bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a 180kD protein in Escherichia coli related to a yeast heavy‐chain myosin
Authors: Casaregola S. , Norris V. , Goldberg M. , Holland I. B. 
Published: October 2006

SummaryA high molecular‐weight protein from Escherichia coli sharing structural ho mo logy at the protein level with a yeast heavy‐chain myosin encoded by the MYO1 gene is described. This 180kD protein (180‐HMP) can be enriched in cell fractions following the procedure normally utilized for the purification of non‐muscle myosins. In Western blots this protein cross‐reacts with a monoclonal antibody against yeast heavy‐chain myosin. Moreover, antibodies raised against the 180kD protein cross‐react with the yeast myosin and with a myosin heavy chain from chicken. Recognition by anti‐180‐HMP antibodies of an overexpressed fragment of yeast myosin encoded by MYO1 allows the localization of one of the shared epitopes to a specific region around the ATP binding site of the yeast myosin heavy chain. The existence of a high molecular‐weight protein with structural similarity to myosin in E. coli raises the possibility that such a protein might generate the force required for movement in processes such as nucleoid segregation and cell division.
Mechanism for induction of adaptive mutations in Escherichia coli
Authors: Boe L. 
Published: October 2006

SummaryWhen bacterial cells are subjected to a strong selective pressure it often induces specific mutations. Here a model is considered in which errors are introduced at random in one of the strands of the DNA molecule: a nick in one of the strands can initiate strand displacement rendering a region of the chromosome single‐stranded. Upon conversion back to double‐stranded DNA there is a certain probability of introducing errors creating a heteroduplex. If an error results in the production of an mRNA molecule encoding a product which provides a selective advantage, growth will be stimulated and the mutation can be immortalized by chromosomal replication. Otherwise, the error can be corrected by the DNA ‘proofreading’ enzymes.
A physical map of the Mycoplasma genitalium genome
Authors: Colman S. D. , Hu P.‐C. , Litaker W. , Bott K. F. 
Published: October 2006

SummaryWe report the construction of a physical map of the genome of the human pathogen Mycoplasma genitalium through the use of pulse‐field gel electrophoresis. The small size and relative simplicity of this genome permit the arrangement of restriction fragments without having to construct linking clones. The size of the genome has been calculated to be approximately 600 kb and several important genetic determinants have been assigned specific loci on the map.
Cloning and sequence analysis of linear plasmid telomeres of the bacterium Borrelia burgdorferi
Authors: Hinnebusch J. , Bergstrom S. , Barbour A. G. 
Published: October 2006

Summary Borrelia burgdorferi, the Lyme disease agent, has double‐stranded linear plasmids with covalently closed ends. DNA at the ends, or telomeres, of two linear plasmids of B. burgdorferi strain B31 was examined. Telomeric sequences from both ends of a 16kb linear plasmid and from one end of a 49kb linear plasmid were cloned and sequenced. An 18bp AT‐rich inverted repeat was found at each end of the 16kb linear plasmid. The sequences of the two ends of this plasmid were different beyond these short inverted terminal repeats. The cloned end of the 49kb linear plasmid had sequence identity with one end of the 16kb linear plasmid. The end sequence common to both plasmids contained a series of phased, short direct repeats and a 52bp palindrome adjacent to a highly AT‐rich region. These findings indicate that Borrelialinear plasmid telomeres have structural features different from those of other known replicons.
Analysis of three nodD genes in Rhizobium leguminosarum biovar phaseoli; nodD 1 is preceded by nolE, a gene whose product is secreted from the cytoplasm
Authors: Davis E. O. , Johnston A. W. B. 
Published: October 2006

SummaryIn a strain of Rhizobium leguminosarum biovar phaseoli, three copies of the regulatory nodulation gene nodD were identified on the Sym plasmid and sequenced. Two were closely linked to each other and the third was near, but not adjacent, to the nodABC genes. Each of these nodD genes could correct the Nod defect of a nodD mutant strain of R. leguminosarum biovar viciae on peas. A truncated form of nodD2 could also correct this mutant, indicating that the C‐terminus of NodD2 is not needed for inducing activity. Upstream of nodD1 and in the same operon is a newly described gene, nolE, whose product appears to be exported into the periplasm. Close to nodD2 is another gene, nolP, with no known counterpart in other rhizobia. Both nolP and nolE‐nodD1 are preceded by ‘nod‐box’ sequences and, in the former case, there appear to be two tandemly repeated nod‐box sequences. Mutations in each of the nodD genes and in the nolE and nolP genes did not abolish nodulation or nitrogen fixation on beans.
Localized transposon Tn5 mutagenesis of the photosynthetic gene cluster of Rhodobacter sphaeroides
Authors: Coomber S. A. , Chaudhri M. , Connor A. , Britton G. , Hunter C. N. 
Published: October 2006

SummaryFour genes essential for bacteriochlorophyll biosynthesis were known to be encoded within a 45 kb region of the Rhodobacter sphaeroides genome, the boundaries of which are defined by puh and puf genes for reaction‐centre and light‐harvesting LH1 complexes. The cluster is represented by eight overlapping inserts cloned in the mobilizable vector pSUP202. We have used localized transposon Tn5 mutagenesis to characterize this cluster further; a total of 87 independent insertions were generated which identify nine genes for bacteriochlorophyll biosynthesis, six for carotenoid biosynthesis, and puhA encoding the reaction‐centre H subunit. This work provides an essential framework for a detailed study of the structure and expression of genes for photosynthesis in this bacterium.
Sequence of the peh gene of Erwinia carotovora: homology between Erwinia and plant enzymes
Authors: Hinton J. C. D. , Grll D. R. , Lalo D. , Plastow G. S. , Salmond G. P. C. 
Published: October 2006

SummaryPolygalacturonase (Peh) and other pectolytic enzymes play a crucial role in the maceration of vegetables by soft rot Erwinia spp. We have sequenced the peh gene of Erwinia carotovora subsp. carotovora, and identified its product as a precursor of molecular weight 42639, and a mature protein of molecular weight 42200. A putative KdgR‐binding site was identified in the region 5’to the peh gene. The Peh protein showed significant homology with Peh from tomato. In addition, we have found homologies between pectin methylesterase and pectate lyase from Erwinia and their counterparts in tomato. These homologies are described, and their significance discussed.
Mycoplasma pneumoniae DNA gyrase genes
Authors: Colman S. D. , Hu P.‐C. , Bott K. F. 
Published: October 2006

SummaryWe have identified a clone from a λEMBL3 library containing a 19kb insert of Mycoplasma pneumoniae DNA which includes the genes that encode both subunits of DNA gyrase. The gyrB gene and the 5’end of the gyrA gene have been subcloned into M13. The gryB gene is 1953bp in length and overlaps the gryA gene by a single base. The nucleotide sequence of these subclones has significant homology to previously reported gyrase genes. In terms of the size of gyrB gene and its proximity to the gyrA gene, M. pneumoniae is more similar to Bacillus subtilis than to Escherichia coli.
Genetic variation at the omp2 porin locus of the brucellae: species‐specific markers
Authors: Ficht T. A. , Bearden S. W. , Sowa B. A. , Marquis H. 
Published: October 2006

SummaryThe omp2 locus of Brucella abortus is composed of two closely related genes (omp2a and omp2b) that encode, and potentially both express, homologous porin proteins. Genetic variation at this locus is revealed in the form of restriction‐fragment‐length polymorphisms which can be used to distinguish the type strains of all six Brucella species. Five of the six species contain single copies of omp2a and omp2b, whereas Brucella ovis appears to have two copies of the omp2a gene. The implications of these results with regard to the physiological functions of the omp2a and the omp2b gene products, phylogeny of the genus, and species‐specific adaptation are discussed.
Characterization of the virB operon of an Agrobacterium tumefaciens Ti plasmid: nucleotide sequence and protein analysis
Authors: Shirasu K. , Morel P. , Kado C. I. 
Published: October 2006

SummaryThe virulence regulon of the Agrobacterium tumefaciens TiC58 plasmid is composed of six operons, virA, virB, virG, virC, virD and virE, which direct the transfer of T‐DNA into plant cells. The 9.5kbp virB operon is the largest of these operons and its entire nucleotide sequence was determined and found to contain eleven open reading frames (ORFs). Gene fusions of each VirB ORF to T7φ10 were made and over‐expressed in Escherichia coli to confirm that they encode proteins of predicted size. Hydrophobic analysis of these peptide sequences revealed nine proteins that contain hydrophobic spanning regions including signal‐peptide‐like sequences. These data suggest that the majority of VirB proteins may associate with bacterial cell membranes, while the two additional proteins possess a potential ATP‐binding site. Strong homologies in amino acid sequences were observed between nopaline‐ and octopine‐type plasmids. Specific differences in amino acid sequence encoded by VirB ORFs of nopaline and octopine Ti plasmid and a functional role of the gene products are discussed.
Apo forms of cytochrome C550 and cytochrome cd1 are translocated to the periplasm of Paracoccus denitrificans in the absence of haem incorporation caused by either mutation or inhibition of haem synthesis
Authors: Page M. D. , Ferguson S. J. 
Published: October 2006

SummaryAn apo form of cytochrome C550 can be detected by immunoblotting cell‐free extracts of a mutant of Paracoccus denitrificans that is deficient in c‐type cytochromes. This apoprotein is found predominantly in the periplasm, the location of the holocytochrome in the wild‐type organism, indicating that translocation of the polypeptide occurs in the absence of haem attachment. The polypeptide molecular weight, as judged by sodium dodecyl sulphate/polyacrylamide gel electrophoresis, is indistinguishable from that of the holoprotein and the chemically prepared apoprotein; this suggests that the N‐terminal signal sequence is removed in the mutant as in the wild‐type organism. In the presence of levulinic acid, an inhibitor of haem biosynthesis, apocytochrome c550 and aponitrite reductase (cytochrome cd1) accumulated in the periplasm of wild‐type cells. Synthesis of these apoproteins was blocked by chloramphenicol. Thus in P. denitrificans the synthesis of these polypeptides is neither autoregulated nor regulated by the availability of haem. That the apoproteins appear in the periplasm argues against the possibility of polypeptide/haem co‐transport from cytoplasm to periplasm. These observations are related to, and contrasted with, the biosynthesis of c‐type cytochromes in eukaryotic cells.
Immunocytochemical analysis of P‐fimbrial structure: localization of minor subunits and the influence of the minor subunit FsoE on the biogenesis of the adhesin
Authors: Riegman N. , Hoschützky H. , van Die I. , Hoekstra W. , Jann K. , Bergmans H. 
Published: October 2006

SummaryAntibodies recognizing the non‐adhesive minor P‐fimbrial subunrt protein E and the P‐fimbrial adhesin were used in an immunocytochemical analysis of P‐fimbrial structure. It was demonstrated that P‐fimbriae of the serotypes F71, F72 and F11 carry their adhesin in a complex with protein E. These complexes are commonly found at the tip of the fimbrial structure. In P‐fimbriae of serotype F9, expressed by the uropathogenic Escherichia coli strain 21086, adhesin‐protein E complexes are localized at the tips as well as along the shafts of the fimbriae. Protein E of F71 fimbriae (FsoE) plays a catalysing role in the biogenesis of the adhesin, but has no effect on the eventual localization of the adhesin.
COBIOTECH's Role in Biotechnology Worldwide
Authors: Gerhardt Philipp 
Published: October 2006

SummaryCurious or sceptical friends often ask, ‘What and why is COBIOTECH? What is it doing?’. After serving as President during its formative first years, I attempt here to provide information for the curious and allay concerns of the sceptics about COBIOTECH's emerging role in biotechnology internationally.
Post‐transcriptional control in the polycistronic operon environment: studies of the atp operon of Escherichia coli
Authors: McCarthy J. E. G. 
Published: October 2006

SummaryPost‐transcriptional control mechanisms assume special significance in polycistronic operons. Differential gene expression in the atp operon of Escherichia coli is primarily attributable to translational control and, to a lesser extent, to control of mRNA stability. At the same time, the polycistronic environment influences, to varying degrees, the relative importance of the different types of post‐transcriptional control. The present article briefly reviews more recent results obtained through studies of the atp operon. Investigations of the pathway and kinetics of mRNA decay have yielded new information about the role of degradative mechanisms in the overall scheme of control. Moreover, translational coupling has been shown to feature as a major form of interaction between the atp genes. The relevance of these and other data is discussed in the wider context of the post‐transcriptional control mechanisms generally available to E. coli.
Overproduction and purification of the Tn10‐specified inner membrane tetracycline resistance protein Tet using fusions to β‐galactosidase
Authors: Hickman R. K. , McMurry L. M. , Levy S. B. 
Published: October 2006

SummaryTetracycline resistance in the Enterobacteriaceae is mediated by a number of genetically related, usually plasmid‐borne, determinants which specify an efflux system involving an inner membrane protein, Tet. Attempts to overproduce the Tn 10 (Class B)‐encoded Tet in Escherichia coli by cloning the structural gene tet downstream of the λPL promoter under regulation by temperature‐sensitive λ repressor c 1857 were unsuccessful; induction at 42°C resulted in filamentous, non‐viable cells containing little detectable overproduction of the protein. However, cells containing tet fused to lacZ were resistant to tetracycline at 30°C and synthesized modest amounts of a large fusion protein when induced at 42°C. Fusion of the N‐terminal half or the first 38 amino adds of tet to lacZ did lead to increased production of fusion proteins. Fusions could be purified by size or by LacZ immunoaffinity or substrate‐affinity chromatography. In the latter method, selected detergents were required to counteract nonspecific binding of Tet to the adsorbant. Amino acid sequencing of the N‐terminus of Tet–LacZ fusion proteins indicated that most molecules were blocked at this terminus. The sequence of an unblocked subpopulation was consistent with that expected from the nucleotide sequence. A collagen peptide linker, genetically placed between tet and lacZ, allowed recovery of purified Tet protein after collagenase treatment of the purified fusion protein.
Cell‐type‐specific genes expressed late in Dictyostelium development show markedly different responses to 3′ 5′ cyclic AMP
Authors: Richards A. J. , Corney A. J. , Hames B. D. 
Published: October 2006

SummaryThe maintenance of late gene expression by 3′ 5′ cyclic AMP was re‐examined using several newly isolated cell‐type‐specific genes. Expression of all the prespore‐enriched genes ceased immediately upon disaggregation of developing cells and pre‐existing mRNA was rapidly degraded. For most genes, cAMP had little or no effect either alone or in combination with conditioned medium factors. The expression of the non‐cell‐type‐specific genes 7E and 2C also ceased upon cell disaggregation but cAMP triggered a full re‐induction of expression although the timing of the response differed markedly between these two genes. In contrast to earlier interpretations, these data argue that for none of these late prespore genes is cAMP alone sufficient for the maintenance of expression. The responses of the two prestalk mRNAs examined were gene‐specific. Prestalk 5D mRNA decayed slowly upon disaggregation and was partially stabilized by cAMP whereas prestalk 5G mRNA increased upon disaggregation and was inhibited by cAMP.
Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli
Authors: Schlensog V. , Böck A. 
Published: October 2006

SummaryThrough complementation of a trans‐acting regulatory mutation a gene has been cloned whose product is required for the formate induction of the anaerobic expression of the formate hydrogenlyase structural genes. By restriction analysis, and from the size of the encoded protein, the gene could be identified as being equivalent to fhlA described by Sankar et al. (1988). The nucleotide sequence of the fhlA gene was determined and it was shown to code for a protein with a calculated Mr of 78467. Analysis of the derived amino acid sequence showed that the carboxy‐terminal domain of FHLA shares considerable sequence similarity with NIFA and NTRC, which are the ‘regulators’ of two‐component regulatory systems. Carboxy‐terminal truncation of, and introduction of amino‐terminal deletions in, the fhlA gene delivered inactive gene products. When overexpressed, FHLA mediates activation of expression of the formate dehydrogenase and hydrogenase structural genes in the presene of formate also under aerobic growth conditions. FHLA appears to bind to the upstream regulatory sequence (URS) in the 5′ flanking region of the fdhF gene since activation of fdhF expression was dependent on the presence of the URS.
The role of direct oligonucleotide repeats in gonococcal pilin gene variation
Authors: Hill S. A. , Morrison S. G. , Swanson J. 
Published: October 2006

SummaryPrevious studies indicate that gonococcal pilin phase and antigenic variation occur by intragenomic pilin gene recombination, the outcome of which resembles that of gene conversion. During such transitions, the expressed complete pilin gene (pilE) acquires a novel sequence corresponding to that of a silent pilin gene (pilS). In the present study, we find that internal deletions of pilE can produce pilus−/pilus+ phase transitions: direct oligonucleotide repeats in the pilin‐encoding portion of pilE bracket the deleted segments. A novel, orthodox pilE is formed upon repair of the internal deletions, with pilS sequence probably acting as a template for repair. Such deletion/repair of pilE is suggested as a principal mechanism underlying gonococcal pilus variation.
Lipid involvement in protein translocation in Escherichia coli
Authors: de Vrije G. J. , Batenburg A. M. , Killian J. A. , de Kruijff B. 
Published: October 2006

SummarySignal peptides play an essential role in protein trans‐location. This review summarizes the current knowledge of the structure of signal peptides and signal peptide‐lipid interactions and addresses the possibility that signal peptide‐lipid interactions initiate membrane translocation of precursor proteins. A new model for protein translocation in Escherichia coli is proposed, which includes as central features con‐formational changes of the signal peptide and signal‐peptide‐induced local changes in membrane organization (non‐bilayer lipids).
Identification and cloning of nodulation genes and host specificity determinants of the broad host‐range Rhizobium leguminosarum biovar phaseoli strain CIAT899
Authors: Vargas C. , Martinez L. J. , Megias M. , Quinto C. 
Published: October 2006

Summary Rhizobium Ieguminosarum biovar phaseoli type II strain CIAT899 nodulates a wide range of hosts: Phaseolus vulgaris (beans), Leucaena esculenta (leucaena) and Macroptilium atropurpureum (siratro). A nodulation region from the symbiotic plasmid has been isolated and characterized. This region, which is contained in the overlapping cosmid clones pCV38 and pCV117, is able to induce nodutes in beans, leucaena and siratro roots when introduced in strains cured for the symbiotic plasmid, pSym. In addition, this cloned region extends the host range of Rhizobium meliloti and R. leguminosarum biovar (bv.) trifolii wild‐type strains to nodulate beans. Analysis of constructed subclones indicates that a 6.4 kb Hin dlll fragment contains the essential genes required for nodule induction on all three hosts. Rhizobium leguminosarum bv. phaseoli type I strain CE3 nodulates only beans. However, CE3 transconjugants harbouring plasmid pCV3802 (which hybridized to a nodD heterologous probe), were capable of eliciting nodules on leucaena and siratro roots. Our results suggest that the CIAT899 DNA region hybridizing with the R. meliloti nodD detector is involved in the extension of host specificity to promote nodule formation in P. vulgaris, L. esculenta and M. atropurpureum.
Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis
Authors: Snapper S. B. , Melton R. E. , Mustafa S. , Kieser T. , Jr W. R.Jacobs 
Published: October 2006

SummaryRecent development of vectors and methodologies to introduce recombinant DNA into members of the genus Mycobacterium has provided new approaches for investigating these important bacteria. While most pathogenic mycobacteria are slow‐growing, Mycobacterium smegmatis is a fast‐growing, non‐pathogenic species that has been used for many years as a host for mycobacteriophage propagation and, recently, as a host for the introduction of recombinant DNA. Its use as a cloning host for the analysis of mycobacterial genes has been limited by its inability to be efficiently transformed with plasmid vectors. This work describes the isolation and characterization of mutants of M. smegmatis that can be transformed, using electroporation, at efficiencies 104 to 105 times greater than those of the parent strain, yielding more than 105 transformants per μg of plasmid DNA. The mutations conferring this efficient plasmid transformation (Ept) phenotype do not affect phage transfection or the integration of DNA into the M. smegmatis chromosome, but seem to be specific for plasmid transformation. Such Ept mutants have been used to characterize plasmid DNA sequences essential for replication of the Mycobacterium fortuitum plasmid pAL5000 in mycobacteria by permitting the transformation of a library of hybrid plasmid constructs. Efficient plasmid transformation of M. smegmatis will facilitate the analysis of mycobacterial gene function, expression and replication and thus aid in the development of BCG as a multivalent recombinant vaccine vector and in the genetic analysis of the virulence determinants of pathogenic mycobacteria.