bluuebunny/crossref_metadata_2025 huggingface dataset:
Dechlorination and para-hydroxylation of polychlorinated phenols by Rhodococcus chlorophenolicus
Authors: Apajalahti J H , Salkinoja-Salonen M S
Published: November 2016

In this paper we show that a polychlorophenol degrader Rhodococcus chlorophenolicus PCP-I initially attacked polychlorinated phenols (pentachlorophenol, 2,3,4,5-, 2,3,4,6-, and 2,3,5,6-tetrachlorophenol, and 2,3,5- and 2,3,6-trichlorophenol) by tetra- or trichlorohydroquinone-producing para-hydroxylation. The novel hydroxyl group was set in position 4, whether or not a substrate had chlorine substituent in this position. The hydroxyl was in each case derived from water molecules, as was shown by following the incorporation of oxygen from H2(18)O into the reaction products. Nevertheless, the para-hydroxylation reaction required the presence of molecular oxygen, whereas further metabolism of the reaction product, tetrachlorohydroquinone, proceeded also in anaerobiosis. All polychlorinated phenols were readily transformed at 41 degrees C, but none were transformed at 44 degrees C. In contrast to this, tetrachlorohydroquinone was metabolized at a high rate at 50 degrees C, but was not metabolized at 55 degrees C. Polychlorinated phenols were specific inducers of the para-hydroxylating enzymes; para-hydroxylated reaction products did not induce these enzymes. On the other hand, the degradation of tri- and tetrachlorohydroquinone was induced by any of the chlorophenols and also by hydroquinones.
Verification of the protein in the outer membrane of Bdellovibrio bacteriovorus as the OmpF protein of its Escherichia coli prey
Authors: Talley B G , McDade R L , Diedrich D L
Published: November 2016

Two research groups showed that several Bdellovibrio strains incorporated into their outer membranes intact OmpF porin proteins derived from their Escherichia coli prey. These results could not be reproduced by another group using Bdellovibrio bacteriovorus 109J. They showed that a major protein appearing in the Bdellovibrio Triton X-100-insoluble outer membrane was coded for by the bdellovibrios. We reconciled these results by examining the strain used by this group and by reviving a freeze-dried culture of strain 109J which had been stored for almost 9 years. B. bacteriovorus 109J failed to acquire substantial amounts of the OmpF protein from E. coli ML35, and a protein coded for by the bdellovibrios was expressed in its place. However, B. bacteriovorus 109J incorporated the OmpF protein from rough K-12 strains of E. coli, and the revived 9-year-old culture of B. bacteriovorus 109J incorporated more of the OmpF protein from the smooth E. coli ML35 than did its contemporary counterpart. The protein isolated from the outer membrane of the bdellovibrios was identified as the OmpF protein of E. coli by its protease peptide profile on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by Western blot analysis. This confirmed that bdellovibrios relocalize outer membrane proteins from their prey, but relocalization may be an unstable trait which can be influenced by the prey.
Electron microscopy of nickel-containing methanogenic enzymes: methyl reductase and F420-reducing hydrogenase
Authors: Wackett L P , Hartwieg E A , King J A , Orme-Johnson W H , Walsh C T
Published: November 2016

Methanogens catalyze the hydrogen-dependent eight-electron reduction of carbon dioxide to methane. Two of the key catalysts in the eight-electron reduction pathway are the nickel-containing enzymes F420-reducing hydrogenase and methyl reductase. In the present study, the structures of these archaebacterial enzymes from Methanobacterium thermoautotrophicum delta H have been determined by electron microscopy. By negative stain techniques, F420 hydrogenase was found to be a ring structure with a diameter of 15.7 nm and an inner channel 4 nm in diameter. Shadow-casting experiments demonstrated that the rings were 8.5 nm deep, indicating a holoenzyme molecular weight of 8.0 X 10(5). Methyl reductase appeared to be an oligomeric complex of dimensions 8.5 by 9 by 11 nm, with a central stain-penetrating region. The morphology and known subunit composition suggest a model in which the subunits are arranged as an eclipsed pair of open trimers. Methyl reductase was also found in the form of larger aggregates and in paracrystalline arrays derived from highly concentrated solutions. The extremely large size of F420 hydrogenase and the methyl reductase supramolecular assemblies may have relevance in vivo in the construction of multiprotein arrays that function in methane biogenesis.
Inhibition of adhesive activity of K88 fibrillae by peptides derived from the K88 adhesin
Authors: Jacobs A A , Venema J , Leeven R , van Pelt-Heerschap H , de Graaf F K
Published: November 2016

A cyanogen bromide fragment derived from the K88ab adhesin inhibited the hemagglutinating activity of K88 fibrillae. Smaller fragments which inhibited the adherence of K88 fibrillae to erythrocytes or to intestinal epithelial cells were obtained by digestion of K88ab fibrillae with alpha-chymotrypsin. Active peptides were isolated from the digestion mixture and identified as Ser-Leu-Phe and Ala-Ile-Phe. Both tripeptides correspond to the peptide stretches Ser-148-Leu-Phe-150 and Ala-156-Ile-Phe-158, respectively, which are part of conserved regions in the primary structure of the K88 variants ab, ac, and ad. The isolated tripeptides inhibited the hemagglutinating activity of purified K88 fibrillae in the 1 to 5 microM range, while adherence of the fibrillae to intestinal epithelial cell brush borders was inhibited in the 10 to 50 microM range. Furthermore, the tripeptides were capable of eluting attached bacteria from agglutinated erythrocytes. The inhibitory activity of the isolated peptides was confirmed by testing various synthetic peptides for their ability to inhibit the interaction of the different K88 variants with various species of erythrocytes. The significance of these findings for the localization of the receptor-binding domain is discussed.
Common mechanism of ampC beta-lactamase induction in enterobacteria: regulation of the cloned Enterobacter cloacae P99 beta-lactamase gene
Authors: Lindberg F , Normark S
Published: November 2016

Expression of the chromosomal beta-lactamase from the ampC gene in inducible in both Enterobacter cloacae and Citrobacter freundii. Cloning of ampC as well as its regulatory gene, ampR, from E. cloacae P99 revealed a gene organization indentical to that of C. freundii in the corresponding region. Although almost no similarities could be found between the restriction maps of ampC and ampR in the two species, the genes cross-hybridize. Also, both ampR gene products have a size of about 31,000. The regulatory features of E. cloacae beta-lactamase induction are very similar to those in C. freundii, i.e., beta-lactamase synthesis is repressed by AmpR in the absence, and stimulated in the presence, of inducer. The AmpR function can be transcomplemented between the two species, but there are quantitative regulatory aberrations in such hybrids, in contrast to the total complementation obtained within each system. These results suggest that the mechanism of beta-lactamase induction is the same in E. cloacae, C. freundii, and other gram-negative bacteria with inducible chromosomal beta-lactamase expression.
Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product
Authors: Keil H , Saint C M , Williams P A
Published: November 2016

The entire operon coding for the enzymes responsible for conversion of toluenes to benzoates has been cloned from TOL plasmid pWW53 and the position of the genes accurately located. The coding region was 7.4 kilobase pairs (kbp) long, and the gene order was operator-promoter region (OP1)-a small open reading frame-xylC (1.6 kbp)-xylA (2.9 kbp)-xylB (1.8 kbp). Within the coding region there was considerable homology with the isofunctional region of the archetypal TOL plasmid pWW0. A central region of 2.9 kbp complemented an xylA (for xylene oxygenase) mutant of Pseudomonas putida mt-2 and was also capable of conferring the ability to convert indole to indigo on strains of Escherichia coli and P. putida. This reaction has been reported previously only for dioxygenases involved in aromatic catabolism but not for monooxygenases. It is proposed that the region encodes xylene oxygenase activity capable of direct monohydroxylation of indole to 3-hydroxyindole (oxindole), which then spontaneously dimerizes to form indigo.
Effect of cell cycle position on thermotolerance in Saccharomyces cerevisiae
Authors: Plesset J , Ludwig J R , Cox B S , McLaughlin C S
Published: November 2016

We showed that the heat killing curve for exponentially growing Saccharomyces cerevisiae was biphasic. This suggests two populations of cells with different thermal killing characteristics. When exponentially growing cells separated into cell cycle-specific fractions via centrifugal elutriation were heat shocked, the fractions enriched in small unbudded cells showed greater resistance to heat killing than did other cell cycle fractions. Cells arrested as unbudded cells fell into two groups on the basis of thermotolerance. Sulfur-starved cells and the temperature-sensitive mutants cdc25, cdc33, and cdc35 arrested as unbudded cells were in a thermotolerant state. Alpha-factor-treated cells arrested in a thermosensitive state, as did the temperature-sensitive mutant cdc36 when grown at the restrictive temperature. cdc7, which arrested at the G1-S boundary, arrested in a thermosensitive state. Our results suggest that there is a subpopulation of unbudded cells in exponentially growing cultures that is in G0 and not in G1 and that some but not all methods which cause arrest as unbudded cells lead to arrest in G0 as opposed to G1. It has been shown previously that yeast cells acquire thermotolerance to a subsequent challenge at an otherwise lethal temperature during a preincubation at 36 degrees C. We showed that this acquisition of thermotolerance was corrected temporally with a transient increase in the percentage of unbudded cells during the preincubation at 36 degrees C. The results suggest a relationship between the heat shock phenomenon and the cell cycle in S. cerevisiae and relate thermotolerance to transient as well as to more prolonged residence in the G0 state.
Loss of aldehyde dehydrogenase in an Escherichia coli mutant selected for growth on the rare sugar L-galactose
Authors: Zhu Y , Lin E C
Published: November 2016

Escherichia coli K-12 converts L-fucose to dihydroxyacetone phosphate (C-1 to C-3) and L-lactaldehyde (C-4 to C-6) by a pathway specified by the fuc regulon. Aerobically, L-lactaldehyde serves as a carbon and energy source by the action of an aldehyde dehydrogenase of broad specificity; the product, L-lactate, is then converted to pyruvate. Anaerobically, L-lactaldehyde serves as an electron acceptor to regenerate NAD from NADH by the action of an oxidoreductase; the reduced product, L-12-propanediol, is excreted. A strain selected for growth on L-galactose (a structural analog of L-fucose) acquired a broadened inducer specificity because of an altered fucR gene encoding the activator protein for the fuc regulon (Y. Zhu and E. C. C. Lin, J. Mol. Evol. 23:259-266, 1986). In this study, a second mutation that abolished aldehyde dehydrogenase activity was discovered. The L-fucose pathway converts L-galactose to dihydroxyacetone phosphate and L-glyceraldehyde. Aldehyde dehydrogenase then converts L-glyceraldehyde to L-glycerate, which is toxic. Loss of the dehydrogenase averts the toxicity during growth on L-galactose, but reduces by one-half the aerobic growth yield on L-fucose. When mutant cells induced in the L-fucose system were incubated with radioactive L-fucose, accumulation of radioactivity occurred if the substrate was labeled at C-1 but not if it was labeled C-6. Complete aerobic utilization of carbons 4 through 6 of L-fucose depends not only on an adequate activity of aldehyde dehydrogenase to trap L-lactaldehyde as its anionic acid but also on the lack of L-1,2-propanediol oxidoreductase activity, which converts L-lactaldehyde to a readily excreted alcohol.
Amino sugars in the glycoprotein toxin from Bacillus thuringiensis subsp. israelensis
Authors: Pfannenstiel M A , Muthukumar G , Couche G A , Nickerson K W
Published: November 2016

The carbohydrate content of purified Bacillus thuriniensis subsp. israelensis crystal toxin was determined by six biochemical tests, column chromatography on an amino acid analyzer, and the binding of 11 fluorescent lectins. The crystals contained approximately 1.0% neutral sugars and 1.7% amino sugars. The amino sugars consisted of 70% glucosamine and 30% galactosamine. No N-acetylneuraminic acid (sialic acid) was detected. The presence of amino sugars was confirmed by the strong binding of fluorescent wheat germ agglutinin and the weak binding of fluorescent soybean agglutinin. These lectins recognize N-acetyl-D-glucosamine and N-acetyl-D-galactosamine, respectively. The lectin-binding sites appeared evenly distributed among the protein subunits of the crystal. The sugars were covalently attached to the crystal toxin because wheat germ agglutinin still bound alkali-solubilized toxin which had been boiled in sodium dodecyl sulfate, separate by polyacrylamide gel electrophoresis, and transferred to nitrocellulose membranes. This study demonstrates the covalent attachment of amino sugars and indicates that the B. thuringiensis subsp. israelensis protein toxins should be viewed as glycoprotein toxins. The crystals used in the present study were purified on sodium bromide density gradients. Studies employing crystals purified on Renografin density gradients can give artificially high values for the anthrone test for neutral sugars.
In vivo regulation of histidine ammonia-lyase activity from Streptomyces griseus
Authors: Kroening T A , Kendrick K E
Published: November 2016

The enzyme histidine ammonia-lyase (histidase) is required for growth of Streptomyces griseus on L-histidine as the sole source of nitrogen. Histidase was induced by the inclusion of histidine in the medium, regardless of the presence of other carbon and nitrogen sources. Histidase activity was increased by a shift of culture incubation temperature from 30 to 37 degrees C. Conversely, upon induction of sporulation by either phosphate starvation or nutritional downshift, histidase underwent rapid inactivation. Nutrient replenishment fully reversed histidase inactivation while simultaneously permitting reinitiation of vegetative growth. In contrast to histidase inactivation during sporulation, histidase was activated after transition of a vegetatively growing culture to stationary phase. Although neither activation nor inactivation required de novo protein synthesis, inactivation appeared to involve a heat-labile protein. The results indicate that histidase activity is regulated in vivo by a process that responds to changes in the growth phase of the organism.
Nucleotide sequence encoding the flavoprotein and iron-sulfur protein subunits of the Bacillus subtilis PY79 succinate dehydrogenase complex
Authors: Phillips M K , Hederstedt L , Hasnain S , Rutberg L , Guest J R
Published: November 2016

The nucleotide sequence of a 2.7-kilobase segment of DNA containing the sdhA and sdhB genes encoding the flavoprotein (Fp, sdhA) and iron-sulfur protein (Ip, sdhB) subunits of the succinate dehydrogenase of Bacillus subtilis was determined. This sequence extends the previously reported sequence encoding the cytochrome b558 subunit (sdhC) and completes the sequence of the sdh operon, sdhCAB. The predicted molecular weights for the Fp and Ip subunits, 65,186 (585 amino acids) and 28,285 (252 amino acids), agreed with the values determined independently for the labeled Fp and Ip antigens, although it appeared that the B. subtilis Fp was not functional after expression of the sdhA gene in Escherichia coli. Both subunits closely resembled the corresponding Fp and Ip subunits of the succinate dehydrogenase (SDH) and fumarate reductase of E. coli in size, composition, and amino acid sequence. The sequence homologies further indicated that the B. subtilis SDH subunits are equally related to the SDH and fumarate reductase subunits of E. coli but are less closely related than are the corresponding pairs of E. coli subunits. The regions of highest sequence conservation were identifiable as the catalytically significant flavin adenine dinucleotide-binding sites and cysteine clusters of the iron-sulfur centers.
An alkaline shift induces the heat shock response in Escherichia coli
Authors: Taglicht D , Padan E , Oppenheim A B , Schuldiner S
Published: November 2016

Activation of heat shock response was observed after an alkaline shift of extracellular pH: it peaked at 5 to 10 min, as was previously reported for the heat-induced response, and was dependent on a functional rpoH gene, which is the positive regulator of the heat shock response. An induction of over sixfold was observed for dnaK and groE. The response was induced by the alkalization of extracellular pH but not by the alkalization of intracellular pH. An acidic shift of extracellular pH failed to activate the heat shock response, showing that the response is specific to the alkaline shift.
Genetic expression of enzyme I activity of the phosphoenolpyruvate:sugar phosphotransferase system in ptsHI deletion strains of Salmonella typhimurium
Authors: Chin A M , Sutrina S , Feldheim D A , Saier M H
Published: November 2016

Mutants expressing a novel enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system, termed enzyme I, were isolated from strains of Salmonella typhimurium which were deleted for the HPr and enzyme I structural genes. The mutations lay in a newly defined gene, termed ptsJ, which mapped on the S. typhimurium chromosome between the ptsHI operon and the cysA gene.
Variations between the nucleotide sequences of Tn1, Tn2, and Tn3 and expression of beta-lactamase in Pseudomonas aeruginosa and Escherichia coli
Authors: Chen S T , Clowes R C
Published: November 2016

Using S1 nuclease assays, we located the sites of initiation of transcription of the beta-lactamase gene on Tn1 and Tn2. Transcription in Tn2, like that in Tn3, occurred from the P3 promoter, whereas transcription in Tn1 was initiated by two stronger and overlapping promoters, Pa and Pb. The nucleotide sequences of Tn1 and Tn2 were determined over a 1,195-base-pair segment constituting most of the sequences of the tnpR and bla genes and the intervening region. There were six base-pair differences between Tn1 and Tn3. One in the bla regulatory region accounted for the presence of the Pa and Pb promoters, and another in the bla structural gene is consistent with the isoelectric focusing difference found between the Tn1 and Tn3 enzymes. In contrast, there were 24 base-pair differences between Tn2 and Tn3, most of them clustered in one segment of the tnpR gene.
Purification and properties of 2,3-dihydroxybiphenyl dioxygenase from polychlorinated biphenyl-degrading Pseudomonas pseudoalcaligenes and Pseudomonas aeruginosa carrying the cloned bphC gene
Authors: Furukawa K , Arimura N
Published: November 2016

2,3-Dihydroxybiphenyl dioxygenase, involved in biphenyl and polychlorinated biphenyl degradation, was purified from cell extracts of polychlorinated biphenyl-degrading Pseudomonas pseudoalcaligenes KF707 and Pseudomonas aeruginosa PAO1161 carrying the cloned bphC gene (encoding 2,3-dihydroxybiphenyl dioxygenase). The purified enzyme contained ferrous iron as a prosthetic group. The specific activities decreased with the loss of ferrous iron from the enzyme, and the activity was restored by incubation with ferrous iron in the presence of cysteine. Addition of ferric iron caused the complete inactivation of the enzyme. The molecular weight was estimated to be 250,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a single band with a molecular weight of 31,000, indicating that the enzyme consists of eight identical subunits. The enzyme was specific only for 2,3-dihydroxybiphenyl with a Km value of 87 microM. No significant activity was observed for 3,4-dihydroxybiphenyl, catechol, or 3-methyl- and 4-methylcatechol. The molecular weight, subunit structure, ferrous iron requirement, and NH2-terminal sequence (starting with serine up to 12 residues) were the same between the two enzymes obtained from KF707 and PAO1161 (bphC).
Pyruvate decarboxylase of Zymomonas mobilis: isolation, properties, and genetic expression in Escherichia coli
Authors: Neale A D , Scopes R K , Wettenhall R E , Hoogenraad N J
Published: November 2016

Pyruvate decarboxylase (EC 4.1.1.1) from Zymomonas mobilis purified to homogeneity by using dye-ligand and ion-exchange chromatography. Antibodies produced against the enzyme and the amino-terminal sequence obtained for the pure enzyme were used to select and confirm the identity of a genomic clone encoding the enzyme selected from a genomic library of Z. mobilis DNA cloned into pUC9. The genomic fragment encoding the enzyme expressed high levels of pyruvate decarboxylase in Escherichia coli. Possible RNA polymerase and ribosome-binding sites have been identified in the 5'-untranslated region of the pyruvate decarboxylase gene.
Molecular cloning and characterization of the Streptomyces hygroscopicus alpha-amylase gene
Authors: Hoshiko S , Makabe O , Nojiri C , Katsumata K , Satoh E , Nagaoka K
Published: November 2016

We have isolated and sequenced a gene (amy) coding for alpha-amylase (EC 3.2.1.1.) from the Streptomyces hygroscopicus genome (H. Hidaka, Y. Koaze, K. Yoshida, T. Niwa, T. Shomura, and T. Niida, Die Stärke 26:413-416, 1974). Amylase was purified to obtain amino acid sequence information which was used to synthesize oligonucleotide probes. amy-containing Escherichia coli cosmids identified by hybridization did not express amylase activity. Subcloning experiments indicated that amy could be expressed from the lac promoter in E. coli or from its own promoter in S. lividans. The amy nucleotide sequence indicated that it coded for a protein of 52 kilodaltons (478 amino acids). Secreted alpha-amylase contained amino- and carboxy-terminal as well as internal amino acid sequences which were consistent with the nucleotide sequence. The 30-residue leader sequence showed similarities to those found in other procaryotes. The DNA sequence 5' to the amy structural gene contained a sequence complementary to the 3'-terminal sequence of 16S rRNA of S. lividans (M. J. Bibb and S. N. Cohen, Mol. Gen. Genet. 187:265-277, 1982). The transcriptional start points of amy were determined by mung bean nuclease mapping, but the promoter of amy was not similar to the consensus sequence found in other procaryotes.
Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette
Authors: Arps P J , Winkler M E
Published: November 2016

We constructed a series of recombinant plasmids containing a kanamycin resistance (Kmr) cassette upstream from, within, and downstream from hisT, which encodes the tRNA modification enzyme pseudouridine synthase I. These Kmr insertions were then crossed directly into the bacterial chromosome. We determined growth characteristics, assayed in vivo hisT expression, and mapped in vivo hisT operon transcripts for the Kmr insertion mutants. We also analyzed polypeptides synthesized in minicells from plasmids containing Kmr cassettes. The combined results from these experiments demonstrate new features concerning the structure and expression of the complex operon that contains hisT. We show that the minimum size of the operon is approximately 3,500 base pairs and that it contains at least four genes, which are arranged in the order usg-2 (pdxB), usg-1, hisT, and dsg-1 and encode polypeptides with apparent molecular masses of 42,000, 45,000, 31,000, and 17,000 daltons, respectively. Of these genes, only the functions of usg-2 (pdxB) and hisT are known, and genetic evidence suggests that these two genes do not require usg-1 or dsg-1 for function, usg-2 (pdxB) is required for growth of bacteria on minimal medium at 37 degrees C. In contrast, the three genes at the end of the hisT operon are dispensable and form a transcription unit that is expressed from a relatively strong internal promoter. The phenotypes of the Kmr insertion mutants and results from gene expression experiments further confirm the position of the internal promoter and locate additional genetic signals in the DNA sequence around hisT. The experiments reported here also indicate several interesting properties of the Kmr cassette as a tool for probing complex operons.
An unusual genetic link between vitamin B6 biosynthesis and tRNA pseudouridine modification in Escherichia coli K-12
Authors: Arps P J , Winkler M E
Published: November 2016

We characterized several unusual phenotypes caused by stable insertion mutations in a gene that is located upstream in the same operon from hisT, which encodes the tRNA modification enzyme pseudouridine synthase I. Mutants containing kanamycin resistance (Kmr) cassettes in this upstream gene, which we temporarily designated usg-2, failed to grow on minimal plus glucose medium at 37 and 42 degrees C. However, usg-2::Kmr mutants did form oddly translucent, mucoid colonies at 30 degrees C or below. Microscopic examination revealed that cells from these translucent colonies were spherical and seemed to divide equatorially. Addition of D-alanine restored the shape of the mutant cells to rods and allowed the mutants to grow slowly at 37 degrees C and above. By contrast, addition of the common L-amino acids prevented growth of the usg-2::Kmr mutants, even at 30 degrees C. Furthermore, prolonged incubation of usg-2::Kmr mutants at 37 and 42 degrees C led to the appearance of several classes of temperature-resistant pseudorevertants. Other compounds also supported growth of usg-2::Kmr mutants at 37 and 42 degrees C, including glycolaldehyde and the B6 vitamers pyridoxine and pyridoxal. This observation suggested that usg-2 was pdxB, which had been mapped near hisT. Complementation experiments confirmed that usg-2 is indeed pdxB, and inspection of the pyridoxine biosynthetic pathway suggests explanations for the unusual phenotypes of pdxB::Kmr mutants. Finally, Southern hybridization experiments showed that pdxB and hisT are closely associated in several enterobacterial species. We consider reasons for grouping pdxB and hisT together in the same complex operon and speculate that these two genes play roles in the global regulation of amino acid metabolism.
Essential DNA sequence for the replication of Rts1
Authors: Itoh Y , Kamio Y , Terawaki Y
Published: November 2016

The promoter sequence of the mini-Rts1 repA gene encoding the 33,000-dalton RepA protein that is essential for replication was defined by RNA polymerase protection experiments and by analyzing RepA protein synthesized in maxicells harboring mini-Rts1 derivatives deleted upstream of or within the presumptive promoter region. The -10 region of the promoter which shows homology to the incII repeat sequences overlaps two inverted repeats. One of the repeats forms a pair with a sequence in the -35 region, and the other forms a pair with the translation initiation region. The replication origin region, ori(Rts1), which was determined by supplying RepA protein in trans, was localized within 188 base pairs in a region containing three incII repeats and four GATC sequences. Dyad dnaA boxes that exist upstream from the GATC sequences appeared to be dispensable for the origin function, but deletion of both dnaA boxes from ori(Rts1) resulted in reduced replication frequency, suggesting that host-encoded DnaA protein is involved in the replication of Rts1 as a stimulatory element. Combination of the minimal repA and ori(Rts1) segments, even in the reverse orientation compared with the natural sequence, resulted in reconstitution of an autonomously replicating molecule.
Alteration of surface properties in a Tn5 mutant strain of Rhizobium trifolii 0403
Authors: Gardiol A E , Hollingsworth R I , Dazzo F B
Published: November 2016

A symbiotically defective mutant strain of Rhizobium trifolii, UR251, was obtained by transposon Tn5 mutagenesis of R. trifolii 0403 rif and recognized by its partially ineffective (Fix +/-) phenotype on white clover plants. UR251 had a single Tn5 insertion in plasmid DNA, a wild-type plasmid pattern, and no detectable Mu DNA sequences originally present in the vector used for Tn5 mutagenesis. Agglutination by the clover lectin trifoliin A and attachment to clover root hairs was higher with UR251 than with the wild-type strain. The capsular polysaccharide (CPS) of UR251 was altered, as shown by a slower rate of CPS depolymerization with a CPS beta-lyase, PD-I; more pyruvate and less acetate and 3-hydroxybutanoate noncarbohydrate substitutions as quantitated by 1H nuclear magnetic resonance; and a higher pyruvyl transferase activity (enzymatic pyruvylation of lipid-bound saccharides). The site of increased pyruvylation in the CPS of UR251 was on the terminal galactose of the branch of the repeating oligosaccharide unit. These results show that the level of noncarbohydrate substitutions of the CPS as well as pyruvyl transferase activity are altered in R. trifolii UR251 and that trifoliin A-binding ability and clover root hair attachment are improved in this mutant strain of R. trifolii 0403 rif.
Multiple SecA protein isoforms in Escherichia coli
Authors: Liebke H H
Published: November 2016

To define the anti-SecA-LacZ antiserum, immunoprecipitates produced with either whole anti-SecA-LacZ rabbit antiserum or affinity-purified antibodies were used to analyze nondenatured lysates of Escherichia coli. The antiserum contains antibodies that recognize different proteins. Antibody purified by preadsorption to the SecA-LacZ hybrid protein precipitated only the SecA protein from extracts. In contrast, antibody purified from the intact SecA protein precipitated several additional proteins with SecA protein. Ribosomal protein L7L12 is one of the polypeptides coprecipitated with SecA protein by antibody purified by immunoadsorption to the intact SecA protein as well as by unfractionated anti-SecA-LacZ antiserum. Two-dimensional gel electrophoresis of the SecA protein immunoprecipitated by either antiserum or purified antibody indicated that the SecA protein exists in at least two, and probably four, isoforms. Only one of the SecA isoforms is present in a ribosomal preparation.
Evidence that the Bacteroides thetaiotaomicron chondroitin lyase II gene is adjacent to the chondro-4-sulfatase gene and may be part of the same operon
Authors: Guthrie E P , Salyers A A
Published: November 2016

The chondroitin lyase II gene from Bacteroides thetaiotaomicron has previously been cloned in Escherichia coli on a 7.8-kilobase (kb) fragment (pA818). In E. coli, the chondroitin lyase II gene appeared to be expressed from a promoter that was about 0.5 kb from the beginning of the gene. However, when a subcloned 5-kb fragment from pA818 which contained the chondroitin lyase II gene and the promoter from which the gene is expressed in E. coli was introduced into B. thetaiotaomicron on a multicopy plasmid (pEG800), the chondroitin lyase specific activity of B. thetaiotaomicron was not altered. Further evidence that the promoter that is recognized in E. coli may not be the promoter from which the chondroitin lyase II gene is transcribed in B. thetaiotaomicron was obtained by making an insertion in the B. thetaiotaomicron chromosome at a point which is 1 kb upstream from the chondroitin lyase II gene. This insertion stopped synthesis of the chondroitin lyase II gene product, as would be predicted if the gene was part of an operon and was transcribed in B. thetaiotaomicron from a promoter that was at least 1 kb upstream from the chondroitin lyase II gene. A region of pA818 which was adjacent to the chondroitin lyase II gene and which included the region used to make the insertional mutation was found to code for chondro-4-sulfatase, an enzyme that breaks down one of the products of the chondroitin lyase reaction. The upstream insertion mutant of B. thetaiotaomicron which stopped synthesis of chondroitin lyase II had no detectable chondro-4-sulfatase activity. This mutant was still able to grow on chondroitin sulfate, although the rate of growth was slower than that of the wild type.
Activities of the RNAI and RNAII promoters of plasmid pBR322
Authors: Lin-Chao S , Bremer H
Published: November 2016

The synthesis rates of the replication control RNAs of plasmid pBR322, RNAI, an inhibitor of replication, and RNAII, the preprimer, have been determined by hybridizing in vivo pulse-labeled RNA to specific, single-stranded DNA probes for RNAI and RNAII. In Escherichia coli growing in glycerol minimal medium, RNAI transcripts were made at a rate of one molecule per 30 s per plasmid; RNAII was transcribed fivefold less, at a rate of one molecule per 3 min per plasmid. It is estimated that only 1 in 20 prepriming events leads to replication.
Cloning and characterization of the 5' region of the cell wall protein gene operon in Bacillus brevis 47
Authors: Yamagata H , Adachi T , Tsuboi A , Takao M , Sasaki T , Tsukagoshi N , Udaka S
Published: November 2016

Bacillus brevis 47 secretes vast amounts of proteins derived from both middle wall protein (MWP) and outer wall protein into the medium. The 5' region of the cell wall protein gene operon was cloned into Bacillus subtilis and subsequently into B. brevis 47. On the basis of the nucleotide sequence analysis, an open reading frame coding for MWP was identified on the cloned DNA fragment. Two potential translation initiation sites for the MWP gene are located tandemly in the same reading frame. Each of the sites contains a sequence highly homologous to the 3' end of B. brevis rRNA and an initiation codon. The translational fusion of the 5' region of the MWP gene with the Bacillus licheniformis alpha-amylase gene resulted in the efficient expression of the alpha-amylase gene in B. brevis 47. Of the two potential translation initiation sites, the one located upstream could be eliminated without affecting the expression of the MWP-alpha-amylase fusion gene, suggesting that MWP is synthesized in a precursor form with a signal peptide of 23 amino acid residues. S1 nuclease mapping of the cell wall protein gene transcripts suggested the possibility of the existence of several promoters in the 5' region within 300 base pairs from the translation initiation sites; one promoter was definitely localized within this part of the 5' region, and it was capable of expressing a heterologous gene fusion at a high level. The roles of the apparent structural complexity of the 5' region of the cell wall protein gene operon are discussed in connection with the efficient gene expression.
Chemotaxis in Escherichia coli: construction and properties of lambda tsr transducing phage
Authors: Callahan A M , Frazier B L , Parkinson J S
Published: November 2016

The tsr gene of Escherichia coli, located at approximately 99 min on the chromosomal map, encodes a methyl-accepting protein that serves as the chemoreceptor and signal transducer for chemotactic responses to serine and several repellents. To determine whether any other chemotaxis or motility genes were located in the tsr region, we constructed and characterized two lambda tsr transducing phages that each contain about 12 kilobases of chromosomal material adjacent to tsr. lambda tsr70 carries sequences from the promoter-proximal side of tsr; lambda tsr72 carries sequences from the promoter-distal side of tsr. Restriction maps of the bacterial inserts in these phages and Southern hybridization analyses of the bacterial chromosome indicated that the tsr gene is transcribed in the counterclockwise direction on the genetic map. Insert deletions were isolated in lambda tsr70 and transferred into the host chromosome to examine the null phenotype of tsr. All such strains exhibited wild-type swimming patterns and chemotactic responses to a variety of stimuli, but were specifically defective in serine taxis and other Tsr-mediated responses. In addition, UV programming experiments demonstrated that Tsr and several of its presumptive degradation products were the only bacterial proteins encoded by lambda tsr70 and lambda tsr72 that required host FlbB/FlaI function for expression. These findings indicate that there are probably no other chemotaxis-related genes in the tsr region. A series of tsr point mutations were isolated by propagating lambda tsr70 on a mutD host and used to construct a fine-structure map of the tsr locus. These mutations should prove valuable in exploring structure-function relationships in the Tsr transducer.
Isolation and genetic analysis of mutations allowing the degradation of furans and thiophenes by Escherichia coli
Authors: Abdulrashid N , Clark D P
Published: November 2016

Successive mutations of Escherichia coli yielded a strain that was able to degrade a variety of heterocyclic oxygen- and sulfur-containing ring compounds. In particular, this strain could use both furan-2-carboxylic acid and thiophene-2-carboxylic acid as sole carbon and energy sources. Nitrogen-containing heterocyclic compounds were not degraded. This mutant was isolated by selecting first for oxidation of furan derivatives and then for thiophene degradation. Genetic analysis revealed that mutations in three novel genes, thdA (12 min), thdC (92 min), and thdD (98 min), were required for thiophene degradation. In addition, constitutively at both of the previously characterized fadR and atoC loci was required for efficient thiophene breakdown. The pathway of furan and thiophene degradation remains obscure, but the inability of our mutants to degrade 5-nitro- or 5-bromo-substituted furan derivatives suggests that hydroxylation at position 5 may be involved. Thiophene derivatives were toxic when they were present at concentrations of 0.1% or greater; however, addition of trace amounts of phenylalanine plus tyrosine greatly reduced this effect.
Tn5 insertion in the polynucleotide phosphorylase (pnp) gene in Escherichia coli increases susceptibility to antibiotics
Authors: McMurry L M , Levy S B
Published: November 2016

A Tn5 insertional mutation on the Escherichia coli chromosome which caused a severalfold increase in susceptibility to structurally and functionally diverse antibiotics was found to map within the gene for polynucleotide phosphorylase (pnp) and to inactivate this enzyme, which is involved in RNA breakdown. The mutation also decreased the growth rate 10 to 25% and increased the rate of tetracycline uptake about 30%. The hypersensitivity due to the insertion was only partially complemented by a cloned pnp gene.
Characterization of suppressible mutations in the viomycin phosphotransferase gene of the Streptomyces enteric plasmid pVE138
Authors: Paradiso M J , Roberts G , Streicher S L , Goldberg R B
Published: November 2016

The viomycin phosphotransferase gene (vph) is expressed and confers resistance to viomycin in both Streptomyces spp. and members of the family Enterobacteriaceae. We report the isolation of UGA (opal) and UAG (amber) mutations in the vph gene of shuttle plasmid pVE138. We found that the five UGA mutations in vph resulted in a temperature-sensitive phenotype in Salmonella typhimurium. Su- strains are Vior at 28 degrees C and Vios at 37 degrees C, whereas Su+UGA strains are Vior at both 28 and 37 degrees C. The single amber mutation isolated was not temperature sensitive and resulted in the expected Vios phenotype in Su- strains and Vior in Su+UAG strains.
Cloning of Rhizobium leguminosarum genes for competitive nodulation blocking on peas
Authors: Dowling D N , Samrey U , Stanley J , Broughton W J
Published: November 2016

One type of competitive interaction among rhizobia is that between nonnodulating and nodulating strains of Rhizobium leguminosarum on primitive pea genotypes. Pisum sativum cv. Afghanistan nodulates effectively with R. leguminosarum TOM, and this can be blocked in mixed inoculations by R. leguminosarum PF2, which does not nodulate this cultivar. We termed this PF2 phenotype Cnb+, for competitive nodulation blocking. Strain PF2 contains three large plasmids including a 250-kilobase-pair symbiotic (Sym) plasmid. Transfer of this plasmid, pSymPF2, to nonblocking rhizobia conferred the Cnb+ phenotype on recipients in mixed inoculations on cultivar Afghanistan with TOM. A library of the PF2 genome constructed in the vector pMMB33 was used to isolate two cosmid clones which hybridize to pSymPF2. These cosmids, pDD50 and pDD58, overlapped to the extent of 23 kilobase pairs and conferred a Cnb+ phenotype on recipient Cnb- rhizobia, as did pSD1, a subclone from the common region.
Ultrastructural localization of carbohydrates on thin sections of Staphylococcus aureus with silver methenamine and wheat germ agglutinin-gold complex
Authors: Morioka H , Tachibana M , Suganuma A
Published: November 2016

Postembedding staining of intracellular carbohydrates on thin sections of Staphylococcus aureus was studied by the silver methenamine and the wheat germ agglutinin-gold techniques. Staining of silver grains was observed on both the cell wall and the cross wall. The staining was interpreted to be due to teichoic acid. Labeling by wheat germ agglutinin-gold particles was observed on both the cell wall and the cross wall, and the staining pattern resembled that of silver methenamine staining. Therefore, the labeling was considered to be due to N-acetylglucosamine of teichoic acid. The combination of two types of cytochemical techniques was useful to localize and characterize the carbohydrates of the bacterial cell.
Cloning and expression in Escherichia coli of a Klebsiella ozaenae plasmid-borne gene encoding a nitrilase specific for the herbicide bromoxynil
Authors: Stalker D M , McBride K E
Published: November 2016

An enzyme (nitrilase) that converts the herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) to its metabolite 3,5-dibromo-4-hydroxybenzoic acid was shown to be plasmid encoded in the natural soil isolate Klebsiella ozaenae. The bromoxynil-specific nitrilase was expressed in Escherichia coli by direct transfer and stable maintenance in E. coli of a naturally occurring 82-kilobase K. ozaenae plasmid. Irreversible loss of the ability to metabolize bromoxynil both in E. coli and K. ozaenae was associated with the conversion of the 82-kilobase plasmid to a 68-kilobase species. In E. coli this conversion was the result of a host recA+-dependent recombinational event. A gene, designated bxn, encoding the bromoxynil-specific nitrilase was constitutively expressed in K. ozaenae and E. coli and subcloned on a 2.6-kilobase PstI DNA segment. The polarity and the location of the gene were determined by assaying hybrid constructs of the bromoxynil-specific nitrilase gene fused with the heterologous lac promoter.
Isolation and characterization of an aminolevulinate-requiring Rhodobacter capsulatus mutant
Authors: Wright M S , Cardin R D , Biel A J
Published: November 2016

Using transposon Tn5 mutagenesis, we isolated a mutant strain of Rhodobacter capsulatus that requires aminolevulinate for growth. Southern blot analysis indicated that this strain has a single Tn5 insertion. The addition of 0.1 mM aminolevulinate to the medium allowed the mutant to grow either aerobically or photosynthetically with generation times similar to those of the parental strain. When grown photosynthetically, bacteriochlorophyll accumulation increased with increasing aminolevulinate concentration. The mutant strain had only 10% of the normal aminolevulinate synthase activity, but it had a normal level of porphobilinogen synthase activity. The requirement for aminolevulinate could be satisfied by porphobilinogen, hemin, or protoporphyrin. While the mutant grew well on agar plates containing any of these substrates, growth in liquid media containing hemin or protoporphyrin was poor. Introduction of an R' factor containing all the known R. capsulatus bch genes into the mutant strain did not relieve the requirement for aminolevulinate, suggesting that the Tn5 insertion is not within the bch region.
The mRNA for an inducible chloramphenicol acetyltransferase gene is cleaved into discrete fragments in Bacillus subtilis
Authors: Ambulos N P , Duvall E J , Lovett P S
Published: November 2016

cat-86 is a promoter-deficient plasmid gene that encodes chloramphenicol acetyltransferase (CAT). Insertion of a promoter at a site 144 base pairs 5' to the cat-86 coding sequence activates transcription of the gene and allows cat-86 to specify chloramphenicol-inducible CAT activity in Bacillus subtilis. Induction of cat-86 by chloramphenicol has been shown to result from a regulatory event that activates translation of cat-86 mRNA that is present in cells before the addition of inducer (E. J. Duvall and P. S. Lovett, Proc. Natl. Acad. Sci. USA 83:3939-3943, 1986). In the present study we show an unusual property of cat-86 mRNA. Full-length cat-86 transcripts, consisting of 920 nucleotides (nt), are cleaved in B. subtilis to yield two predominant fragmentation products: an 810-nt species that lacks sequences present at the 5' end of the 920-nt species and a 720-nt species that lacks sequences present at the 3' end of the 920-nt species. A third fragmentation product consisting of 620 nt may result from the cleavage of a single 920-nt transcript at both the 5' and 3' ends. The sequences which are missing from the 720- and 620-nt species suggest that these transcripts cannot be translated into functional CAT. The 810-nt species lacks sequences from the 5' regulatory region, and it is not yet certain whether or not translation of this species can be induced by chloramphenicol. The ratio of 920-nt molecules/720-nt molecules in rifampin-treated cells is increased when the cells are grown in chloramphenicol. Therefore, induction may partially stabilize full-length cat-86 transcripts against inactivation by a novel processing-like system.
Bacillus subtilis rRNA promoters are growth rate regulated in Escherichia coli
Authors: Deneer H G , Spiegelman G B
Published: November 2016

rRNA promoters from the rrnB locus of Bacillus subtilis and from the rrnB locus of Escherichia coli were fused to the gene for chloramphenicol acetyltransferase (CAT). The level of expression of CAT in E. coli showed growth rate dependence when the CAT gene was linked to either E. coli or B. subtilis tandem promoters. The downstream promoter of the tandem Bacillus pair showed growth rate regulation, while the upstream promoter did not, whereas for the E. coli tandem promoters, only the upstream promoter was growth rate regulated.
A new methionine locus, metR, that encodes a trans-acting protein required for activation of metE and metH in Escherichia coli and Salmonella typhimurium
Authors: Urbanowski M L , Stauffer L T , Plamann L S , Stauffer G V
Published: November 2016

We isolated an Escherichia coli methionine auxotroph that displays a growth phenotype similar to that of known metF mutants but has elevated levels of 5,10-methylenetetrahydrofolate reductase, the metF gene product. Transduction analysis indicates that the mutant carries normal metE, metH, and metF genes; the phenotype is due to a single mutation, eliminating the possibility that the strain is a metE metH double mutant; and the new mutation is linked to the metE gene by P1 transduction. Plasmids carrying the Salmonella typhimurium metE gene and flanking regions complement the mutation, even when the plasmid-borne metE gene is inactivated. Enzyme assays show that the mutation results in a dramatic decrease in metE gene expression, a moderate decrease in metH gene expression, and a disruption of the metH-mediated vitamin B12 repression of the metE and metF genes. Our evidence suggests that the methionine auxotrophy caused by the new mutation is a result of insufficient production of both the vitamin B12-independent (metE) and vitamin B12-dependent (metH) transmethylase enzymes that are necessary for the synthesis of methionine from homocysteine. We propose that this mutation defines a positive regulatory gene, designated metR, whose product acts in trans to activate the metE and metH genes.