bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large genomic rearrangements of the unstable region in Streptomyces ambofaciens are associated with major changes in global gene expression
Authors: Dary A. , Kaiser P. , Bourget N. , Thompson C. J. , Simonet J. M. , Decaris B. 
Published: October 2006

SummaryGlobal gene expression is dramatically altered by genomic rearrangements in Streptomyces ambofaciens RP181110. Partial genome mapping of two derivatives of strain RP181110 (strains NSA205 and NSA228) revealed rearrangements located in the unstable region of the genome (deletion in strain NSA228; deletion and amplification in strain NSA205). Computerized comparisons of pulse‐labelled proteins separated by two‐dimensional electrophoresis have revealed numerous differences in gene expression among the three strains during both exponential and stationary phases of growth: 31 proteins were absent in both mutant strains, 16 were absent only in strain NSA228, 17 were absent only in strain NSA205 and 9 were found to be present or over expressed in strain NSA205. Thus, in spite of the scarcity of genetic markers in the unstable region and its dispensability for growth under laboratory conditions, these results suggest that it includes genes which are actively expressed. Spontaneous gene amplifications, which occur frequently in this region of the chromosome, can further activate their expression.
Protein–nucleoside contacts in the interaction between the replication terminator protein of Bacillus subtilis and the DNA terminator
Authors: Langley D. B. , Smith M. T. , Lewis P. J. , Wake R. G. 
Published: October 2006

SummaryThe interaction between the DNA replication terminator, IRI, of Bacillus subtilis and its cognate replication terminator protein (RTP) has been examined by the technique of missing nucleoside interference (MNI). IRI contains two adjacent binding sites (A and B) for RTP dimers. The B site is proximal to the replication fork arrest site. The present results have shown that nucleoside contacts with RTP in the two sites are very different. There are more extensive contacts of nucleosides in both strands of the B site with RTP compared with the A site. The data also strongly suggest that filling by RTP of the B site occurs first and is needed for subsequent co‐operative filling of an overlapping A site. The A site alone binds RTP poorly. The findings are consistent with interaction occurring between RTP dimers bound to adjacent sites of IRI, which would explain why RTP bound to the B site alone cannot cause replication fork arrest.
Interactions between the Escherichia coli cyclic AMP receptor protein and RNA polymerase at Class II promoters
Authors: West David , Williams Roy , Rhodius Virgil , Bell Andrew , Sharma Naveen , Zou Chao , Fujita Nobuyuki , Ishihama Akira , Busby Stephen 
Published: October 2006

SummaryThe effects of a number of mutations in crp have been measured at different cyclic AMP receptor protein (CRP)‐dependent Class II promoters, where the CRP‐binding site is centred around 411/2 base pairs upstream from the transcription start point. The amino acid substitutions HL159 and TA158 result in reduced CRP‐dependent activation, but the reduction varies from one Class II promoter to another. Deletions in the C‐terminus of the RNA polymerase alpha subunit suppress the effects of HL159 and TA158. The role of the C‐terminus of alpha at these promoters is assessed. Other changes at E58, K52 and E96 affect CRP activity specifically at Class II promoters and their role is discussed.
Secondary sites for integration mediated by the Tn21 integrase
Authors: Francia M. Victoria , Cruz Fernando de la , Lobo Juan M.Garcí 
Published: October 2006

SummaryThe integrase encoded by the integron of the transposon Tn21 can mediate the site‐specific fusion of two plasmids if there is a recombination hot spot (59 bp element) in one of them and the sequence GWTMW in the other. The use of this latter, loosely defined site explains how antibiotic‐resistance genes could first become associated with integrons.
A Mycobacterium leprae‐specific gene encoding an immunologically recognized 45 kDa protein
Authors: De Wit Tobias F. Rinke , Clark‐Curtiss Josephine E. , Abebe Feseha , Kolk Arend H. J. , Janson Anneke A. M. , Agterveld Miranda van , Thole Jelle E. R. 
Published: October 2006

SummaryBy screening a Mycobacterium leprae lambda gt11 expression library with a serum from an Ethiopian lepromatous leprosy (LL) patient a clone was isolated (LL4) belonging to hybridization group III of a panel of previously isolated M. leprae clones. Members of this hybridization group encode a serologically recognized 45 kDa protein. The complete DNA sequences of the partially overlapping clones LL4 and L1 (hybridization group III) are presented and these revealed the presence of an open reading frame (ORF) predicting a protein with a molecular size of 42 448 Da. Southern hybridizations on total genomic DNA of M. Ieprae, Mycobacterium tuberculosis and eight atypical mycobacteria showed that the LL4 DNA fragment is specific for M. Ieprae DNA even under low‐stringency conditions. The M. Ieprae specificity of LL4 DNA was further confirmed by the polymerase chain reaction using four different sets of primers. Western blotting analyses showed that the M. Ieprae 45 kDa protein is frequently recognized by antibodies from leprosy patients and that this recognition is specific since no antibodies could be detected in sera of tuberculosis patients. T‐cell proliferation assays also demonstrated T‐cell recognition by leprosy patients and healthy contacts of the M. Ieprae 45 kDa protein. The specificity of the LL4 DNA region and the 45 kDa antigen that is encoded by hybridization group III could provide unique tools for the development of M. Ieprae‐specific immunological and DNA reagents.
Molecular and genetic characterization of superoxide dismutase in Haemophilus influenzae type b
Authors: Kroll J. S. , Langford P. R. , Saah J. R. , Loynds B. M. 
Published: October 2006

SummaryOxygen free radicals present a serious potential threat to microbial survival, through their ability to inflict Indiscriminate damage on proteins and DNA. Superoxide dismutase (SOD, EC 1.15.1.1), among other oxygen‐metabolizing enzymes, is essential to prevent these toxic molecules from accumulating in the bacterial cytosol during aerobic metabolism. The gene sodA, encoding manganese‐containing SOD ([Mn]‐SOD), has been cloned from a virulent strain of Haemophilus influenzae type b using degenerate oligonucleotides encoding regions of the gene conserved across different bacterial species. The gene product has been identified as [Mn]‐SOD by its similarity at key amino acid residues to known examples of the enzyme, by expression of enzymatically active protein from cloned DNA expressed in Escherichia coli, and by demonstration that an in‐frame deletion in the gene abolishes this activity. In contrast to the situation in E. coli, this [Mn]‐SOD is the only active SOD detected in H. influenzae. In further contrast to E. coli, [Mn]‐SOD gene expression in H. influenzae has been found to be only partially repressed under anaerobic conditions. When expressed in E. coli the gene is regulated by Fur and Fnr, and the promoter region, identified experimentally, has been found to contain nucleotide sequence motifs similar to the Fur‐ and Fnr‐binding sequences of E. coli, suggesting the involvement of analogues of these aerobiosis‐ responsive activators in H. influenzae gene expression.
Branched Escherichia coli cells
Authors: Åkerlund Thomas , Nordström Kurt , Bernander Rolf 
Published: October 2006

SummaryfWe report that the normally rod‐shaped bacterium Escherichia coli can form branched cells. These were found in strains in which chromosome replication or nucleoid segregation was disturbed, e.g. in minB mutants, intR1 strains, and in strains exhibiting stable DNA replication. Often, chromosome DNA was found to be located in the branch point of the cells. The branching frequency was dependent upon the growth medium: in rich medium no branched cells were found, whereas in minimal medium containing acetate and casamino acids the frequency of branched cells was increased. The genetic background of the strains also affected the tendency to branch. Furthermore, electron microscopy of thin‐sectioned branched cells revealed additional membrane‐like structures, which were not observed in wild‐type cells. Finally, the branched cells are compared with bacteria that normally branch, and probable causes for branching in E. coli are discussed.
Morphogenesis‐independent regulation of actin transcript levels in the pathogenic yeast Candida albicans
Authors: Delbrück Sebastian , Ernst Joachim F. 
Published: October 2006

SummaryThe transcript level of the Candida albicans ACT1 gene (encoding actin) is strongly regulated during induction of hyphal morphogenesis. ACT1 mRNA declines rapidly during starvation pretreatment and quickly recovers in media inducing morphogenesis. The C. albicans URA3 and LEU2 mRNAs, as well as an ACT1 promoterILAC4 fusion, are regulated similarly. The regulation of ACT1ILAC4 and unaltered mRNA stabilities suggest transcriptional regulation during morphogenesis. However, by individually testing morphogenesis induction parameters, it is shown that starvation and growth phase, but not hyphal formation, are responsible for ACT1 transcript regulation; this conclusion is confirmed by analyses of morphological mutants and by inhibition of hyphal development. Thus, the specific morphogenesis‐induction conditions, but not morphogenesis per se, affect transcript levels in C. albicans.
Transaldolase mutants in the yeast Kluyveromyces lactis provide evidence that glucose can be metabolized through the pentose phosphate pathway
Authors: Jacoby J. , Hollenberg C. P. , Heinisch J. J. 
Published: October 2006

SummaryWe have isolated the gene encoding transaldolase from Kluyveromyces lactis (KITALI) by screening a genomic library of this yeast using the TAL1 gene of Saccharomyces cerevisiae as a radioactive probe. The clone isolated contained an open reading frame of 1002 bp, encoding a protein with 76% identical residues in the deduced amino acid sequences as compared to Tal from S. cerevisiae. KITAL1 can complement a tal1 deletion of S. cerevisiae for enzymatic activity. The transcription start of KITAL1 was located at ‐69 bp relative to the ATG translation start codon. Deleting a large part of the open reading frame from the genome did not lead to any obvious phenotype. Transaldolase was not produced in such mutants as shown by immunological detection. In combination with a double null‐mutant in the genes encoding the phosphofructokinase subunits in K. lactis (Klpfk1 Klpfk2 Kltal1), the cells lost their ability to grow on glucose. We take this as strong evidence that glucose is metabolized via the pentose phosphate pathway in this yeast when glycolysis is blocked. In addition, by tetrad analysis we detected a close linkage to KIPFK1 and inferred that KITAL1 is localized on chromosome I.
Interaction of a redox‐sensitive DNA‐binding factor with the 5′‐flanking region of the micF gene in Escherichia coli
Authors: Gidrol Xavier , Farr Spencer 
Published: October 2006

SummaryThe product of the micF gene is an endogenous anti‐sense RNA which down‐regulates the expression of a major outer membrane protein, OmpF, in E. coli. We report here that two DNA‐binding factors compete for the same site in the promoter region of the micF gene: RSBF, a high‐affinity redox‐sensitive DNA‐binding factor that responds to an active oxygen species other than hydrogen peroxide or superoxide anions; and HRBF a heat‐resistant DNA‐binding factor. Both RSBF and HRBF bind to the same DNA sequence, 5′‐TTAAAATCAATAACTTATTCTTAA3‐′, located upstream of the transcription start site of the micF gene. We present evidence that RSBF could be the controlling factor of a novel regulon involved in the response to oxidative stress in E. coli.
Repair of cyclobutane pyrimidine dimers and 6‐4 photoproducts in the fission yeast Schizosaccharomyces pombe
Authors: McCready Shirley , Carr Antony M. , Lehmann Alan R. 
Published: October 2006

SummaryWe have measured repair of both of the major lesions induced by ultraviolet irradiation (cyclobutane pyrimidine dimers and 6‐4 photoproducts) in wild‐type Schizosaccharomyces pombe and in selected rad mutants, including mutants with deletions in genes from the main phenotypic groups. We find that rad13Δ, rad15 and rad16Δ, which are the S. pombe homologues of the excision‐defective Saccharomyces cerevisiae rad2, rad3 and rad1, respectively, repair lesions somewhat more slowly than the wild type, but still have considerable repair capacity. rad2Δ, also a presumed excision‐defective mutant, behaves similarly. radS and rad9δ, which belong to different phenotypic groups, repair lesions at the same rate as wild‐type cells. These findings provide new evidence that S. pombe has a second repair system for removing ultraviolet damage, which is absent in S. cerevisiae. Surprisingly, this second mechanism repairs lesions very efficiently; its possible nature is discussed.
The ompS gene of Vibrio cholerae encodes a growth‐phase‐dependent maltoporin
Authors: Lå Hannu , Palva E. Tapio 
Published: October 2006

SummaryThe outer membrane of Vibrio cholerae contains a maltose‐inducible major protein, OmpS (43 kDa), that is common to different isolates. Nucleotide sequence analysis of the corresponding structural gene, ompS, revealed an open reading frame encoding a 412‐amino‐acid polypeptide. The amino acid sequence of OmpS is similar to that of LamB, the Escherichia coli maltoporin, and to ScrY of Klebsilla pneumoniae, although the antigenic determinants of these proteins are different. The cloned ompS gene complemented an ompS mutation of V. cholerae and the corresponding polypeptide could function as a maltoporin in a LamB‐ mutant of E. coli. The promoter region of ompS is highly homologous to the malK‐lamB promoter of E. coli and the ompS gene is controlled by MalT in E. coli. This indicates that the same kind of regulatory mechanism is used to activate the ompS expression in V. cholerae and malK‐lamB expression in E. coli. An ompS‐lacZ transcriptional fusion was used to demonstrate a dual control in ompS expression; the ompS gene is responsive to the inducers maltose and trehalose but in their absence it is also expressed in response to growth‐phase. These different modes of induction might be of importance during different stages of V. cholerae infection.
Linear plasmids and chromosomes in bacteria
Authors: Hinnebusch Joe , Tilly Kit 
Published: October 2006

SummaryLinear plasmids and chromosomes were unknown in prokaryotes until recently but have now been found in spirochaetes, Gram‐positive bacteria, and Gram‐negative bacteria. Two structural types of bacterial linear DNA have been characterized. Linear plasmids of the spirochaete Borrelia have a covalently closed hairpin loop at each end and linear plasmids of the Gram‐positive filamentous Streptomyces have a covalently attached protein at each end. Replicons with similar structures are more frequent in eukaryotic cells than in prokaryotes. Linear genomic structures are probably more common in bacteria than previously recognized, however, and some replicons may interconvert between circular and linear isomers. The molecular biology of these widely dispersed elements provides clues to explain the origin of linear DNA in bacteria, including evidence for genetic exchange between prokaryotes and eukaryotes.
The chromosomal DNA of Streptomyces lividans 66 is linear
Authors: Lin Yi‐Shing , Kieser Helen M. , Hopwood David A. , Chen Carton W. 
Published: October 2006

SummaryTwo copies of a DNA sequence similar or identical to one end of the linear plasmid SLP2 were found on the Streptomyces lividans chromosome. Restriction mapping showed that these sequences represented free ends. Electrophoretic retardation and glass‐binding studies indicated that the telomeres carry covalently bound proteins. Moreover, the chromosome migrated as an 8Mb linear DNA in pulsed‐field gel electrophoresis. A similar finding with the chromosomes of six other Streptomyces species suggested that a linear chromosome may be characteristic of the genus. The S. lividans chromosome can be circularized by joining the two ends by artificial targeted recombination or by spontaneous deletions spanning both telomeres. Thus the chromosome appears to be able to exist, in viable bacteria, as a linear or a circular molecule.
The genus‐specific lipopolysaccharide epitope of Chlamydia is assembled in C. psittaci and C. trachomatis by glycosyltransferases of low homology
Authors: Mamat U. , Baumann M. , Schmidt G. , Brade H. 
Published: October 2006

SummaryChlamydiae possess a genus‐specific epitope that is located on the lipopolysaccharide (LPS) and is composed of a 3‐deoxy‐d‐manno‐octulosonic acid (Kdo) trisaccharide of the sequence αKdo‐(2→8)–αKdo–(2→4)‐αKdo. In Chlamydia trachomatis, this trisaccharide is biosynthetically generated through the action of a multi‐functional Kdo‐transferase encoded by the gene gseA. gseA of Chlamydia psittaci 6BC was cloned and expressed in a rough mutant (Re chemotype) of Escherichia coli (strain F515) that contains an LPS with only two α2→4‐linked Kdo residues. Recombinant strains were able to add the immunodominant Kdo residue in a α2→8‐linkage to the parental LPS, as determined by SDS–PAGE and Western blot analysis using a monoclonal antibody against the genus‐specific epitope. The DNA sequence of gseA was determined and aligned to that published recently for C. trachomatis serovar L2. Most surprisingly, the two deduced amino acid sequences shared only an overall homology of 67%. Thus, gseA exhibits species specificity at the DNA level, whereas its gene product results in the synthesis of a carbohydrate antigen with genus specificity.
The conserved proline‐rich Motif is not essential for energy transduction by Escherichia coliTonB protein
Authors: Larsen Ray A. , Wood Gwendolyn E. , Postle Kathleen 
Published: October 2006

SummaryTonB protein functions as an energy transducer, coupling cytoplasmic membrane electrochemical potential to the active transport of vitamin B12 and Fe(III)–siderophore complexes across the outer membrane of Escherichia coli and other Gram‐negative bacteria. Accumulated evidence indicates that TonB is anchored in the cytoplasm, but spans the periplasmic space to interact physically with outer membrane receptors. It has been presumed that this ability is caused by a conserved (Glu–Pro)n–(Lys–Pro)m repeat motif, predicted to assume a rigid, linear conformation of sufficient length to reach the outer membrane. Based on in vitro studies with synthetic peptides and purified FhuA outer membrane receptor, it has been suggested that this region contains a site that directly binds outer membrane receptors and is essential for energy transduction. We have found a TonB lacking the (Glu–Pro)n–(Lys–Pro)m, repeat motif (TonBΔ(66–100)). TonBΔ(66–100) is fully capable of irreversible 80 adsorption, except under physiological circumstances where the periplasmic space is expanded. Based on the ability of TonBΔ(66–100) to interact with outer membrane receptors and components of the energy transduction apparatus under normal physiological conditions, it is evident that the TonB proline‐rich region has no role in energy transduction other than to provide a physical extension sufficient to reach the outer membrane.
Differential regulation of two myo‐inositol transporter genes of Saccharomyces cerevisiae
Authors: Nikawa J. , Hosaka K. , Yamashita S. 
Published: October 2006

SummaryWe previously isolated two distinct Saccharomyces cerevisiae myo‐inositol transporter genes, ITR1 and ITR2 (Nikawa et al., 1991). Here, we studied the regulation of their expression by measuring steady‐state mRNA levels and β‐galactosidase activities of lacZ fusion genes under different conditions. The results show that the expression of the two ITR genes is differently regulated: ITR1 was repressed by inositol and choline whereas ITR2 was constitutive. Deletion analysis of the ITR1 upstream region and comparison with the upstream regions of other genes involved in phospholipid synthesis indicate that the octamer sequence 5′‐TTCACATG‐3′ is important for the expression and inositol/choline regulation of the ITR1 gene.
The appearance of the UmuD'C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis
Authors: Sommer Suzanne , Bailone Adriana , Devoret Raymond 
Published: October 2006

SummaryThe process of SOS mutagenesis in Escherichia coli requires (i) the replisome enzymes, (ii) RecA protein, and (iii) the formation of the UmuD'C protein complex which appears to help the replisome to resume DNA synthesis across a lesion. We found that the UmuD'C complex is an antagonist of RecA‐mediated recombination. Homologous recombination in an Hfr x F‐ cross decreased as a function of the UmuD'C cell concentration; this effect was challenged by increasing RecA concentration. Recombination of a u.v.‐damaged F‐lac with the lac gene of an F‐ recipient was reduced by increasing the UmuD'C concentration while lac mutagenesis increased, showing an inverse relationship between recombination and SOS mutagenesis. We explain our data with the following model. The kinetics of appearance of the UmuD'C complex after DNA damage is slow, reaching a maximum after an hour. Within that period, excision and recombinational repair have had time to occur. When the UmuD'C concentration relative to the number of residual RecA filaments, not resolved by recombinational repair, becomes high enough, UmuD'C proteins provide a processive factor for the replisome to help replication bypass and repel the standing RecA filament. Thus, at a high enough concentration, the UmuD'C complex will switch repair from recombination to SOS mutagenesis.
DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo
Authors: Plumbridge Jacqueline , Kolb Annie 
Published: October 2006

SummaryBinding sites for the Nag repressor overlap the transcription start sites of the divergent nagE and nagB genes, such that the centres of the sites are separated by nine turns of the B‐DNA helix. Mutations which prevent repressor binding to either site or alter the phasing of the binding sites result in simultaneous derepression of both genes. An additional mutation which restores the phasing of the two sites permits repression. These observations show that repression is the result of co‐operative binding of the repressor to its two sites, resulting in the formation of a loop of DNA.