‐iron conditions using sera from patients with trichomoniasis further revealed the synthesis by T. vaginalis of at least 19 iron‐regulated immunogens, and patients' sera also detected the lactoferrin receptor. These data not only show the overall importance of iron to the biology of this protozoan, but illustrate the in vivo iron modulation of gene expression of the biofunctional lactoferrin receptor and other immunogens.
Ferrioxamine uptake in Yersinia enterocolitica: characterization of the receptor protein FoxA
Authors: Báumler Andreas J. , Hantke Klaus 
Published: October 2006

SummaryThe gene for the high‐affinity outer membrane ferrioxamine receptor FoxA of Yersinia enterocolitica was cloned in Escherichia coli K‐12. A foxA mutant of Yersinia could be complemented by the cloned DNA fragment. The FoxA encoding region was sequenced and an open reading frame encoding 710 amino acids, including a signal sequence of 26 amino acids, was deduced. The mature FoxA protein consisted of 684 amino acids and had a molecular mass of 75768 Da. FoxA shared 33% amino acid sequence homology with FhuA, the ferrichrome receptor of Escherichia coli. Based on the homologies with FhuA and other TonB‐dependent receptors a topological model of FoxA is presented.
IRE1 encodes a putative protein kinase containing a membrane‐spanning domain and is required for inositol phototrophy in Saccharomyces cerevisiae
Authors: Nikawa Jun‐Ichi , Yamashita Satoshi 
Published: October 2006

SummaryA novel gene, IRE1, of Saccharomyces cerevisiae was cloned through genetic complementation of a myo‐ inositol auxotrophic mutant. The predicted amino acid sequence indicated that IRE1 encodes a protein of 126983 Da with two highly hydrophobic regions, probably a signal sequence and a membrane‐spanning region. The carboxy‐terminal region of IRE1 showed close sequence similarity to the catalytic domains of protein kinases. Disruption of the IRE1 locus caused myo‐inositol auxotrophy. The IRE1 product is very likely a protein kinase required for myo‐inositol synthesis.
Molecular genetic analysis of the Rhizobium meliloti fixK promoter: identification of sequences involved in positive and negative regulation
Authors: Waelkens F. , Foglia A. , Morel J.‐B. , Fourment J. , Batut J. , Boistard P. 
Published: October 2006

SummaryTranscription of the Rhizobium meliloti fixK gene is induced in symbiotic and microaerobic growth conditions by the FixL/FixJ modulator/effector pair. Transcription of fixK is also negatively autoregulated. By 5’deletion analysis, the involvement in negative regulation of a DNA region between ‐514 and ‐450 with respect to the transcription start was demonstrated. Site‐directed mutagenesis allowed us to show that a sequence homologous to the binding site of the Escherichia coli Fnr protein, centred at position ‐487, participates in this effect. However, deletion or mutagenesis of this Fnr‐like sequence does not completely eliminate FixK‐dependent repression, which suggests that either an additional DNA region is involved in negative regulation or that it is mediated at the level of fixLJ transcription. Deletion analysis also allowed the definition of a DNA region involved in FixJ‐mediated activation of the fixK promoter, between ‐79 and ‐42. Different point mutations in the ‐60, ‐45 and ‐35 regions were shown to affect promoter activity. In some cases, the activity of mutant promoters could be partly or fully restored by increasing the expression of the fixLJ regulatory genes. In an E. coli strain harbouring a plasmid with fixLJ under the control of an inducible (p‐tac) promoter.
The spo0A gene is implicated in the maintenance of non‐complementing diploids in Bacillus subtilis
Authors: Le Dérout J. , Thaler David S. , Guillén Nancy , Hirschbein Luisa 
Published: October 2006

Summary Bacillus subtilis can exist in a diploid state in which two genetically distinct chromosomes co‐exist in the same cell and yet only one of them is expressed, thereby determining the phenotype. Such cells are called non‐complementing diploids (Ncds). In this study, two types of experiments are reported which indicate that a previously known pleiotropic gene, spo0A, plays a role in the maintaining the diploid state, as follows, (i) When protoplasts of two Spo0A mutant strains were fused, the resulting products continued to segregate cells of both parental phenotypes for many more divisions than had been reported previously, (ii) When a stable Ned (an Ncd in which the unexpressed markers are not spontaneously activated at a detectable level) harbouring a chloramphenicol acetyltransferase gene on the silent chromosome was transformed with spo0A null alleles the transformants often expressed chloramphenicol acetyltransferase activity. Together these results indicate that the spo0A gene is involved in maintenance of the diploid state in both unstable and stable Ncds.
Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli
Authors: Sauter M. , Böhm R. , Böck A. 
Published: October 2006

SummaryIn‐frame deletions were introduced into each of the eight genes of the hyc operon coding for products required for the formation of the formate hydrogenlyase (FHL) system. The deletions were transferred to the chromosome and the resulting mutants were analysed for development of formate dehydrogenase H and hydrogenase 1, 2 and 3 activity. It was found that hycA, the promoter‐proximal gene, is a regulatory gene and that it codes for a product counteracting transcriptional activation by FhlA. Deletions within the hycB to hycH genes specifically affected formate dehydrogenase H activity or hydrogenase 3 activity, or both. None of the mutations affected hydrogenase 1 or 2 activity. A model is proposed for the functional interaction of the different hyc operon gene products in the formate hydrogenlyase complex, which is based on the results of the mutational analysis, on the determination of the subcellular localization of the FdhF, HycE, HycF and HycG polypeptides and on the similarity of hyc gene product sequences with those from other hydrogenase systems. HycH, the product of the most promoter‐distal gene, does not seem to form part of the functional FHL complex but rather is required for the conversion of a precursor form of the large subunit of hydrogenase 3 into the mature form.
Involvement of a possible chaperonin in the efficient expression of a cloned CryllA δ‐endotoxin gene in Bacillus thuringiensis
Authors: Crickmore Neil , Ellar David J. 
Published: October 2006

SummaryThe Bacillus thuringiensis cryllAδ‐endotoxin gene is found as the third‐gene in a three‐gene operon, with a sporulation‐dependent promoter lying upstream of the first gene, orf1. We show here that the polypeptide product of the middle gene (orf2) is required for efficient expression of the toxin gene. In the absence of a functional ORF2 polypeptide the toxin does not form the crystalline inclusions characteristic of other known Bacillus thuringiensis toxins. We discuss the importance of this finding with respect to the possible role of chaperonins in the crystallization of these proteins.
icsB: a Shigella flexneri virulence gene necessary for the lysis of protrusions during intercellular spread
Authors: Allaoui Abdelmounaaïm , Mounier Joëlle , Prévost Marie‐Christine , Sansonetti Philippe J. , Parsot Claude 
Published: October 2006

Summary Shigella flexneri causes bacillary dysentery by invading epithelial cells of the colonic mucosa. We have characterized the icsB gene which is located on the virulence plasmid pWR100. After inactivation of icsB, the mutant strain remained invasive, but formed abnormally small plaques on HeLa cell monolayers, colonized only the peripheral cells of Caco‐2 islets, and was unable to provoke a keratoconjunctivitis in guinea‐pigs. Examination of infected HeLa cells showed that the icsB mutant was able to lyse the phagocytic vacuole and to form protrusions at the surface of infected cells, but, unlike the wild type, remained trapped in protrusions surrounded by two membranes. These results indicate that IcsB is involved in the lysis of the protrusions, a step necessary for intercellular spread.
In vivo characterization of tus gene expression in Escherichia coli
Authors: Roecklein Bryan A. , Kuempel Peter L. 
Published: October 2006

SummaryThe tus gene encodes a DNA‐binding protein (Tus) that inhibits replication forks at specific block‐sites within the terminus region of the Escherichia coli chromosome. One of these block‐sites, TerB, is adjacent to the tus gene. Using primer extension and a promoter fusion to characterize in vivo expression, we have demonstrated that the tus transcription start site is within TerB, and that Tus protein autoregulates expression at this weak promoter We have also demonstrated that a minority of tus transcripts are initiated from an upstream region that contains two additional open reading frames. This readthrough transcription into tus is reduced in the presence of Tus protein.