bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlamydia trachomatis Mip‐like protein has peptidylprolyl cis/trans isomerase activity that is inhibited by FK506 and rapamycin and is implicated in initiation of chlamydial infection
Authors: Lundemose Anker G. , Kay John E. , Pearce John H. 
Published: October 2006

SummaryThe Mip‐like protein of Chlamydia trachomatis has sequence similarity with both the Mip protein of Legionella pneumophila, a virulence factor necessary for optimal intracellular infection, and FK506‐binding proteins (FKBPs) of both prokaryotic and eukaryotic origin. FKBPs contain a site for peptidyl‐prolyl cis/trans isomerase activity, which is blocked upon binding of the drugs, FK506 or rapamycin. In this paper we report that the recombinant chlamydial Mip‐like protein exhibits a peptidyl‐prolyl cis/trans isomerase activity which is inhibited by either rapamycin or FK506. To assess the role of the Mip‐like protein in chlamydial infection, rapamycin or FK506 (25μM), were used in either treatment of chlamydial organisms prior to inoculation, or were present at different intervals through the infection. Pretreatment of organisms alone reduced infectivity for McCoy cells by 30%, with inhibition rising to 80% on more prolonged exposure from 0 to 8h and 8 to 16 h post‐inoculation and declining thereafter. When drug was present during the developmental cycle at intervals from 0 to 24h post‐inoculation abnormal chlamydiae were induced in residual inclusions. The results suggest that inhibition of the isomerase of the Mip‐like protein interferes with one or more early events in the infective process that determine productive intracellular infection.
Molecular analysis of spv virulence genes of the salmonella virulence plasmids
Authors: Gulig Paul A. , Danbara Hirofumi , Guiney Donald G. , Lax Alistair J. , Norel Françoise , Rhen Mikael 
Published: October 2006

SummaryGenes on an 8 kb region common to the virulence plasmids of several serovars of Salmonella are sufficient to replace the entire plasmid in enabling systemic infection in animal models. This virulence region encompasses five genes which previously have been designated with different names from each investigating laboratory. A common nomenclature has been devised for the five genes, i.e. spv for salmonella plasmid virulence. The first gene, spvR, encodes a positive activator for the following four genes, spvABCD. DNA sequence analysis of the spv genes from Salmonella typhimurium. Salmonella dublin, and Salmonella choleraesuis demonstrated extremely high conservation of the DNA and amino acid sequences. The spv genes are induced at stationary phase and in carbon‐poor media, and optimal expression is dependent on the katF locus. The cirulence functions of the spv genes are not known, but these genes may increase the growth rate of salmonellae in host cells and affect the interaction of salmonellae with the host immune system.
The Rad3 protein from Saccharomyces cerevisiae: a DNA and DNA:RNA helicase with putative RNA helicase activity
Authors: Deschavanne Patrick J. , Harosh Itzik 
Published: October 2006

SummaryThe Rad3 protein from Saccharomyces cerevisiae is a DNA helicase which participates in the repair of ultraviolet‐irradiated DNA and is Inhibited in the presence of DNA containing thymine dimers. This protein is also involved in mitotic recombination and spontaneous mutagenesis and is essential for cell viability in the absence of DNA damage. Furthermore, the Rad3 protein also exhibits a DNA:RNA helicase activity in which there is a significant preference for a partial DNA:RNA hybrid rather than a partial duplex DNA substrate, which suggests that this protein might be involved in DNA repair within transcriptionally active genes. Finally, the Rad3 protein contains the DEAH motif and shares high amino acid sequence similarity with the DEAD family of RNA helicase proteins, suggesting that it might also possess an RNA helicase activity.
Involvement of the RNA polymerase α subunit C‐terminal region in co‐operative interaction and transcriptional activation with OxyR protein
Authors: Tao Kazuyuki , Fujita Nobuyuki , Ishihama Akira 
Published: October 2006

SummaryThe role of the α subunit of Escherichia coli RNA polymerase in transcription activation by the OxyR protein was investigated using in‐vitro‐reconstituted RNA polymerase containing α subunits carrying C‐terminal truncations or an amino acid substitution. Mutant RNA polymerases failed to respond to transcription activation of the E. coli OxyR‐dependent promoters. DNase I footprinting analysis indicates that the OxyR protein exerts a co‐operative effect on the binding of wild‐type RNA polymerase, but not the mutant RNA polymerases, to the katG promoter. Together, these results suggest that direct protein‐protein contact between the OxyR protein and the C‐terminal contact site I region of the RNA polymerase α subunit plays an essential role in transcription activation at the OxyR‐dependent promoters.
Antisense RNA mediates transcriptional processing in an archaebacterium, indicating a novel kind of RNase activity
Authors: Stolt Pelte , Zillig Wolfram 
Published: October 2006

SummaryStrains of the extremely halophilic archaebacterium Halobacterium salinarium that are lysogenic for the phage φH produce an antisense RNA transcript complementary to the first 151 nucleotides (nt) of the early lytic phage transcript T1. This is the first case of antisense control of gene expression in an archaebacterium. We show through transformation of H. salinarium that the antisense RNA functions in trans, rendering the early lytic phage transcript T1 susceptible to specific cleavage by an unidentified RNase of unique endonucleolytic activity. The single‐stranded ends of RNA are cut off at the ends of the 151 nt RNA duplex, removing the ribosomal binding sites from the first open reading frame of transcript T1 but without concominant digestion of the products.
Organization of Lrp‐binding sites upstream of ilvlH in Salmonella typhimurium
Authors: Wang Qing , Sacco Margherita , Ricca Ezio , Lago Carmine T. , DeFelice Maurilio , Calvo Joseph M. 
Published: October 2006

SummaryLrp, a major regulatory protein in Escherichia coli, controls the expression of numerous operons, including ilvlH. Lrp binds to six sites upstream of ilvlH, and Lrp binding is required for ilvlH expression. We show here that an Lrp‐like protein is also present in Salmonella typhimurium. This protein can bind both E. coli and S. typhimurium ilvlH DNA, as can E. coli Lrp. Methidiumpropyl‐EDTA footprinting studies were performed with purified E. coli Lrp and S. typhimurium ilvlH DNA. Six binding sites were defined, three of them being similar to corresponding sites in E. coli, and three being organized differently. A consensus derived from six S. typhimurium sites is compatible with that derived from a similar analysis of E. coli sequences.
Molecular characterization of the enniatin synthetase gene encoding a multifunctional enzyme catalysing N‐methyldepsipeptide formation in Fusarium scirpi
Authors: Haese Angela , Schubert Monika , Herrmann Matthias , Zocher Rainer 
Published: October 2006

SummaryThe gene encoding the multifunctional enzyme enniatin synthetase from Fusarium scirpi (esyn1) was isolated and characterized by transcriptional mapping and expression studies in Escherichia coli. This is the first example of a gene encoding an N‐methyl peptide synthetase. The nucleotide sequence revealed an open reading frame of 9393 bp encoding a protein of 3131 amino acids (Mr 346 900). Two domains designated EA and EB within the protein were identified which share similarity to each other and to microbial peptide synthetase domains. In contrast to the N‐terminal domain EA, the carboxyl terminal domain EB is interrupted by a 434‐amino‐acid portion which shows local similarity to a motif apparently conserved within adenine and cytosine RNA and DNA methyltransferases and therefore seems to harbour the N‐methyl‐transferase function of the multienzyme.
The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule
Authors: Chen Carton W. , Yu Tin‐Wein , Lin Yi‐Shing , Kieser Helen M. , Hopwood David A. 
Published: October 2006

SummaryThe SLP2 plasmid had previously been demonstrated genetically to exist In Streptomyces lividans by its ability to promote conjugation and to elicit‘pocks’on recipient (SLP2−) cultures, but it had not been physically detected. Using pulsed‐field gel electrophoresis, a 50kb linear DNA was isolated from SLP2+ but not SLP2− strains of S. lividans, and from Streptomyces coelicolor and Streptomyces parvulus strains to which SLP2 had been transferred by conjugation or transformation. We conclude that this linear DNA is SLP2. The terminal fragments of SLP2 were cloned. The determined sequences revealed a 44 bp imperfect terminal inverted repeat. The terminal 12 bp sequence of SLP2 was identical to those of two other Streptomyces linear plasmids, pSLA2 and pSCL, and similar to the terminal sequences of another Streptomyces linear plasmid, SCP1. The termini of SLP2 DNA were resistant to digestion by λ exonuclease and ExoIII. A truncated (probably crippled) copy of Tn4811 is present on the plasmid. While the SLP2 plasmid exists as a tree form in the host, a 15.7 kb sequence corresponding to the segment of SLP2 from Tn4811 to the right terminus is also present (at a copy number similar to the free form) elsewhere in the genome of S. lividans. Furthermore, SLP2 is partially homologous to a newly discovered 650 kb linear plasmid in S. parvulus.
Recombination‐deficient mutants of Salmonella typhimurium are avirulent and sensitive to the oxidative burst of macrophages
Authors: Buchmeier Nancy A. , Lipps Craig J. , So Magdalene Y. H. , Heffron Fred 
Published: October 2006

SummaryMutations in the genes recA and recBC were constructed in the virulent Salmonella typhimurium strain 14028s. Both the recA and recBC mutants were attenuated in mice. The mutants were also sensitive to killing by macrophages in vitro. The recombination mutants were no longer macrophage sensitive in a variant line of J774 macrophage‐like cells that fail to generate superoxide. This suggests that repair of DNA damage by Salmonella is necessary for full virulence in vivo and that the oxidative burst of phagocytes is one source of such DNA damage.
In vitro transcription in Chlamydia psittaci and Chlamydia trachomatis
Authors: Mathews Sarah A. , Douglas Annemarie , Sriprakash K. S. , Hatch Thomas P. 
Published: October 2006

SummaryExtracts of Chlamydia psittaci and Chlamydia trachomatis were used to transcribe molecularly cloned chlamydial genes in vitro. The extracts were prepared by Iysing reticulate bodies, obtaining the 10000 ×g centrifugation pellet, and eluting RNA polymerase from the pellet by treatment with 2M KCI to yield a fraction designated SS2. Some in vitro transcription was initiated from non‐chlamydial promoters and a small amount of transcription was from endogenous DNA template in SS2. However, optimal transcription from exogenous templates required chlamydial promoter sequences, and primer extension analysis indicated that chlamydia promoter‐specific in vitro transcription was initiated from the same start sites recognized in vivo. A monoclonal antibody that was generated against Escherichia coliσ;70 and which immunologically cross‐reacts with C. trachomatisσ;66 inhibited in vitro transcription of vector and cloned chlamydial DNA, suggesting that transcriptional initiation in the SS2 fraction is mediated by CT66. An in vitro transcription assay based on detection of transcripts of specific lengths was applied to the chlamydial system; this assay and others described here should be useful in defining chlamydial promoters and other transcriptional regulatory elements.
Expression of the pspA gene stimulates efficient protein export in Escherichia coli
Authors: Kleerebezem Michiel , Tommassen Jan 
Published: October 2006

SummaryExpression of several mutant forms of outer membrane protein PhoE of Escherichia coli, which are disturbed in normal biogenesis, resulted in high expression of a 26kDa protein. This 26kDa protein fractionated as a peripherally bound inner membrane protein. It appeared to be identical to a previously identified protein (PspA = phage shock protein A) of unknown function that is induced upon infection of E. coli with filamentous phages. PspA was not expressed upon synthesis of mutant PhoE proteins in a secB mutant, nor upon expression of a PhoE mutant that lacks the signal sequence, suggesting that entrance into the export pathway of prePhoE is essential for induction. PspA synthesis was also induced under other conditions that are known to block the export apparatus, i.e. in secA, secD and secF mutants when grown at their non‐permissive temperature or upon induction of the synthesis of MalE‐LacZ or LamB‐LacZ hybrid proteins. The inducing conditions for PspA synthesis suggested a rote for this protein in export. In vivo pulse‐chase experiments showed that the translocation of (mutant) prePhoE and of the precursors of other exported proteins was retarded in a pspA mutant strain. Also, in in vitro translocation assays, a role for PspA in protein transport could be demonstrated.
Two genes present on a transposon‐like structure in Lactococcus lactis are involved in a Clp‐family proteolytic activity
Authors: Huang Dao Chao , Huang Xian Fang , Novel Georges , Novel Madeleine 
Published: October 2006

SummaryThe lactose‐protease plasmid pUCL22 of Lactococcus lactis subsp. lactis strain CNRZ270 contained two inverted copies of IS 1076 flanking a region of 3.7 kb. This internal region was sequenced and found to contain two large open reading frames, ORF1 and ORFP in opposite orientations. ORF1 consists of 2289 bp; the deduced 763‐amino‐acid sequence is similar to the ATPases of the ClpA family. It contains two well‐conserved consensus ATP‐binding sites. It was named ClpL. ORFP consists of 930 bp encoding a protein of 310 amino acids. No similarity with any known protein was found in GenBank data for ORFP. Increased ATP‐dependent proteolytic activity was detected in extracts from Escherichia coli cells expressing the clpL and ORFP genes.
A positive feedback loop controls transcription of the spo0F gene, a component of the sporulation phosphorelay In Bacillus subtilis
Authors: Strauch Mark A. , Wu Jiunn‐Jong , Jonas Robert H. , Hoch James A. 
Published: October 2006

SummaryThe spo0Fgene of Bacillus subtilisencodes a protein that functions as a secondary messenger in a phosphorelay system controlling the initiation of sporulation. Transcription of the spo0F gene was known to be dependent on an intact gene for the transcription regulator Spo0A. In vitro footprint analysis revealed that Spo0A protein bound to two locations in the spo0F promoter region. Deletion of a 40 bp region upstream of one of the promoters (P2) abolished the activation of spo0Fexpression that occurs at the onset of stationary phase and sporulation. This 40 bp region contains a Spo0A‐binding site. These observations are consistent with a hypothesis that Spo0A binding to this region is responsible for activating spo0F transcription. Additionally, Spo0A binding at a downstream site could modulate the level of this activation. Since Spo0F protein is required for the formation of Spo0A∼P (the form needed for transcriptional activation) a positive feedback loop controls transcription of spo0F.
Translation across the 5′‐splice site interferes with autocatalytic splicing
Authors: Öhman‐Hedén Marie , Åhgren‐Stálhandske Agneta , Hahne Solveig , Sjöberg Britt‐Marie 
Published: October 2006

SummaryThe bacteriophage T4 nrdB gene, encoding the ribonucleotide reductase small subunit, contains a self‐splicing group IA2 intron with an ochre codon in frame with the preceding exon sequence. The stop codon was changed to an amino acid codon and splicing efficiency was compared with that of the wild type in the presence and absence of translation. In vivo the mutant has a much tower efficiency for producing a mature transcript than the wild type. Also, the relative production of the full‐length translation product is correspondingly lower in the mutant than in the wild type. These results confirm the importance of the stop codon, which spans the splice site of the nrdB intron.The occurrence of stop codons in 56 group I introns in protein‐encoding genes was investigated. In 33 of those translation is terminated upstream of the first common elements of the catalytic core, of group I introns. In the rest translation is terminated in intron regions outside the heart of the catalytic core, with one exception.Our observations suggest that in situations where transcription and translation are coupled events there has been an evolutionary pressure to preserve stop codons in the 5′‐region of these introns or to prevent translational termination from occurring in vital parts of the introns.
Ribosome activity and modification of 16S RNA are influenced by deletion of ribosomal protein S20
Authors: Rydén‐Aulin Monica , Shaoping Zhang , Kylsten Per , Isaksson Leif A. 
Published: October 2006

SummaryA spontaneous mutant of Escherichia coli K‐12 was isolated that shows an increased misreading ability of all three nonsense codons together with an inability to grow at 42° C. It is demonstrated that the mutation is a deletion of the gene rpsT, coding for ribosomal protein S20. The loss of this protein not only influences the decoding properties of the ribosome; the modification pattern of 16S ribosomal RNA is also changed. This leads to a deficiency in the ability of the mutant to associate its 30S subunits with 50S subunits to form 70S ribosomes. It is suggested that two modified bases, m5C and m62A, are directly or indirectly essential for association of subunits to functional ribosomes in the rpsT mutant strain. Two other modifications were also studied; m2G which is not affected at all and m3U which is undermodified in both active and inactive subunits and, therefore, not involved in subunit association.
Mitochondrial transcription: is a pattern emerging?
Authors: Jaehning Judith A. 
Published: October 2006

SummaryDespite the striking similarities of RNA polymerases and transcription signals shared by eubacteria, archaebacteria and eukaryotes, there has been little indication that transcription in mitochondria is related to any previously characterized model. Only in yeast has the subunit structure of the mitochondrial RNA polymerase been determined. The yeast enzyme is composed of a core related to polymerases from bacteriophage T7 and T3, and a promoter recognition factor similar to bacterial sigma factors. Soluble systems for studying mitochondrial transcript initiation in vitro have been described from several organisms, and used to determine consensus sequences at or near transcription start sites. Comparison of these sequences from fungi, plants, and amphibians with the T7/T3 promoter suggests some intriguing similarities. Mammalian mitochondrial promoters do not fit this pattern but instead appear to utilize upstream sites, the target of a transcriptional stimulatory factor, to position the RNA polymerase. The recent identification of a possible homologue of the mammalian upstream factor in yeast mitochondria may indicate that a pattern will eventually be revealed relating the transcriptional machineries of all eukaryotic mitochondria.
Influence of pH on bacterial gene expression
Authors: Olson Eric R. 
Published: October 2006

SummaryBacteria respond to changes in internal and external pH by adjusting the activity and synthesis of proteins associated with many different processes, including proton translocation, amino acid degradation, adaptation to acidic or basic conditions and virulence. While, for many of these examples, the physiological and biological consequence of the pH‐induced response is clear, the mechanism by which the transcription/translation machinery is signalled is not. These examples are discussed along with several others in which the function of the gene or protein remains a mystery.
Organization of the genes necessary for hydrogenase expression in Rhodobacter capsulatus. Sequence analysis and identification of two hyp regulatory mutants
Authors: Colbeau Annette , Richaud Pierre , Toussaint Bertrand , Caballero F. Javier , Elster Christine , Delphin Christian , Smith Russell L. , Chabert Jacqueline , Vignais Paulette M. 
Published: October 2006

SummaryA 25kbp DNA fragment from the chromosome of Rhodobacter capsulatus B10 carrying hydrogenase (hup) determinants was completely sequenced. Coding regions corresponding to 20 open reading frames were identified. The R. capsulatus hydrogenase‐specific gene (hup and hyp) products bear significant structural identity to hydrogenase gene products from Escherichia coli (13), from Rhizobium liguminosarum (16), from Azotobacter vinelandii (10) and from Alcaligenes eutrophus (11). The sequential arrangement of the R. capsulatus genes is: hupR2‐hupU‐hypF‐hupS‐hupL‐hupM‐hupD‐hupF‐hupG‐hupH‐huoJ‐hupK‐hypA‐hypB‐hupR1‐hypC‐hypD‐hypE‐ORF19‐ORF20, all contiguous and transcribed from the same DNA strand. The last two potential genes do not encode products that are related to identified hydrogenase‐specific gene products in other species. The sequence of the 12 R. capsulatus genes underlined above is presented. The mutation site in two of the Hup− mutants used in this study, RS13 and RCC12, was identified in the hypF gene (deletion of one G) and in the hypD qene (deletion of 54 bp), respectively. The hypF gene product shares 45% identity with the product of hydA from E. coli and the product of hypF from R. leguminosarum. Those products present at their N‐terminus a Cys arrangement typical of zinc‐finger proteins. The G deletion in the C‐terminal region of hypF in the RS13 mutant
Characterization of a Bacillus subtilis SecA mutant protein deficient in translocation ATPase and release from the membrane
Authors: van der Wolk J. , Klose M. , Breukink E. , Demel R. A. , de Kruijff B. , Freudl R. , Driessen A. J. M. 
Published: October 2006

SummarySecA is the precursor protein binding subunit of the bacterial precursor protein translocase, which consists of the SecY/E protein as integral membrane domain. SecA is an ATPase, and couples the hydrolysis of ATP to the release of bound precursor proteins to allow their proton‐motive‐force‐driven translocation across the cytoplasmic membrane. A putative ATP‐binding motif can be predicted from the amino acid sequence of SecA with homology to the consensus Walker A‐type motif. The role of this domain is not known. A lysine residue at position 106 at the end of the glycine‐rich loop in the A motif of the Bacillus subtilis SecA was replaced by an asparagine through site‐directed mutagenesis (K106N SecA). A similar replacement was introduced at an adjacent lysine residue at position 101 (K101N SecA). Wild‐type and mutant SecA proteins were expressed to a high level and purified to homogeneity. The catalytic efficacy (kcat/km) of the K106N SecA for lipid‐stimulated ATP hydrolysis was only 1% of that of the wild‐type and K101N SecA. K106N SecA retained the ability to bind ATP, but its ATPase activity was not stimulated by precursor proteins. Mutant and wild‐type SecA bind with similar affinity to Escherichia coli inner membrane vesicles and insert into a phospholipid mono‐layer, in contrast to the wild type, membrane insertion of the K106N SecA was not prevented by ATP. K106N SecA blocks the ATP and proton‐motive‐force‐dependent chase of a translocation intermediate to fully translocated proOmpA. It is concluded that the GKT motif in the amino‐terminal domain of SecA is part of the catalytic ATP‐binding site. This site may be involved in the ATP‐driven protein recycling function of SecA which allows the release of SecA from its association with precursor proteins, and the phospholipid bilayer.