bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double, independent mutational events in the rpsL gene of Escherichia coli: an example of hypermutability?
Authors: Timms Andrew R. , Bridges Bryn A. 
Published: October 2006

SummaryA proportion (up to 20%) of newly arising streptomycin‐dependent (SmD) colonies of Escherichia coli WP2 contain bacteria where, in addition to a known SmD‐determining (primary) mutation in the rpsL gene, there is a further ancillary mutation in the same gene. These ancillary mutations occur at 10 sites between 11 and 201 bp away from the primary mutation. Ancillary mutations have been found in mutant colonies arising both spontaneously and after treatment with ultraviolet light and some have been found repeatedly. Ancillary mutations were frequently found to occur in mixed clones with an excess of bacteria carrying only the primary SmD mutation. No ancillary mutations were found in an adjacent non‐coding region and there were no coding sequence changes that did not alter the amino acid specified. Although a selective advantage for bacteria containing ancillary mutations could not be demonstrated directly in every case, some small advantage must be presumed to have occurred to explain the absence of mutations at the other sites and particularly at third (wobble) codon positions. Ancillary mutations appear to occur fairly early in the life of a newly arisen SmD mutant clone in some sort of hypermutable process. Whether they are noticed appears to depend on their conferment of some selective advantage on the bacteria carrying them. While the ancillary mutations within rpsL lie close to, and may be consequent upon the formation of a primary SmD mutation, their mechanism of formation appears to be at least to some extent independent and does not involve the recA or umuC genes. Ancillary mutations were also detected in bacteria lacking reverse transcriptase or transcription repair coupling factor.
Retarded RNA turnover in Escherichia coli: a means of maintaining gene expression during anaerobiosis
Authors: Georgellis Dimitris , Barlow Tamara , Arvidson Staffan , von Gabain Alexander 
Published: October 2006

SummaryIn this study, we extend earlier observations on the influence of growth rate on mRNA stability and rRNA processing in Escherichia coli during continuous culture, to the effect of anaerobiosis. During slow anaerobic growth (generation time 700 min) both ompA and bla mRNA had a prolonged half‐life compared to that during slow aerobic growth and the processing of 9S RNA was even more profoundly retarded, which indicated a general slowing of mRNA turnover. The latter was confirmed by a nearly fourfold increase in the functional half‐life of bulk mRNA. In spite of this difference in stability, steady state levels of RNA, as judged by those of the ompA and 9S transcripts, were the same in aerobic and anaerobic cells at a given growth rate. Furthermore, we found that RNA synthesis during anaerobiosis was a fraction of that observed during slow aerobic growth and it is proposed that this offsets the general increase in mRNA stability. Our data therefore suggest that a constant level of RNA is maintained by matching the rate of decay to the level of RNA synthesis.
FtsZ ring in bacterial cytokinesis
Authors: Lutkenhaus Joe 
Published: October 2006

SummaryFtsZ is localized to a cytokinetic ring at the cell division site in bacteria. In this review a model is discussed that suggests that FtsZ self assembles into a ring at a nucleation site formed on the cytoplasmic membrane under cell‐cycle control. This model suggests that formation of the cytokinetic FtsZ ring initiates and coordinates the circumferential invagination of the cytoplasmic membrane and cell wall, leading to formation of the septum. It is also suggested that this process may be conserved among the peptidoglycan‐containing eubacteria. In addition, similarities between FtsZ and tubulin are discussed.
Translation elongation factor 3: a fungus‐specific translation factor?
Authors: Belfield Graham P. , Tuite Mick F. 
Published: October 2006

SummaryFungi appear to be unique in their requirement for a third soluble translation elongation factor. This factor, designated elongation factor 3 (EF‐3), was first described in the yeast Saccharomycescerevisiae and has subsequently been identified in a wide range of fungal species Including Candida albicans and Schizo‐saccharomyces pombe. EF‐3 exhibits ribosome‐dependent ATPase and GTPase activities that are not intrinsic to the fungal ribosome, but which are essential for translation elongation. Recent studies on the structure of EF‐3 from several fungal species have shown that it consists of a repeated domain, with each domain containing the expected putative ATP‐ and GTP‐binding motifs. Overall, EF‐3 shows striking amino acid similarity to members of the ATP‐binding Cassette (ABC) family of membrane‐associated transport proteins although EF‐3 is not itself directly membrane‐associated. Regions of the EF‐3 polypeptide also show structural homology with other translation‐associated factors including aminoacyl‐tRNA synthetases and the Escherichia coli ribosomal protein S5. While the precise role of EF‐3 in the translation elongation cycle remains to be defined, recent evidence suggests that it may be involved in optimizing accuracy during mRNA decoding at the ribosomal A site. Furthermore, the essential nature of EF‐3 with respect to the fungal cell indicates that it may be an effective antifungal target. Its apparently ubiquitous occurrence throughout the fungal kingdom also suggests that it may be a useful fungal taxonomic marker.
Assembly of the Escherichia coli F1F0 ATPase, a large multimeric membrane‐bound enzyme
Authors: Brusilow William S. A. 
Published: October 2006

SummaryThe F1F0 proton translocating ATPase of Escherichia coli is a large membrane‐bound enzyme complex consisting of more than 20 polypeptides that are encoded by the unc operon. Besides being a system for analysing the enzymology of ATP synthesis and energy coupling, the ATPase is a model system for determining how large oligomeric membrane‐bound proteins are synthesized and assembled. The assembly of the ATPase involves differential gene expression and assembly of the subunits within the membrane and with each other. This review discusses the influence of F1 subunits on the assembly and proton permeability of the F0 proton channel, and the possible advantages to assembly of the particular arrangement of genes in the unc operon.
Orientation of porin channels in the outer membrane of Bordetella pertussis
Authors: Kocsis E. , Trus B. L. , Steven A. C. , Smith P. R. , Hannah J. H. , Brennan M. J. , Kessel M. 
Published: October 2006

SummaryWe have examined the surface topography and channel connectivity of a naturally crystalline porin that is known to be functional, and whose structure has not been perturbed by detergent extraction, A three‐dimensional density map, calculated from two independent tilt series of negatively stained cell envelopes, reveals three separate channels per trimer on one side (the ‘smooth’ side), and a single common opening at the other (‘rough’) side. This arrangement is consistent with the molecular structures recently determined at high resolution by X‐ray crystallography for three other porins after detergent solubilization, and implies that the Bordetella pertussis porin may have the same kind of folding. Surface relief maps calculated from electron micrographs of cell envelopes contrasted by unidirectional shadowing clearly show that the side with single opening (i.e. the rough side) represents the external surface.
Erwinia stewartii WtsA, a positive regulator of pathogenicity gene expression, is similar to Pseudomonas syringae pv. phaseolicola HrpS
Authors: Frederick R. D. , Majerczak D. R. , Coplin D. L. 
Published: October 2006

Summary Erwinia Stewartii contains a large cluster of wts genes that are required by this bacterium for pathogenicity on com plants. Three complementation groups within the right half of this cluster, wtsA, wtsC, and ivtsB, were previously identified. In this study, WtsA was found to be a positive activator of ivfsB::lacZ expression. The WtsA locus was sequenced and a single open reading frame is present within the wtsA locus, which has the capacity to encode a 323 amino acid polypeptide. A corresponding 38kDa protein was observed in Escherichia coli minicells containing the cloned wtsA gene. The predicted WtsA polypeptide has significant similarity to HrpS from Pseudomonas syringae pv. phaseolicola, as well as other members of the NtrC class of prokaryotic regulatory proteins. Similar to other genes activated by NtrC regulators, wtsB::lacZ expression in E. coli was dependent upon rpoN.
Differentiation of Pseudomonas aeruginosa into the alginate‐producing form: inactivation of mucB causes conversion to mucoidy
Authors: Martin D. W. , Schurr M. J. , Mudd M. H. , Deretic V. 
Published: October 2006

SummaryMucoidy in Pseudomonas aeruginosa is a critical virulence factor associated with chronic respiratory infections in cystic fibrosis. A cluster of three tightly linked genes. algU, mucA and mucB located at 67.5 min, controls development of mucoid phenotype. This locus is allelic with a group of mutations (muc) associated with conversion into constitutively mucoid forms. One of the genes previously characterized in this region, algU, is absolutely required for the transcriptional activation of algD, a critical event in the establishment of mucoidy. AlgU is homologous to the alternative sigma factor σ;H (Spo0H) controlling sporulation and competence in Bacillus. Two genes downstream of algU, mucA and mucB were further characterized in this study. Previous complementation studies have demonstrated that mucA is required for suppression of mucoidy in the muc‐2 strain PAO568. In this work, complementation analysis indicated that, in addition. mucB was required for suppression of mucoidy in the muc‐25 strain PAO581, and for enhanced complementation of the muc‐2 mutation in PAO568. The complete nucleotide sequence of mucA and mucH was determined. Insertional inactivation of mucB on the chromosome of the standard genetic strain PAO resulted in mucoid phenotype, and in a strong transcriptional activation of algD. Thus, a loss of mucB function is sufficient to cause conversion of P. aeruginosa into the mucoid phenotype. Since the algU‐mucA‐mucB region is a general site where muc mutations have been mapped, it is likely that mucB participates in the emergence of mucoid forms. Both mucA and mucB play a regulatory role in concert with the sigma‐like factor AlgU; all three genes, along with signal transduction and histone‐like elements, control differentiation of P. aeruginosa into the mucoid phenotype.
The Myf fibrillae of Yersinia enterocolitica
Authors: Iriarte Maite , Vanooteghem Jean‐Claude , Delor Isabelle , Diaz Ramon , Knutton Stuart , Cornelis Guy R. 
Published: October 2006

SummaryThe Myf antigen produced by Yersinia enterocolitica appeared as a proteic polymer composed of 21 kDa subunits. By transposon mutagenesis we isolated Myf‐defective mutants. Those allowed us to clone and sequence a 4.4 kb chromosomal locus involved in Myf production. This region was found to contain three genes that we called myfA, myfB and myfC. Genes myfB and myfC encode an assembly machine related to those involved in the synthesis of many fimbriae; MyfB, the putative chaperone, possesses the consensus residues of the PapD family and MyfC encodes a putative outer‐membrane protein. MyfA, the major subunit, was found to be 44% identical to the pH 6 antigen of Y.pestis. Myf is thus the K enterocolitica counterpart of this antigen, but it is by far not so well conserved as the other virulence determinants such as the Yops, suggesting that Myf and pH 6 antigen do not necessarily play the same role in Y. enterocolitica and Y. pestis. The study of the prevalence of myfA in various species of Yersinia reveaied that, like the yst enterotoxin gene, its presence is restricted to the pathogenic serotypes of Y. enterocolitica. By immuno‐gold labelling, Myf appeared as a layer of extracellular material extending locally 2μm from the bacterial surface, indicative of a fibrillar structure.
Inhibition of translational initiation in Saccharomyces cerevisiae by secondary structure: the roles of the stability and position of stem‐loops in the mRNA leader
Authors: Oliveira Caria C. , van den Heuvel Joop J. , McCarthy John E. G. 
Published: October 2006

SummaryA new modular gene‐expression system for use in studies of translational control in Saccharomyces cerevisiae was constructed. A GAL::PGK fusion promoter (GPF) directed the inducible synthesis of mRNAs initiated at a single major site. A series of leader sequences were tested in combination with each of two reporter genes (encoding chloramphenicol acetyl transferase (cat) and luciferase (luc)). Stem‐loop structures of three different sizes and predicted stabilities were inserted into each of two different unique restriction sites in the leader. After correction for relative mRNA abundance, a stem‐loop of predicted stability equivalent to approximately −18kcal mol−1 inhibited translation by up to 89%. The degree of inhibition exerted by the other stem‐loops correlated positively with their predicted stabilities. Combinations of two stem‐l oops at different sites yielded an inhibitory effect greater than that of either individual stem‐loop alone. Similar inhibitory effects were observed with both reporter genes. However, inhibition of translation, particularly of the cat gene, was more effective when the stem‐loop was positioned close to the start codon rather than at the 5′ end of the leader. The observed results reflect an important form of post‐transcriptional control that is expected to act on a large number of genes in yeast.
NAD+ binding to the Escherichia coli K+‐uptake protein TrkA and sequence similarity between TrkA and domains of a family of dehydrogenases suggest a role for NAD+ in bacterial transport
Authors: Schlosser Andreas , Hamann Angela , Bossemeyer Dirk , Schneider Erwin , Bakker Evert P. 
Published: October 2006

SummaryThe nucleotide sequence of trkA, a gene encoding a surface component of the constitutive K+‐uptake systems TrkG and TrkH from Escherichia coli, was determined. The structure of the TrkA protein deduced from the nucleotide sequence accords with the view that TrkA is peripherally bound to the inner side of the cytoplasmic membrane. Analysis by a dot matrix revealed that TrkA is composed of similar halves. The M‐terminal part of each TrkA half (residues 1–130 and 234–355, respectively) is similar to the complete NAD+‐binding domain of NAD+‐dependent dehydrogenases. The C‐terminal part of each TrkA half (residues 131–233 and 357–458, respectively) aligns with the first 100 residues of the catalytic domain of glyceraldehyde‐3‐phosphate dehydrogenase. Strong u.v. illumination at 252 nm led to cross‐linking of NAD+ or NADH, but not of ATP to the isolated TrkA protein.
Identification of a new nuclear gene (CEM1) encoding a protein homologous to a β‐keto‐acyl synthase which is essential for mitochondrial respiration in Saccharomyces cerevisiae
Authors: Harington A. , Herbert C. J. , Tung B. , Getz G. S. , Slonimski P. P. 
Published: October 2006

SummaryWe have analysed a new gene, CEM1, from Saccharomyces cerevisiae. Inactivation of this gene leads to a respiratory‐deficient phenotype. The deduced protein sequence shows strong similarities with β‐keto‐acyl synthases or condensing enzymes. Typically, enzymes of this class are involved in the synthesis of fatty acids or similar molecules. An analysis of the mitochondrial lipids and fatty acids shows no major difference between the wild type and deleted strains. Implying that the CBM1 gene product is not involved in the synthesis of the bulk fatty acids. Thus it Is possible that the CEM1 protein is involved in the synthesis of a specialized molecule, probably related to a fatty acid, which is essential for mitochondrial respiration.
Escherichia coli endoribonuclease RNase E: autoregulation of expression and site‐specific cleavage of mRNA
Authors: Mudd Elisabeth A. , Higgins Christopher F. 
Published: October 2006

SummaryMutations in the Escherichia coli rne (ams) gene have a general effect on the rate of mRNA decay in vivo. Using antibodies we have shown that the product of the rne gene is a polypeptide of relative mobility 180kDa. However, proteolytic fragments as small as 70kDa, which can arise during purification, also exhibit RNase E activity, in vitro studies demonstrate that the rne gene product, RNase E, is an endoribonuclease that cleaves mRNA at specific sites. RNase E cleaves rne mRNA and autoregulates the expression of the rne gene. In addition we demonstrate RNase E‐dependent endonucleolytic cleavage of ompA mRNA, at a site known to be rate‐determining for degradation and reported to be cieaved by RNase K. Our data are consistent with RNase K being a proteolytic fragment of RNase E.
An accessory gene, lipB, required for the production of active Pseudomonas glumae lipase
Authors: Frenken Leon G.J. , Bos J. Wil , Visser Chris , Müller Wally , Tommassen Jan , Verrips C. Theo 
Published: October 2006

Summary Pseudomonas glumae PG1 is able to secrete lipase into the extracellular medium. The lipase is produced as a precursor protein, with an N‐terminal signal sequence. A second open reading frame (ORF) was found immediately downstream of the lipase structural gene, lip A, a situation found for the lipases of some other Pseudomonas species. Inactivation of this ORF resulted in a lipase‐negative phenotype, indicating its importance in the production of active extracellular lipase. The ORF, lipB, potentially encodes a protein of 353‐amtno‐acid residues, having a hydrophobic N‐terminal (amino acids 1 to 90) and a hydrophilic C‐terminal part. As a first step in determining the role of LipB, its subcellular location was determined. The protein was found to fractionate with the inner membranes. The expression of fusions of lipB fragments with phoA revealed an Nin–Cout topology for the LipB protein, which was confirmed by protease accessibility studies on EDTA‐permeabilized cells and on inverted inner membrane vesicles. These and other results indicate that most of the LipB polypeptide is located in the periplasm and anchored to the inner membrane by an an N‐terminal transmembrane helix, located between amino acids 19 and 40.
Role of the lipB gene product in the folding of the secreted lipase of Pseudomonas glumae
Authors: Frenken Leon G. J. , de Groot Arjan , Tommassen Jan , Verrips C. Theo 
Published: October 2006

SummaryThe LipB protein of Pseudomonas glumae is essential for the production of active extracellular lipase encoded by the lipA gene. When lipase is overproduced in P. glumae in the absence of a functional lipB gene, the enzyme accumulates intracellularly in an inactive conformation. Heterologous expression of the lipase in Pseudomonas aeruginosa, Bacillus subtilis and Escherichia coli indicated that LipB is not directly involved in the trans location of the lipase across the inner or outer membrane. However, the presence of LipB was essential for obtaining active lipase and had a profound influence on the stability of the protein to proteolytic degradation. Inactive iipase, produced in the absence of LipB could be activated in vitro by unfolding and refolding, which demonstrates that LipB activity is not responsible for an essential covalent modification of the enzyme. We propose that LipB is a lipase‐specific foldase. Furthermore, proper folding of the lipase in the periplasm appears to be essential for Xcp‐mediated translocation across the outer membrane.
Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites
Authors: Mojica F. J. M. , Juez G. , Rodriguez‐Valera F. 
Published: October 2006

SummaryTwo genomic sequences from the halophilic archaeon Haloferax mediterranei, where we had found PstI restriction‐pattern modifications depending on the salinity of the growth medium, have been studied. A markedly salt‐dependent differential expression has been detected in the nearby regions. Two of the open reading frames characterized correspond to two of the differentially expressed transcripts. In both cases the PstI sites were included in purine–pyrimidine alternancies suggestive of Z‐DNA structures and located in non–coding regions with frequent repetitive motifs. A long alternating adenine‐thymine tract also appears in the upstream regions of one of these open reading frames. A possible role of local DNA configuration in osmoregulation in this organism is discussed.
Isolation of a putative fimbrial adhesin from Bordetella pertussis and the identification of its gene
Authors: Willems Rob J. L. , Geuijen Cecile , van der Heide Han G. J. , Matheson Mary , Robinson Andrew , Versluis Leone F. , Ebberink Rob , Theelen Joop , Mooi Frits R. 
Published: October 2006

SummaryWe report the purification of a minor Bordetella pertussis fimbrial subunit, designated FimD, and the identification of its gene (fimD.) FimD could be purified from the bulk of major fimbrial subunits by exploiting the fact that major subunit‐subunit interactions are more stable in the presence of SDS than minor‐major subunit interactions. To locate the gene for FimD, internal peptides of FimD were generated, purified and sequenced. Subsequently, an oligonucleotide probe, based on the primary sequence of one peptide, was used to clone fimD. The primary structure of FimD, derived from the DNA sequence of its gene, showed homology with a number of fimbrial adhesins. Most pronounced homology was observed with MrkD, a fimbrial adhesin derived from Klebsieila pneumoniae. These observations suggest that FimD may represent a B. pertussis fimbrial adhesin. With a fimD‐specific probe we detected the presence of a fimD homologue in Bordetella parapertussis and Bordetella bron‐chiseptica but not in Bordetella avium. Cloning and sequencing revealed that the B. parapertussis and B. bronchiseptica fimD product differed from the B. pertussis fimD product in 20 and 1 amino acid residues, respectively. Since B. bronchiseptica is normally not a human pathogen, but causes respiratory disease in a wide range of non‐human mammalian species, this may suggest that FimD recognizes a receptor that is well conserved in mammalian species. An in‐frame deletion in fimD completely abolished FimD expression and also affected the expression of the major subunits Fim2 and Fim3 suggesting that, in contrast to other adhesins that are minor components of fimbriae, FimD is required for formation of the fimbrial structure.
Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl‐tRNA out of 41 similar contestants
Authors: Nierhaus Knud H. 
Published: October 2006

SummaryThree tRNA binding sites, the A, P and E sites, have been demonstrated on ribosomes of bacterial, archaebacterial and eukaryotic origin. In all these cases the first and the third site, the A and the E site, are allosterically coupled in the sense of a negative co‐operativity. Therefore, the allosteric three‐site model seems to be a generally valid description of the ribosomal elongation phase, where in a cycle of reactions the nascent peptide chain is prolonged by one amino acid. The molecular concept of the allosteric three‐site model explains the astonishing ability of the ribosome to select the correct substrate out of a large number of very similar substrates, and it provides a framework within which the mechanisms of the elongation factors could be understood.Molecular recognition: the special case of the ribosomal selection of the correct aminoacyl‐tRNA