bluuebunny/crossref_metadata_2025 huggingface dataset:
Overproduction of the xylS gene product and activation of the xylDLEGF operon on the TOL plasmid
Authors: Inouye S , Nakazawa A , Nakazawa T
Published: November 2016

The effect of high-level expression of the regulatory gene xylS of the Pseudomonas putida TOL plasmid on the activation of the xylDLEGF operon was investigated in Escherichia coli. The xylS gene was placed downstream from the tac promoter, and the resultant fusion was cloned in cis to the xylDLEGF operon. The expression of the operon was monitored by the level of catechol 2,3-dioxygenase, whose structural gene xylE was placed directly after the operator-promoter region of xylDLEGF. xylS transcription was also determined by reverse transcriptase mapping of mRNA. Overproduction of the xylS gene product elicited constitutive high expression of the xylDLEGF operon even in the absence of the inducer for the operon. The results were consistent with a cascade model for the positive control of the xylDLEGF operon by the xylR and xylS genes (S. Inouye, A. Nakazawa, and T. Nakazawa, Proc. Natl. Acad. Sci. USA, in press): m-xylene, a substrate of the degradative pathway, binds to the xylR gene product; the m-xylene-xylR product complex activates the xylS gene; and the xylS product thus synthesized de novo activates the xylDLEGF operon.
Identification of flagellar hook and basal body gene products (FlaFV, FlaFVI, FlaFVII and FlaFVIII) in Salmonella typhimurium
Authors: Homma M , Ohnishi K , Iino T , Macnab R M
Published: November 2016

The flagellar genes flaFV, flaFVII, and flaFVIII of Salmonella typhimurium were cloned, and their presence on a given plasmid was verified by complementation of Escherichia coli mutants defective in the homologous genes. The gene products were identified by radiolabeling in a minicell system as being proteins of the following molecular masses: FlaFV, 42 kilodaltons (kDa); FlaFVI, 32 kDa; FlaFVII, 30 kDA; and FlaFVIII, 27 kDa. These data, together with isoelectric focusing data, confirm gene product assignments of flagellar components made indirectly from mutant studies. Flagellar components are transported by either a signal peptide-dependent or a flagellar-specific pathway. Consistent with its location in the outer membrane ring of the basal body, protein FlaFVIII seems to use the signal peptide-dependent pathway, since it was synthesized in a precursor form and processed, presumably by peptide cleavage, to a mature form; the maturation process was inhibited by addition of a proton ionophore. Proteins synthesized in minicells were localized as follows: FlaFVI was localized to the soluble fraction (cytoplasm); pre-FlaFVIII and FlaFVIII were localized to the particulate fraction (membrane or high-molecular-weight aggregate); FlaFV and FlaFVII were localized to both fractions. The significance of these locations in terms of known or suspected roles in the flagellar apparatus is discussed.
Iron uptake in Mycelia sterilia EP-76
Authors: Adjimani J P , Emery T
Published: November 2016

The cyclic trihydroxamic acid, N,N',N''-triacetylfusarinine C, produced by Mycelia sterilia EP-76, was shown to be a ferric ionophore for this organism. The logarithm of the association constant k for the ferric triacetylfusarinine C chelate was determined to be 31.8. Other iron-chelating agents, such as rhodotorulic acid, citric acid, and the monomeric subunit of triacetylfusarinine C, N-acetylfusarinine, delivered iron to the cells by an indirect mechanism involving iron exchange into triacetylfusarinine C. In vitro ferric ion exchange was found to be rapid with triacetylfusarinine C. Gallium uptake rates comparable to those of iron were observed with the chelating agents that transport iron into the cell. Ferrichrome, but not ferrichrome A, was also capable of delivering iron and gallium to this organism, but not by an exchange mechanism. Unlike triacetylfusarinine C, the 14C-ligand of ferrichrome was retained by the cell. A midpoint potential of -690 mV with respect to the saturated silver chloride electrode was obtained for the ferric triacetylfusarinine C complex, indicating that an unfavorable reduction potential was not the reason for the use of a hydrolytic mechanism of intracellular iron release from the ferric triacetylfusarinine C chelate.
Organization of phosphoribulokinase and ribulose bisphosphate carboxylase/oxygenase genes in Rhodopseudomonas (Rhodobacter) sphaeroides
Authors: Gibson J L , Tabita F R
Published: November 2016

A heterologous phosphoribulokinase (PRK) gene probe was used to analyze two recombinant plasmids isolated from a Rhodopseudomonas (Rhodobacter) sphaeroides gene library. These plasmids were previously shown to carry the genes for form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBPC/O). Southern blot hybridization analysis indicated that there were two PRK genes linked to the RuBPC/O coding sequences. Restriction mapping showed the arrangement of the duplicate sets of PRK and RuBPC/O to be distinct. Subcloning of the hybridizing PRK sequences downstream of the lac promoter of pUC8 allowed expression of the two PRK enzymes in Escherichia coli. Analysis of the purified proteins by sodium dodecyl sulfate-slab gel electrophoresis revealed polypeptides with molecular weights of 32,000 and 34,000 corresponding to the form I and form II PRKs, respectively. Preliminary experiments on sensitivity to NADH regulation suggested that the two PRK enzymes differ in catalytic properties.
Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases
Authors: Dorman C J , Higgins C F
Published: November 2016

Expression of fimA, the structural gene for type 1 fimbriae of Escherichia coli, is phase variable. Significant homologies were identified between the recombinases which control fimbrial phase variation, FimB and FimE, and the integrase class of site-specific recombinases. Normal expression of fimA was shown to require the integration host factor (IHF). Mutations in either the himA-or the himD (hip) gene, which encode the alpha and beta subunits of IHF, respectively, prevented phase variation and locked expression of fimA in either the "on" or "off" phase. In addition, both himA and himD lesions caused a sevenfold reduction in expression of a phi(fimA-lacZ) operon fusion in strains in which fimA was locked in the on phase. Thus, IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter. A mechanism by which IHF may exert control over fimA expression is discussed.
Comparison of dnaA nucleotide sequences of Escherichia coli, Salmonella typhimurium, and Serratia marcescens
Authors: Skovgaard O , Hansen F G
Published: November 2016

The dnaA genes of Salmonella typhimurium and Serratia marcescens, which complemented the temperature-sensitive dnaA46 mutation of Escherichia coli, were cloned and sequenced. They were very homologous to the dnaA gene of E. coli. The 63 N-terminal amino acids and the 333 C-terminal amino acids of the corresponding DnaA proteins were identical. The region in between, corresponding to 71 amino acids in E. coli, exhibited a number of changes. This variable region coincided with a nonhomologous region found in the comparison of E. coli dnaA and Bacillus subtilis "dnaA" genes. The regions upstream of the genes were also homologous. The ribosome-binding area, one of the promoters, the DnaA protein-binding site, and many GATC sites (Dam methyltransferase-recognition sequence) were conserved in these three enteric bacteria.
Characterization of 2,3-dihydroxybenzoic acid from Nocardia asteroides GUH-2
Authors: Feistner G J , Beaman B L
Published: November 2016

Culture filtrates of virulent Nocardia asteroides GUH-2 after growth in acetate minimal medium displayed an absorbance maximum at 320 nm. After isolation by polyamide extraction and anion chromatography, a UV-active compound with this absorbance was shown to be 2,3-dihydroxybenzoic acid (DHB) by nuclear magnetic resonance, gas chromatographic, and mass spectrometric techniques. DHB production under several culture conditions was quantified by a standard high-pressure liquid chromatography assay. Under iron deficiency conditions, N. asteroides GUH-2 excreted up to 11 mg of DHB per liter into the culture medium. No DHB was detected when N. asteroides GUH-2 was grown in an iron-rich medium. With the less virulent strain N. asteroides 10905, DHB was not found under any condition tested.
Analysis of transfer genes and gene products within the traB-traC region of the Escherichia coli fertility factor, F
Authors: Moore D , Wu J H , Kathir P , Hamilton C M , Ippen-Ihler K
Published: November 2016

A series of plasmids that carry overlapping segments of F DNA encoding the genes in the traB-traC interval was constructed, and a restriction enzyme map of the region was derived. Plasmids carrying deletions that had been introduced at an HpaI site within this interval were also isolated. The ability of these plasmids to complement transfer of F lac plasmids carrying mutations in traB, traV, and traW, and traC was analyzed. The protein products of the plasmids were labeled in UV-irradiated cells and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. These analyses showed that the product of traV is a polypeptide that migrates with an apparent molecular weight of 21,000. It was not detected when [35S]methionine was used to label plasmid products, but was readily detected in 14C-amino acid labeling experiments. A 21,500-dalton product appeared to stem from the region assigned to traP. A 9,000-dalton product was found to stem from a locus, named traR, that is located between traV and traC. No traW activity could be detected from the region of tra DNA examined. Our data also indicated that traC is located in a more promoter-proximal position than suggested on earlier maps. The plasmids constructed are expected to be useful in studies designed to identify the specific functions of the traB, -P, -V, -R, and -C products.
Western blot (immunoblot) analysis of the fimbrial antigens of Bacteroides nodosus
Authors: Anderson B J , Mattick J S , Cox P T , Kristo C L , Egerton J R
Published: November 2016

The roles of the fimbrial subunit and the putative basal protein antigens in the serological classification of Bacteroides nodosus have been examined by Western blot (immunoblot)-antibody binding studies of fimbriae isolated from a wide range of strains representative of different serogroups and serotypes. Fimbrial subunits were recognized by antiserum against the homologous serogroup but not generally by heterologous antisera, whereas recognition of the basal antigen was independent of serological classification. Secondary cross-reaction patterns among fimbrial subunits indicated that some serogroups may be more closely related than others. Examples include serogroups C and G and serogroups D and H. Similar analyses of isolates classified within serotypes A1 and A2, with serotype-specific antisera, showed that this subdivision is also determined by the fimbrial subunit and that significant variation does occur even at this level. These studies suggest that the various serogroups and serotypes of B. nodosus comprise a series of overlapping sets of antigenically related strains.
Comparative organization of nitrogen fixation-specific genes from Azotobacter vinelandii and Klebsiella pneumoniae: DNA sequence of the nifUSV genes
Authors: Beynon J , Ally A , Cannon M , Cannon F , Jacobson M , Cash V , Dean D
Published: November 2016

In the facultative anaerobe Klebsiella pneumoniae 17 nitrogen fixation-specific genes (nif genes) have been identified. Homologs to 12 of these genes have now been isolated from the aerobic diazotroph Azotobacter vinelandii. Comparative studies have indicated that these diverse microorganisms share striking similarities in the genetic organization of their nif genes and in the primary structure of their individual nif gene products. In this study the complete nucleotide sequence of the nifUSV gene clusters from both K. pneumoniae and A. vinelandii were determined. These genes are identically organized on their respective genomes, and the individual genes and their products exhibit a high degree of interspecies sequence homology.
Expression of a cloned Bacillus thuringiensis crystal protein gene in Escherichia coli
Authors: Schnepf H E , Wong H C , Whiteley H R
Published: November 2016

The expression in Escherichia coli of a cloned crystal protein gene from Bacillus thuringiensis was investigated through the use of fusions of the crystal protein gene promoter to beta-galactosidase and catechol oxidase genes. Analysis of deletion and insertion derivatives of the crystal protein gene promoter showed that a region of B. thuringiensis DNA located between 87 and 258 base pairs upstream from the transcription initiation site caused reduced transcription from this promoter. Insertion of Tn5 145 base pairs upstream from the transcription initiation site resulted in overproduction of the crystal protein. S1 nuclease mapping experiments failed to detect transcription from an outwardly directed promoter in Tn5, indicating that the overproduction resulted from the disruption or repositioning of the transcription-suppressing region.
Malate dehydrogenase in phototrophic purple bacteria: purification, molecular weight, and quaternary structure
Authors: Tayeh M A , Madigan M T
Published: November 2016

The citric acid cycle enzyme malate dehydrogenase was purified to homogeneity from the nonsulfur purple bacteria Rhodobacter capsulatus, Rhodospirillum rubrum, Rhodomicrobium vannielii, and Rhodocyclus purpureus. Malate dehydrogenase was purified from each species by either a single- or a two-step protocol: triazine dye affinity chromatography was the key step in purification of malate dehydrogenase in all cases. Purification of malate dehydrogenase resulted in a 130- to 240-fold increase in malate dehydrogenase specific activity, depending on the species, with recoveries ranging from 30 to 70%. Homogeneity of malate dehydrogenase preparations from the four organisms was determined by sodium dodecyl sulfate and nondenaturing polyacrylamide gel electrophoresis; a single protein band was observed in purified preparations by both techniques. The molecular weight of native malate dehydrogenases was determined by four independent methods and estimated to be in the range of 130,000 to 140,000 for the enzyme from R. capsulatus, R. rubrum, and R. vannielii and 57,000 for that from R. purpureus. It is concluded that malate dehydrogenase from R. capsulatus, R. rubrum, and R. vannielii is a tetramer composed of four identical subunits, while the enzyme from R. purpureus is a dimer composed of two identical subunits.
Cytokinin production by Agrobacterium and Pseudomonas spp
Authors: Akiyoshi D E , Regier D A , Gordon M P
Published: November 2016

The production of cytokinins by plant-associated bacteria was examined by radioimmunoassay. Strains producing trans-zeatin were identified in the genera Agrobacterium and Pseudomonas. Agrobacterium tumefaciens strains containing nopaline tumor-inducing plasmids, A. tumefaciens Lippia isolates, and Agrobacterium rhizogenes strains produced trans-zeatin in culture at 0.5 to 44 micrograms/liter. Pseudomonas solanacearum and Pseudomonas syringae pv. savastanoi produced trans-zeatin at levels of up to 1 mg/liter. In vitro cytokinin biosynthetic activity was measured for representative strains and was found to correlate with trans-zeatin production. The genetic locus for trans-zeatin secretion (tzs) was cloned from four strains: A. tumefaciens T37, A. rhizogenes A4, P. solanacearum K60, and P. syringae pv. savastanoi 1006. Southern blot analysis showed substantial homology of the Agrobacterium tzs genes to each other but not to the two Pseudomonas genes.
Characterization of the promoter, signal sequence, and amino terminus of a secreted beta-galactosidase from "Streptomyces lividans"
Authors: Eckhardt T , Strickler J , Gorniak L , Burnett W V , Fare L R
Published: November 2016

The gene for a secreted 130-kilodalton beta-galactosidase from "Streptomyces lividans" has been cloned, its promoter, signal sequence, and amino terminal region have been localized, and their nucleotide sequence has been determined. The signal sequence extends over 56 amino acids and shows the characteristic-features of signal sequences, including a hydrophilic amino terminus followed by a hydrophobic core near the signal cleavage site. The secretion of beta-galactosidase depends on the presence of the signal sequence. beta-Galactosidase is the major protein in culture supernatants and extracts of strains expressing the cloned beta-galactosidase gene and represents a valuable tool in the study of protein secretion in Streptomyces spp.
Suppression of mutations conferring penicillin tolerance by interference with the stringent control mechanism of Escherichia coli
Authors: Kusser W , Ishiguro E E
Published: November 2016

Mutations in Escherichia coli previously reported (R. E. Harkness and E. E. Ishiguro, J. Bacteriol. 155:15-21, 1983; L. C. Shimmin, D. Vanderwel, R. E. Harkness, B. R. Currie, A. Galloway, and E. E. Ishiguro, J. Gen. Microbiol. 130:1315-1323, 1984) as conferring a temperature-dependent tolerance to lysis induced by inhibitors of peptidoglycan synthesis were suppressed by treatment with inhibitors of the stringent response or by introduction of a relA mutation. The relA+ derivatives of the mutants exhibited a stringent response at the nonpermissive temperature. The consequent inhibition of the autolytic enzyme system (W. Kusser and E. E. Ishiguro, J. Bacteriol. 164:861-865, 1985) was apparently responsible for the lysis-tolerant phenotypes of these mutants.
Genetic and physical analyses of Methylobacterium organophilum XX genes encoding methanol oxidation
Authors: Machlin S M , Tam P E , Bastien C A , Hanson R S
Published: November 2016

When allyl alcohol was used as a suicide substrate, spontaneous mutants and UV light- and nitrous acid-generated mutants of Methylobacterium organophilum XX were selected which grew on methylamine but not on methanol. There was no detectable methanol dehydrogenase (MDH) activity in crude extracts of these mutants, yet Western blots revealed that some mutants still produced MDH protein. Complementation of 50 mutants by a cosmid gene bank of M. organophilum XX demonstrated that three major regions of the genome, each of which was separated by a minimum of 40 kilobases, were required for expression of active MDH. By subcloning and Tn5 insertion mutagenesis of subcloned fragments, at least 11 genes clustered within these three regions were subsequently identified. The identity of the MDH structural gene, which was initially determined by hybridization to the structural gene of Methylobacterium sp. strain AM1, was confirmed by Western blot analysis of an MDH-beta-galactosidase fusion protein.
Nucleotide sequence of the hexA gene for DNA mismatch repair in Streptococcus pneumoniae and homology of hexA to mutS of Escherichia coli and Salmonella typhimurium
Authors: Priebe S D , Hadi S M , Greenberg B , Lacks S A
Published: November 2016

The Hex system of heteroduplex DNA base mismatch repair operates in Streptococcus pneumoniae after transformation and replication to correct donor and nascent DNA strands, respectively. A functionally similar system, called Mut, operates in Escherichia coli and Salmonella typhimurium. The nucleotide sequence of a 3.8-kilobase segment from the S. pneumoniae chromosome that includes the 2.7-kilobase hexA gene was determined. An open reading frame that could encode a 17-kilodalton polypeptide (OrfC) was located just upstream of the gene encoding a polypeptide of 95 kilodaltons corresponding to HexA. Shine-Dalgarno sequences and putative promoters were identified upstream of each protein start site. Insertion mutations showed that only HexA functioned in mismatch repair and that the promoter for hexA transcription was located within the OrfC-coding region. The HexA polypeptide contains a consensus sequence for ATP- or GTP-binding sites in proteins. Comparison of the entire HexA protein sequence to that of MutS of S. typhimurium, which was determined by Haber et al. in the accompanying paper (L. T. Haber, P. P. Pang, D. I. Sobell, J. A. Mankovitch, and G. C. Walker, J. Bacteriol. 170:197-202, 1988), showed the proteins to be homologous, inasmuch as 36% of their amino acid residues were identical. This homology indicates that the Hex and Mut systems of mismatch repair evolved from an ancestor common to the gram-positive streptococci and the gram-negative enterobacteria. It is the first direct evidence linking the two systems.
Regulation of expression of genes coding for small, acid-soluble proteins of Bacillus subtilis spores: studies using lacZ gene fusions
Authors: Mason J M , Hackett R H , Setlow P
Published: November 2016

We constructed in-frame translational fusions of the Escherichia coli lacZ gene with four genes (sspA, sspB, sspD, and sspE) which code for small, acid-soluble spore proteins of Bacillus subtilis, and integrated these fusions into the chromosomes of various B. subtilis strains. With single copies of the fusions in wild-type B. subtilis, beta-galactosidase was synthesized only during sporulation, with the amounts accumulated being sspB much greater than sspE greater than or equal to sspA greater than or equal to sspD. Greater than 97% of the beta-galactosidase was found in the developing forespore, and the great majority was incorporated into mature spores. Less than 2% of the maximum amount of beta-galactosidase was made when these fusions were introduced into B. subtilis strains blocked in stages 0 and II of sporulation, as well as in some stage III mutants. Other stage III mutants, as well as stage IV and V mutants, had no effect on beta-galactosidase synthesis. Increasing the copy number of the sspA-, sspD-, or sspE-lacZ fusions (up to 17-fold for sspE-lacZ) in wild-type B. subtilis resulted in a parallel increase in the amount of beta-galactosidase accumulated (again only in sporulation and with greater than 95% in the developing forespore), with no significant effect on wild-type small, acid-soluble spore protein production. Similarly, the absence of one or more wild-type ssp genes or the presence of multiple copies of wild-type ssp genes had no effect on the expression of the lacZ fusions tested. These data indicate that these ssp-lacZ fusions escape the autoregulation seen for the intact sspA and sspB genes. Strikingly, the kinetics of beta-galactosidase synthesis were identical for all four ssp-lacZ fusions and paralleled those of glucose dehydrogenase synthesis. Similarly, all asporogenous mutants tested had identical effects on both glucose dehydrogenase and ssp-lacZ fusion expression.
Purification of a second alternative nitrogenase from a nifHDK deletion strain of Azotobacter vinelandii
Authors: Chisnell J R , Premakumar R , Bishop P E
Published: November 2016

A second alternative nitrogenase complex (nitrogenase 3) was purified from a nifHDK deletion strain of Azotobacter vinelandii. The active complex is made up of two components, dinitrogenase 3 and dinitrogenase reductase 3. Dinitrogenase 3 contains two protein subunits (alpha, Mr 58,000, and beta, Mr 50,000) which assemble into at least two active configurations: alpha 2 beta 2 (dinitrogenase 3s) and alpha 1 beta 2 (dinitrogenase 3F). Dinitrogenase 3s contains 24 Fe and 18 acid-labile S2-ions per Mr 216,000, and dinitrogenase 3F contains 11 Fe and 9 acid-labile S2-ions per Mr 158,000. Dinitrogenase reductase 3 is composed of two protein subunits of identical Mr (32,500) and contains four Fe and four acid-labile S2- ions per Mr 65,000. On two-dimensional gels, the protein subunits of the nitrogenase 3 complex comigrated with the four Mo-, V-, and NH4+-repressible proteins originally designated as N2ase B: the nitrogenase hypothesized to exist in the alternative N2 fixation system first described in 1980 (P.E. Bishop, D. M. L. Jarlenski, and D. R. Hetherington, Proc. Natl. Acad. Sci. USA 77:7342-7346, 1980). Neutron activation analysis indicated that the nitrogenase 3 complex lacked significant amounts of Mo, V, Cr, Re, and W. Some Zn, however, was found in the dinitrogenase 3S and dinitrogenase 3F preparations. The pattern of substrate reduction efficiency was H+ greater than N2 greater than C2H2. The maximum specific activity found for N2 reduction was 38 nmol of NH3 per min per mg of protein (dinitrogenase 3S). Nitrogenase 3 was found to be extremely sensitive to O2, and activities could not be reproducibly maintained during freezing and thawing.
Isolation and sequencing of a genomic clone encoding aspartic proteinase of Rhizopus niveus
Authors: Horiuchi H , Yanai K , Okazaki T , Takagi M , Yano K
Published: November 2016

A gene encoding Rhizopus niveus aspartic proteinase was isolated from an R. niveus genomic library by using oligonucleotides probes corresponding to its partial amino acid sequence, and its nucleotide sequence was determined. By comparing its deduced amino acid sequence with the amino acid sequence of rhizopuspepsin (5, 26), we concluded that the R. niveus aspartic proteinase gene has an intron within its coding region and that it has a preproenzyme sequence of 66 amino acids upstream of the mature enzyme of 323 amino acids.
Transcription of Bacillus subtilis subtilisin and expression of subtilisin in sporulation mutants
Authors: Ferrari E , Henner D J , Perego M , Hoch J A
Published: November 2016

The start point for transcription of the subtilisin (aprE) gene was determined by primer extension analysis and was found to be at a point significantly different from that identified in a previously published report (S. L. Wong, C. W. Price, D. S. Goldfarb, and R. H. Doi, Proc. Natl. Acad. Sci. USA 81:1184-1188, 1984). An aprE-lacZ fusion was used to analyze expression of the promoter. Deletion analyses of the promoter were performed to determine the extent of the upstream region necessary for activity. This was found to be between -52 and -41 with respect to the transcription start site. Expression of the aprE-lacZ fusion was unimpaired in a mutant deleted for the sigma B subunit of RNA polymerase. Mutations in the gene for the sigma H subunit of RNA polymerase decreased expression of the aprE-lacZ fusion to approximately 25% of that of the wild type. These results leave the identity of the sigma factor responsible for transcription of this gene in question. Mutations in the spo0A gene drastically decreased the activity of the aprE promoter and its upstream deletion derivatives, while the abrB gene, a phenotypic suppressor of spo0 mutations, restored activity of the aprE promoter in all of the deletion derivatives. Thus, inhibition of transcription by the spo0A mutation and its restoration by an abrB mutation could not be separated from the promoter of the aprE gene.
Location of the targets of the hpr-97, sacU32(Hy), and sacQ36(Hy) mutations in upstream regions of the subtilisin promoter
Authors: Henner D J , Ferrari E , Perego M , Hoch J A
Published: November 2016

A number of mutations have been described with pleiotropic effects on the expression of genes for degradative enzymes in Bacillus subtilis. The sacU32(Hy) and sacQ36(Hy) mutations increase the expression of a wide variety of enzymes that degrade biological polymers. The phenotypes caused by mutations at the hpr locus are more restricted; they are known to increase expression of the alkaline and neutral proteases. The alkaline protease (aprE) promoter was analyzed to determine the target site for stimulation by these loci. Deletion of upstream regions of the aprE promoter could abolish or greatly reduce stimulation by mutations at these loci. A region upstream of -200 was necessary for full stimulation by an hpr-97 mutation, whereas a region between -141 and -164 was necessary for full stimulation by the sacU32(Hy) and sacQ36(Hy) mutations. Northern analyses of mRNA preparations showed that the levels of aprE mRNA were increased in strains carrying the sacU32(Hy) or hpr-97 mutation. Moreover, primer extension analysis of these mRNA preparations revealed that the transcription start point was identical to that in a wild-type strain. We hypothesize that upstream activation of the subtilisin promoter mediated by these genes is a mechanism for global responses to a variety of nutritional conditions.
Comparative nucleotide sequence analysis of growth-rate-regulated gnd alleles from natural isolates of Escherichia coli and from Salmonella typhimurium LT-2
Authors: Barcak G J , Wolf R E
Published: November 2016

A comparative study of gnd genes from Escherichia coli strains isolated from natural populations and laboratory strains and from Salmonella typhimurium was undertaken. In the accompanying paper (G. J. Barcak and R. E. Wolf, Jr., J. Bacteriol. 170:365-371, 1988), we showed that the growth-rate-dependent regulation of gnd expression was conserved among four natural E. coli isolates and E. coli B/r in a manner qualitatively similar to that of the gene from E. coli K-12. Here, we report the DNA sequence of the 5' regulatory region and the first 125 codons of the structural gene for the five E. coli gnd genes and the gnd gene from S. typhimurium LT-2. The sequences differed from one another by 5% on the average. All sequences defined putative secondary structures of the mRNA leader, which were previously proposed to be important in the regulation of the K-12 gene. In addition, a sequence between codons 69 and 74, which is highly complementary to the ribosome-binding site of the mRNA, was conserved in all the genes. The sequence data are discussed with respect to potential regulatory consequences.
Nucleotide sequence of the iucD gene of the pColV-K30 aerobactin operon and topology of its product studied with phoA and lacZ gene fusions
Authors: Herrero M , de Lorenzo V , Neilands J B
Published: November 2016

Gene iucD of the aerobactin operon of the Escherichia coli plasmid ColV-K30 encodes a membrane-bound enzyme synthesizing N6-hydroxylysine, the first product of the aerobactin biosynthesis pathway. The entire nucleotide sequence of the cloned iucD gene was determined, from which the primary and some aspects of the secondary structure of the encoded peptide were deduced. E. coli cells harboring multicopy plasmid pVLN12 (iucD+) hyperproduced an approximately 50-kilodalton peptide which was purified and identified as the product of the gene by examination of its amino-terminal sequence. Two iucD'-'lacZ gene fusions were constructed in vitro and four iucD'-'phoA gene fusions were generated in vivo by mutagenesis of iucD with transposon TnphoA (Tn5 IS50L::phoA). Analysis of the corresponding fusion proteins suggested at least two domains of attachment of the IucD protein to the inner side of the cytoplasmic membrane. The first apparent membrane-bound domain was found within the first 25 amino acids of the protein and showed a sequence which resembled that of the signal peptides.
Cloning and expression of the catA and catBC gene clusters from Pseudomonas aeruginosa PAO
Authors: Kukor J J , Olsen R H , Ballou D P
Published: November 2016

A 9.9-kilobase (kb) BamHI restriction endonuclease fragment encoding the catA and catBC gene clusters was selected from a gene bank of the Pseudomonas aeruginosa PAO1c chromosome. The catA, catB, and catC genes encode enzymes that catalyze consecutive reactions in the catechol branch of the beta-ketoadipate pathway: catA, catechol-1,2-dioxygenase (EC 1.13.11.1); catB, muconate lactonizing enzyme (EC 5.5.1.1); and catC, muconolactone isomerase (EC 5.3.3.4). A recombinant plasmid, pRO1783, which contains the 9.9-kb BamHI restriction fragment complemented P. aeruginosa mutants with lesions in the catA, catB, or catC gene; however, this fragment of chromosomal DNA did not contain any other catabolic genes which had been placed near the catA or catBC cluster based on cotransducibility of the loci. Restriction mapping, deletion subcloning, and complementation analysis showed that the order of the genes on the cloned chromosomal DNA fragment is catA, catB, catC. The catBC genes are tightly linked and are transcribed from a single promoter that is on the 5' side of the catB gene. The catA gene is approximately 3 kb from the catBC genes. The cloned P. aeruginosa catA, catB, and catC genes were expressed at basal levels in blocked mutants of Pseudomonas putida and did not exhibit an inducible response. These observations suggest positive regulation of the P. aeruginosa catA and catBC cluster, the absence of a positive regulatory element from pRO1783, and the inability of the P. putida regulatory gene product to induce expression of the P. aeruginosa catA, catB, and catC genes.
Kinetics of toxA and regA mRNA accumulation in Pseudomonas aeruginosa
Authors: Frank D W , Iglewski B H
Published: November 2016

DNA probes specific for an internal portion of the toxA and regA genes were used to examine the synthesis of mRNA during the growth cycle of P. aeruginosa PA103. RNA dot blot analysis revealed that in a low-iron growth medium, the synthesis of regA and toxA mRNA followed a biphasic expression pattern. Analysis of ADP-ribosyltransferase activity also indicated that an early and late phase of exotoxin A synthesis occurred. Utilizing an internal SalI probe, examination of the size distribution of the regA mRNA during the cell cycle indicated that a large transcript (T1) was present at early time points, followed by the appearance of a smaller transcript (T2) during late exponential to early stationary phase. An upstream AvaI regA probe was found to hybridize to the T1 transcript but not to the T2 transcript. The data indicate that at least two separate functional regA mRNA species were produced. Analysis of mRNA accumulation for the regA gene when cells were grown in high-iron medium provided additional evidence for two separately controlled transcripts being produced from the regA chromosomal locus. Both regA transcripts were correlated with exotoxin A transcription and production.
Expression of the gene encoding the 17-kilodalton antigen from Rickettsia rickettsii: transcription and posttranslational modification
Authors: Anderson B E , Baumstark B R , Bellini W J
Published: November 2016

Recently, we reported the molecular cloning and nucleotide sequence analysis of a gene from Rickettsia rickettsii that codes for a 17-kilodalton antigen (17K antigen) and is preceded by sequences closely resembling the -10 and -35 consensus sequences for recognition by Escherichia coli RNA polymerase (Anderson et al., J. Bacteriol. 169:2385-2390, 1987). Experiments described in this report indicate that the start sites for initiating transcription of the 17K antigen gene are identical in the E. coli clone and in intact R. rickettsii. In each case, initiation was shown to begin 9 bases downstream of the presumed Pribnow box sequence (TATACT). A 169-base-pair fragment containing the promoter sequence initiated transcription in both directions when cloned into an E. coli promoter probe vector. The rickettsial fragment was found to contain sequences identical to the -10 region (but not the -35 region) of the E. coli promoter consensus sequence directed away from the 17K antigen gene. The amino-terminal portion (residues 17 to 20) of the deduced amino acid sequence for the 17K antigen contained the tetrapeptide Leu-Gln-Ala-Cys, a sequence that conforms favorably to those described for lipid modification and cleavage by lipoprotein signal peptidase II. The 17K antigen produced by the E. coli clone was shown to be labeled with [3H]palmitate and [3H]glycerol, indicative of lipid modification. In vitro mutagenesis designed to alter the cysteine at residue 20 to a glycine abolished incorporation of [3H]palmitate, suggesting that posttranslational modification occurs via a mechanism similar to that described for other gram-negative bacterial lipoproteins.
Analysis of the Pseudomonas solanacearum polygalacturonase encoded by pglA and its involvement in phytopathogenicity
Authors: Schell M A , Roberts D P , Denny T P
Published: November 2016

A major endopolygalacturonase excreted by Pseudomonas solanacearum was purified to greater than 95% homogeneity and shown to have an isoelectric point of 9.0 and a subunit molecular mass of 52 kilodaltons (kDa). The gene encoding this enzyme (pglA) was isolated from a genomic library of P. solanacearum DNA based on its expression in Escherichia coli and shown to be contained on a 1.8-kilobase DNA fragment. The identity of the pglA gene product and the 52-kDa polygalacturonase was demonstrated by immunoadsorption and isoelectric focusing experiments. The cloned pglA gene was apparently expressed from its own promoter in E. coli and its product was partially secreted into the periplasm. The pglA gene was insertionally inactivated in vitro and used to mutate the chromosomal pglA gene of P. solanacearum by marker exchange mutagenesis. The resulting mutant strain was deficient in production of the 52-kDa polygalacturonase and took twice as long to wilt and kill tomato plants as the wild-type parent in plant bioassay experiments. Complementation in trans with the wild-type cloned pglA gene restored virulence to near wild-type levels. The data indicate that the pglA gene is important, but not absolutely necessary, for pathogenesis.
Aspartate taxis mutants of the Escherichia coli tar chemoreceptor
Authors: Wolff C , Parkinson J S
Published: November 2016

The Tar protein of Escherichia coli belongs to a family of methyl-accepting inner membrane proteins that mediate chemotactic responses to a variety of compounds. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. The periplasmic receptor domain of Tar senses two quite different chemoeffectors, aspartate and maltose. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein. Saturating levels of either aspartate or maltose do not block behavioral responses to the other compound, indicating that the detection sites for these two attractants are not identical. We initiated structure-function studies of these chemoreceptor sites by isolating tar mutants which eliminate aspartate or maltose taxis, while retaining the ability to respond to the other chemoeffector. Mutants with greatly reduced aspartate taxis are described and characterized in this report. When present in single copy in the chromosome, these tar mutations generally eliminated chemotactic responses to aspartate and structurally related compounds, such as glutamate and methionine. Residual responses to these compounds were shifted to higher concentrations, indicating a reduced affinity of the aspartate-binding site in the mutant receptors. Maltose responses in the mutants ranged from 10 to 80% of normal, but had no detectable threshold shifts, indicating that these receptor alterations may have little effect on maltose detection sensitivity. The mutational changes in 17 mutants were determined by DNA sequence analysis. Each mutant exhibited a single amino acid replacement at residue 64, 69, or 73 in the Tar molecule. The wild-type Tar transducer contains arginines at all three of these positions, implying that electrostatic forces may play an important role in aspartate detection.
Transport of diamines by Enterococcus faecalis is mediated by an agmatine-putrescine antiporter
Authors: Driessen A J , Smid E J , Konings W N
Published: November 2016

Enterococcus faecalis ATCC 11700 is able to use arginine and the diamine agmatine as a sole energy source. Via the highly homologous deiminase pathways, arginine and agmatine are converted into CO2, NH3, and the end products ornithine and putrescine, respectively. In the arginine deiminase pathway, uptake of arginine and excretion of ornithine are mediated by an arginine-ornithine antiport system. The translocation of agmatine was studied in whole cells grown in the presence of arginine, agmatine, or glucose. Rapid uncoupler-insensitive uptake of agmatine was observed only in agmatine-grown cells. A high intracellular putrescine pool was maintained by these cells, and this pool was rapidly released by external putrescine or agmatine but not by arginine or ornithine. Kinetic analysis revealed competitive inhibition for uptake between putrescine and agmatine. Agmatine uptake by membrane vesicles was observed only when the membrane vesicles were preloaded with putrescine. Uptake of agmatine was driven by the outwardly directed putrescine concentration gradient, which is continuously sustained by the metabolic process. Uptake of agmatine and extrusion of putrescine by agmatine-grown cells of E. faecalis appeared to be catalyzed by an agmatine-putrescine antiporter. This transport system functionally resembled the previously described arginine-ornithine antiport, which was exclusively induced when the cells were grown in the presence of arginine.
Microcalorimetric monitoring of growth of Saccharomyces cerevisiae: osmotolerance in relation to physiological state
Authors: Blomberg A , Larsson C , Gustafsson L
Published: November 2016

The importance of the physiological state of a culture of Saccharomyces cerevisiae for tolerance to sudden osmotic dehydration was studied, and it was investigated whether specific osmotolerance factors were demonstrable. The microcalorimeter was used to monitor growth, and different physiological states of the culture were selected and their osmotolerance was tested. In addition to cells in the stationary phase, cells from the transition phase between respirofermentative and respiratory catabolism were osmotolerant. S. cerevisiae exhibited ever-changing metabolism during batch growth on either glucose or ethanol as the carbon source. Instantaneous heat production per biomass formation (dQ/dX) and specific activity of sn-glycerol 3-phosphate dehydrogenase (GPDH) (EC 1.1.1.8) were shown to differ for different physiological states. Neither high respiratory activity nor low total cellular activity, nor factors involved in osmoregulation, i.e., intracellular glycerol or activity of GPDH, correlated with the osmotolerant phenotype.
Kinetic study of a change in intracellular ATP level associated with aerobic catabolism of ethanol by Streptococcus mutans
Authors: Fukui K , Kato K , Kodama T , Ohta H , Shimamoto T , Shimono T
Published: November 2016

Streptococcus mutans, a group of lactic acid bacteria and a normal inhabitant of the human oral cavity, generates ATP by substrate-level phosphorylation coupled to oxidation of ethanol (an end product of fermentation of sugars) into acetate in the presence of oxygen (K. Fukui, K. Kato, Kodama, H. Ohta, T. Shima moto, and T. Shimono, Proc. Jpn. Acad. 64B:13-16, 1988). Kinetic measurements were made of the cellular responses of S. mutans FA-1 to ethanol in comparison with those to glucose. In contrast to oxygen-independent acid production from glucose, oxygen was absolutely required for acid production from ethanol. Ethanol elicited a marked increase in the intracellular ATP concentration (ATPi) from a starved level to a steady level which was held constant as long as oxygen was present in the medium. Once oxygen was exhausted, ATPi returned to the starved level without delay. On the contrary, ATPi changes induced by glucose, which were independent of oxygen, followed a rather complicated time course before a steady level was established. Both the steady ATPi and the rate of accompanying oxygen consumption were functions of the ethanol concentration. These two parameters were linearly correlated, indicating that the unimolecular ATP turnover rate, which is independent of the rate of ATP generation in the steady state, can be calculated for cells energized by ethanol. The estimated turnover rate was 1.5 s-1 at 37 degrees C, which is comparable to that for other bacteria energized by glucose under nongrowing conditions.
Structural diversity among methanofurans from different methanogenic bacteria
Authors: White R H
Published: November 2016

An examination of the methanofurans isolated from a wide range of methanogenic bacteria and from Archaeoglobus fulgidus has revealed at least five chromatographically distinct methanofurans. Bacteria from each major genus of methanogenic bacteria have been found to contain a chemically different methanofuran. The nature of the differences in the methanofurans appears to lie in the modification of the side chain attached to the basic core structure of 4-[N-(gamma-L-glutamyl-gamma-L-glutamyl)-p-(beta-aminoethyl)phenoxyme thy l]-2-(amino-methyl)furan. This was supported by the structural elucidation of the methanofuran isolated from Methanobrevibacter smithii, designated methanofuran-c, which was the same as the originally characterized methanofuran except for a hydroxy group at the 2 position of the 4,5-dicarboxyoctanedioic acid moiety of the molecule.
Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells
Authors: Doi M , Wachi M , Ishino F , Tomioka S , Ito M , Sakagami Y , Suzuki A , Matsuhashi M
Published: November 2016

The 6.5-kilobase mre region at 71 min in the Escherichia coli chromosome map, where genes involved in formation of a rod-shaped cell form a gene cluster, was analyzed by in vivo protein synthesis in a maxicell system and by base sequencing of DNA. An open reading frame that may code for a protein with an Mr of about 37,000 on sodium dodecyl sulfate-polyacrylamide gels was found and was correlated with the mreB gene. N-terminal amino acid sequencing of the hybrid mreB-lacZ protein confirmed the production by mreB of a protein of 347 amino acid residues with a molecular weight of 36,958. The amino acid sequence of this protein deduced from the DNA sequence showed close similarity with that of a protein of the ftsA gene which is involved in cell division of E. coli. Three other contiguous genes that formed three proteins with Mrs of about 40,000, 22,000, and 51,000, respectively, were detected downstream of the mreB gene by in vivo protein synthesis. The mreB protein and some of these three proteins may function together in determination of cell shape.
Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties
Authors: Kendall K J , Cohen S N
Published: November 2016

The complete nucleotide sequence of the multicopy Streptomyces plasmid pIJ101 has been determined and correlated with previously published genetic data. The circular DNA molecule is 8,830 nucleotides in length and has a G+C composition of 72.98%. The use of a computer program, FRAME, enabled identification in the sequence of seven open reading frames, four of which, tra (621 amino acids [aa]), spdA (146 aa), spdB (274 aa), and kilB (177 aa), appear to be genes involved in plasmid transfer. At least two of the above genes are predicted to be transcribed by known promoters that are regulated in trans by the products of the korA (241 aa) and korB (80 aa) loci on the plasmid. The segment of the plasmid capable of autonomous replication contains one large open reading frame (rep; 450 aa) and a noncoding region presumed to be the origin of replication. Four other small (less than 90 aa) open reading frames are also present on the plasmid, although no function can be attributed to them. The sequence of the pIJ101 replication segment present in several widely used cloning vectors (e.g., pIJ350 and pIJ702) has also been determined, so that the complete nucleotide sequences of these vectors are now known.