bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleotide sequence and replication characteristics of RepFIB, a basic replicon of IncF plasmids
Authors: Saul D , Spiers A J , McAnulty J , Gibbs M G , Bergquist P L , Hill D F
Published: November 2016

A second autonomous replicon of P307, RepFIB, has been isolated that has significant homology with other replicons in IncFI group plasmids. Eleven homologous repeats of 21 base pairs are present on the sequence and flank an open reading frame capable of coding for a protein of about Mr = 40,000. This protein was identified by maxicell analysis of cloned RepFIB. A series of deletion mutations of RepFIB were inserted into a DNA polymerase I-dependent vector and examined for their replication proficiency in a polA1 strain. These experiments defined a minimal replication region of 1.6 kilobases which includes the three repeats immediately upstream and downstream of the open reading frame. Deletion of a second set of repeats further downstream doubled the copy number of a chimeric plasmid replicating under RepFIB control. It was concluded that these repeats control the copy number of the replicon. Incompatibility tests showed that all three sets of repeats could express incompatibility with a resident RepFIB plasmid.
Deletion mutants of the Escherichia coli K-12 mannitol permease: dissection of transport-phosphorylation, phospho-exchange, and mannitol-binding activities
Authors: Grisafi P L , Scholle A , Sugiyama J , Briggs C , Jacobson G R , Lengeler J W
Published: November 2016

We have constructed a series of deletion mutations of the cloned Escherichia coli K-12 mtlA gene, which encodes the mannitol-specific enzyme II of the phosphoenolpyruvate (PEP)-dependent carbohydrate phosphotransferase system. This membrane-bound permease consists of 637 amino acid residues and is responsible for the concomitant transport and phosphorylation of D-mannitol in E. coli. Deletions into the 3' end of mtlA were constructed by exonuclease III digestion. Restriction mapping of the resultant plasmids identified several classes of deletions that lacked approximately 5% to more than 75% of the gene. Immunoblotting experiments revealed that many of these plasmids expressed proteins within the size range predicted by the restriction analyses, and all of these proteins were membrane localized, which demonstrated that none of the C-terminal half of the permease is required for membrane insertion. Functional analyses of the deletion proteins, expressed in an E. coli strain deleted for the chromosomal copy of mtlA, showed that all but one of the strains containing confirmed deletions were inactive in transport and PEP-dependent phosphorylation of mannitol, but deletions removing up to at least 117 amino acid residues from the C terminus of the permease were still active in catalyzing phospho exchange between mannitol 1-phosphate and mannitol. A deletion protein that lacked 240 residues from the C terminus of the permease was inactive in phospho exchange but still bound mannitol with high affinity. These experiments localize sites important for transport and PEP-dependent phosphorylation to the extreme C terminus of the mannitol permease, sites important for phospho exchange to between residues 377 and 519, and sites necessary for mannitol binding to the N-terminal 60% of the molecule. The results are discussed with respect to the fact that the mannitol permease consists of structurally independent N- and C-terminal domains.
Genes required for developmental signalling in Myxococcus xanthus: three asg loci
Authors: Kuspa A , Kaiser D
Published: November 2016

asg-carrying strains of Myxococcus xanthus arose in a selection for mutants defective in cell-cell signalling during fruiting body development. All 15 asg mutations examined were found to lie in one of three genetic loci, asgA, asgB, or asgC. The loci were defined by linkage to different insertions of transposon Tn5 and molecular cloning of asgA. asg mutants of all three types were deficient in the aggregation of cells into mounds of the sort that normally give rise to fruiting bodies. asg mutants were also deficient in spore formation; sporulation is normally one of the last steps in fruiting body development. Consistent with a requirement for cell-to-cell signalling, at 1 to 2 h asg+-carrying cells release a material called A-factor that can rescue development of asg mutants. asgA, asgB, and asgC mutants released 5% or less of the asg+ level of A-factor, as measured by bioassay. The experimental results are consistent with the hypothesis that a deficiency in A-factor production or release is the primary developmental defect in asg mutants and that aggregation and sporulation depend on A-factor. asg mutations at all three loci also changed the color and morphology of growing colonies, and failure to release A-factor may itself arise from a defect in growing cells.
Basal-body-associated disks are additional structural elements of the flagellar apparatus isolated from Wolinella succinogenes
Authors: Kupper J , Wildhaber I , Gao Z , Baeuerlein E
Published: November 2016

The intact flagella of Wolinella succinogenes, a gram-negative, anaerobic bacterium with a single polar flagellum, were obtained by an improved procedure, introduced recently by Aizawa et al. (S.-J. Aizawa, G. E. Dean, C. J. Jones, R. M. Macnab, and S. Yamaguchi, J. Bacteriol. 161:836-849, 1985) for the flagellum of Salmonella typhimurium. Disks with a diameter of 130 +/- 30 nm, which were attached to the basal body of the isolated intact flagella, could be identified by electron microscopy as additional structural elements of the bacterial flagellar apparatus. In freeze-dried and metal-shadowed samples, two rings of the basal body were detected on one side and a terminal knob was located on the other side of the disks. Suspension of the flagellar apparatus in acidic solution dissociated the flagellar filaments, yielding hook-basal body complexes with and without the associated disks. If whole cells were subjected to low pH, double disks of the same diameter and with a central hole of about 13 nm could be isolated. Similar parallel disks could be seen also in negatively stained whole cells. When uranyl acetate was used for negative staining of the intact flagella, concentric rings were detected on the disks, similar to the concentric membrane rings found by Coulton and Murray (J. W. Coulton and R. G. E. Murray, J. Bacteriol. 136:1037-1049, 1978) on platelike arrays of proteins in outer membrane preparations of Aquaspirillum serpens. Because the disks of W. succinogenes can be isolated together with the flagellar hook-basal body complex, they appear to be basal-body-rather than secondary membrane-associated structures. It is possible that these disks are the bearing or stator of this rotary device.
Genetic diversity of avian and mammalian Chlamydia psittaci strains and relation to host origin
Authors: Fukushi H , Hirai K
Published: November 2016

Genetic relationships were reported for Chlamydia psittaci derived from psittacine birds, pigeons, turkeys, humans, cats, muskrats, cattle, and sheep and for C. trachomatis, including representative strains of the three biovars, through physical analysis of genomic DNA including DNA fingerprinting with restriction endonuclease SalI, DNA-DNA hybridization in solution with S1 nuclease, and Southern analysis with genomic DNA probes. A total of 26 strains were divided into four groups of C. psittaci and two groups of C. trachomatis, on the basis of DNA fingerprints. The six groups of Chlamydia spp. were related to host origin: two avian groups (Av1 and Av2), one feline and muskrat group (Fe1), one ruminant group (Ru1), one C. trachomatis biovars trachoma and lymphogranuloma group (CtHu), and one C. trachomatis mouse biovar group (CtMo), although an ovine abortion strain belonged to the avian group Av2. DNA-DNA hybridization assay and Southern analysis with genomic DNA probes indicated three DNA homology groups in the genus Chlamydia: an avian-feline group (groups Av1, Av2, and Fe1), a ruminant group (group Ru1), and a C. trachomatis group (groups CtHu and CtMo). Furthermore, the Southern analysis indicated that the homologous sequences (DNA homology of at least 14%) within the avian-feline group were distributed along the whole genome, whereas the homologous sequences (DNA homology of less than 24%) among the three DNA homology groups were localized in distinct regions of the genome DNA. These results suggest that Chlamydia spp. are derived from a common ancestor and have diverged into various groups showing restricted host ranges as a natural characteristic and that the species C. psittaci should be differentiated into groups related to host origin and DNA homology.
Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration
Authors: Dempsey L A , Dubnau D A
Published: November 2016

The plasmid pE194 (3.7 kilobases) is capable of integrating into the genome of the bacterial host Bacillus subtilis in the absence of the major homology-dependent RecE recombination system. Multiple recombination sites have been identified on both the B. subtilis chromosome and pE194 (J. Hofemeister, M. Israeli-Reches, and D. Dubnau, Mol. Gen. Genet. 189:58-68, 1983). The B. subtilis chromosomal recombination sites were recovered by genetic cloning, and these sites were studied by nucleotide sequence analysis. Recombination had occurred between regions of short nucleotide homology (6 to 14 base pairs) as indicated by comparison of the plasmid and the host chromosome recombination sites with the crossover sites of the integration products. Recombination between the homologous sequences of the plasmid and the B. subtilis genome produced an integrated pE194 molecule which was bounded by direct repeats of the short homology. These results suggest a recombination model involving a conservative, reciprocal strand exchange between the two recombination sites. A preferred plasmid recombination site was found to occur within a 70-base-pair region which contains a GC-rich dyad symmetry element. Five of seven pE194-integrated strains analyzed had been produced by recombination at different locations within this 70-base-pair interval, located between positions 860 and 930 in pE194. On the basis of these data, mechanisms are discussed to explain the recombinational integration of pE194.
Localization of the replication origin of plasmid pE194
Authors: Dempsey L A , Dubnau D A
Published: November 2016

The pE194 replication origin was localized to a 265-base-pair interval by analyzing the ability of purified pE194 restriction fragments to direct replication of heterologous plasmids. Replication was dependent upon RepF protein supplied in trans. The origin region contained a GC-rich dyad symmetry which may serve as the RepF target.
appR gene product activates transcription of microcin C7 plasmid genes
Authors: Díaz-Guerra L , Moreno F , San Millán J L
Published: November 2016

Microcin C7 (MccC7) is encoded by Escherichia coli plasmid pMccC7. However, some strains of E. coli K-12 carrying this plasmid do not produce this antibiotic. Here we show that these strains differ in the gene locus appR. This chromosomal gene product controls MccC7 production by activating the transcription of some, but not all, MccC7 plasmid genes.
Control mechanism of the Escherichia coli K-12 cell cycle is triggered by the cyclic AMP-cyclic AMP receptor protein complex
Authors: Utsumi R , Noda M , Kawamukai M , Komano T
Published: November 2016

The role of cyclic AMP (cAMP) in the cell cycle of Escherichia coli K-12 was studied in three mutant strains. One was KI1812, in which the cya promoter is replaced by the lacUV5 promoter. In KI1812, isopropyl-beta-D-thiogalactopyranoside induced the synthesis of cya mRNA, and at the same time cell division was inhibited and short filaments containing multiple nuclei were formed. The other strains were constructed as double mutants (NC6707 cya sulB [ftsZ(Ts)] and TR3318 crp sulB [ftsZ(Ts)]). In both double mutants, filamentation was repressed at 42 degrees C, but it was induced again by addition of cAMP in strain NC6707 and introduction of pHA7 containing wild-type crp in TR3318. These results indicate that lateral wall synthesis in the E. coli cell cycle is triggered by the cAMP-cAMP receptor protein complex.
Proteins that interact with GTP during sporulation of Bacillus subtilis
Authors: Mitchell C , Vary J C
Published: November 2016

During sporulation of Bacillus subtilis, several proteins were shown to interact with GTP in specific ways. UV light was used to cross-link [alpha-32P]GTP to proteins in cell extracts at different stages of growth. After electrophoresis, 11 bands of radioactivity were found in vegetative cells, 4 more appeared during sporulation, and only 9 remained in mature spores. Based on the labeling pattern with or without UV light to cross-link either [alpha-32P]GTP or [gamma-32P]GTP, 11 bands of radioactivity were apparent guanine nucleotide-binding proteins, and 5 bands appeared to be phosphorylated and/or guanylated. Similar results were found with Bacillus megaterium. Assuming that GTP might be a type of signal for sporulation, it could interact with and regulate proteins by at least three mechanisms.
Gene conversion in Escherichia coli: the recF pathway for resolution of heteroduplex DNA
Authors: Fishel R , Kolodner R
Published: November 2016

The independent repair of mismatched nucleotides present in heteroduplex DNA has been used to explain gene conversion and map expansion after general genetic recombination. We have constructed and purified heteroduplex plasmid DNAs that contain heteroallelic 10-base-pair insertion-deletion mismatches. These DNA substrates are similar in structure to the heteroduplex DNA intermediates that have been proposed to be produced during the genetic recombination of plasmids. These DNA substrates were transformed into wild-type and mutant Escherichia coli strains, and the fate of the heteroduplex DNA was determined by both restriction mapping and genetic tests. Independent repair events that yielded a wild-type Tetr gene were observed at a frequency of approximately 1% in both wild-type and recB recC sbcB mutant E. coli strains. The independent repair of small insertion-deletion-type mismatches separated by 1,243 base pairs was found to be reduced by recF, recJ, and ssb single mutations in an otherwise wild-type genetic background and reduced by recF, recJ, and recO mutations in a recB recC sbcB genetic background (the ssb mutation was not tested in the latter background). Independent repair of small insertion-deletion-type mismatched nucleotides that were as close as 312 nucleotides apart was observed. There was no apparent bias in favor of the insertion or deletion of mutant sequences.
Presence of the dnaQ-rnh divergent transcriptional unit on a multicopy plasmid inhibits induced mutagenesis in Escherichia coli
Authors: Foster P L , Sullivan A D , Franklin S B
Published: November 2016

In Escherichia coli the dnaQ+ gene, which encodes epsilon, a fidelity subunit of DNA polymerase III, and the rnh+ gene, which encodes RNase H, share a promoter region but are transcribed in opposite directions. The presence of this divergent transcriptional unit on a multicopy plasmid inhibited by as much as 10-fold mutations induced by the SOS-dependent mutagens methyl methanesulfonate and UV light. Mutations in either gene eliminated the effect, suggesting that both genes contribute either directly or indirectly to the antimutagenic phenotype. Neither survival to mutagen exposure nor induction of the SOS response was comparably affected by the presence of the genes. Although the antimutagenic phenotype was partially suppressed by excess UmuDC proteins, which are required for SOS mutagenesis, the presence of the dnaQ+-rnh+ clone also reduced the induction of mutations by N-methyl-N'-nitro-N-nitrosoguanidine in cells deficient for SOS mutagenic processing. The results suggest that the presence of the dnaQ+-rnh+ divergent transcriptional unit interferes with an underlying mutagenic mechanism that is normally facilitated by the proteins induced as part of the SOS response.
Transfer of tra proteins into the recipient cell during bacterial conjugation mediated by plasmid ColIb-P9
Authors: Rees C E , Wilkins B M
Published: November 2016

Selective transfer of the two products of the ColIb primase gene, sog, from donor to recipient cell during conjugation was demonstrated by two independent methods. The transfer of these tra proteins was unidirectional and dependent on DNA transfer. The Sog polypeptides were localized to the cytoplasm of the donor cell, but they appeared to interact with other tra gene products located in the inner membrane. After cell mating, the transferred polypeptides were found to be in the cytoplasm of the recipient cell, and it is estimated that as many as 500 Sog polypeptides were transferred per round of conjugation. It is proposed that these proteins are transferred as a result of an interaction with the single-stranded DNA and that the transferred strand may be coated with Sog polypeptides.
Plasmid dependence of Pseudomonas sp. strain NK87 enzymes that degrade 6-aminohexanoate-cyclic dimer
Authors: Kanagawa K , Negoro S , Takada N , Okada H
Published: November 2016

A bacterial strain, Pseudomonas sp. strain NK87, that can use 6-aminohexanoate-cyclic dimer as the sole source of carbon and nitrogen was newly isolated from wastewater of a factory which produces nylon-6. Two responsible enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (P-EI) and 6-aminohexanoate-dimer hydrolase (P-EII), were found in the NK87 strain, as is the case with Flavobacterium sp. strain KI72, another 6-aminohexanoate-cyclic-dimer-metabolizing bacterium (H. Okada, S. Negoro, H. Kimura, and S. Nakamura, Nature [London] 306:203-206, 1983). The P-EI enzyme is immunologically identical to the 6-aminohexanoate-cyclic-dimer hydrolase of KI72 (F-EI). However, antiserum against the 6-aminohexanoate-dimer hydrolase purified from KI72 (F-EII) did not react with cell extracts of NK87, indicating that the F-EII and P-EII enzymes are immunologically different. Restriction endonuclease analyses show that the NK87 strain harbors at least six plasmids ranging in size from 20 to 80 kilobase pairs (kbp). The P-EI and P-EII genes were cloned in Escherichia coli. Both the P-EI and F-EI probes strongly hybridized with a 23-kbp plasmid in Southern hybridization analyses. The P-EII probe hybridized specifically with an 80-kbp plasmid, but the F-EII probe hybridized with none of the plasmids harbored in NK87. These results indicate that the P-EI gene and P-EII gene are encoded on the 23-kbp and 80-kbp plasmids, respectively.
High homology between 6-aminohexanoate-cyclic-dimer hydrolases of Flavobacterium and Pseudomonas strains
Authors: Tsuchiya K , Fukuyama S , Kanzaki N , Kanagawa K , Negoro S , Okada H
Published: November 2016

The nucleotide sequences of the genes for 6-aminohexanoate-cyclic-dimer hydrolases of Flavobacterium sp. strain K172 (F-nylA) and Pseudomonas sp. NK87 (P-nylA), enzymes essential for the degradation of a by-product of the nylon-6 industry, were obtained by the dideoxynucleotide chain-termination method. A 1,479-base-pair open reading frame starting at a GTG and terminating at a TGA was found for the both of the genes. The P-nylA and F-nylA genes encoded polypeptides of 493 amino acids and had only 10 base substitutions in the coding region, which caused seven amino acid substitutions.
Purification and properties of L-alanine dehydrogenase of the phototrophic bacterium Rhodobacter capsulatus E1F1
Authors: Caballero F J , Cárdenas J , Castillo F
Published: November 2016

In the phototrophic nonsulfur bacterium Rhodobacter capsulatus E1F1, L-alanine dehydrogenase aminating activity functions as an alternative route for ammonia assimilation when glutamine synthetase is inactivated. L-Alanine dehydrogenase deaminating activity participates in the supply of organic carbon to cells growing on L-alanine as the sole carbon source. L-Alanine dehydrogenase is induced in cells growing on pyruvate plus nitrate, pyruvate plus ammonia, or L-alanine under both light-anaerobic and dark-heterotrophic conditions. The enzyme has been purified to electrophoretic and immunological homogeneity by using affinity chromatography with Red-120 agarose. The native enzyme was an oligomeric protein of 246 kilodaltons (kDa) which consisted of six identical subunits of 42 kDa each, had a Stokes' radius of 5.8 nm, an s20.w of 10.1 S, a D20,w of 4.25 x 10(-11) m2 s-1, and a frictional quotient of 1.35. The aminating activity was absolutely specific for NADPH, whereas deaminating activity was strictly NAD dependent, with apparent Kms of 0.25 (NADPH), 0.15 (NAD+), 1.25 (L-alanine), 0.13 (pyruvate), and 16 (ammonium) mM. The enzyme was inhibited in vitro by pyruvate or L-alanine and had two sulfhydryl groups per subunit which were essential for both aminating and deaminating activities.
Ntr-like promoters and upstream regulatory sequence ftr are required for transcription of a developmentally regulated Caulobacter crescentus flagellar gene
Authors: Mullin D A , Newton A
Published: November 2016

The flbG (hook operon or transcription unit II) and flaN (transcription unit I) operons of Caulobacter crescentus have a -12, -24 nucleotide sequence motif that is very similar to those of the Nif and Ntr promoters of enteric bacteria and Rhizobium spp. and a conserved ftr (flagellar gene transcription regulation) sequence, previously designated II-1 (D. A. Mullin, S. A. Minnich, L.-S. Chen, and A. Newton, J. Mol. Biol. 195:939-943, 1987) at approximately -100. We have used site-directed mutagenesis to examine the role of these sequences in the transcriptional regulation of these periodically expressed flagellar genes. Mutations in the flbG promoter that removed the conserved GC at -12, -13, the GG at -24, -25, or an AC base pair at -18, -19 in the nonconserved sequence between the -12, -24 elements completely eliminated detectable transcription. Mutations at other positions resulted in either a slight decrease (position 26), no change (position 15), or an elevated level (position -16 or -19) of the flbG transcript. By contrast, most of these flbG promoter mutations resulted in greatly elevated levels of transcription from the opposing flaN operon. Similar experiments were used to confirm the location of the flaN promoter to a -12, -24 Nif and Ntr sequence motif. Deletion of all or part of the ftr element or point mutations in the sequence drastically reduced the level of flbG transcript and resulted in increased levels of the flaN transcript. Thus, the conserved sequences at -12 and -24 in flbG and flaN are required for transcription of these genes in vivo, and the ftr element is required for transcription of flbG. This analysis also suggested that the ftr sequence and sequences in the flbG promoter are required for the negative autoregulation of the flbG and flaN operons. We speculate that the flbG and flaN promoters and the ftr element interact in some way to mediate the negative control of these divergent transcription units.
Pseudomonas aeruginosa outer membrane protein F: structural role and relationship to the Escherichia coli OmpA protein
Authors: Woodruff W A , Hancock R E
Published: November 2016

A Pseudomonas aeruginosa outer membrane protein F-deficient omega-insertion mutant strain H636, in contrast to its protein F-sufficient parent strain H103, was unable to grow on unsupplemented Proteose Peptone no. 2 broth (Difco Laboratories, Detroit, Mich.). Addition of high concentrations of NaCl, KCl, glucose, sucrose, or potassium succinate permitted growth of strain H636 at rates approaching those of the parent strain H103. Strain H636 cells were 33% shorter and had a 46% smaller cross-sectional area than did the parent strain growing at similar rates on the same medium. These properties of the oprF::omega mutant were analogous to those previously observed for Escherichia coli ompA mutants in an lpp (Braun lipoprotein-deficient) mutant background. Therefore, we compared P. aeruginosa protein F and the E. coli OmpA protein. In addition to many similarities previously described, sequence alignment demonstrated substantial amino acid sequence homology throughout the carboxy-terminal 168 to 180 amino acids of the two proteins. Consistent with this observation, polyclonal antiserum specific for OmpA reacted on Western blots (immunoblots) with protein F. Expression of protein F from the cloned oprF gene in an E. coli ompA lpp double mutant resulted in a 1.7-fold increase in cell length and a 2.1-fold increase in cross-sectional area compared with values for the same mutant containing only the plasmid vector onto which the oprF gene had been cloned. These results favor a structural role for P. aeruginosa protein F and suggest that it is strongly related to the E. coli OmpA protein.
Functions required for vitamin B12-dependent ethanolamine utilization in Salmonella typhimurium
Authors: Roof D M , Roth J R
Published: November 2016

When B12 is available, Salmonella typhimurium can degrade ethanolamine to provide a source of carbon and nitrogen. B12 is essential since it is a cofactor for ethanolamine ammonia-lyase, the first enzyme in ethanolamine breakdown. S. typhimurium makes B12 only under anaerobic conditions; in the presence of oxygen, exogenous B12 must be provided to permit ethanolamine utilization. Genes required for ethanolamine utilization are encoded in the eut operon. For complementation testing, an F' plasmid containing the eut genes was constructed by transposition of the eut operon (flanked by two Tn10 elements) to an existing F plasmid. Complementation tests defined six genes in the eut operon. Three of these genes encode enzymes known to be involved in degradation of ethanolamine: ethanolamine ammonia-lyase (eutB and eutC) and acetaldehyde dehydrogenase (eutE). One gene (eutR) seems to encode a positive regulatory protein required for induction of transcription of eut. The function of one of the remaining two genes (eutA) was shown to be required for ethanolamine utilization only when cyano-B12 or hydroxy-B12 were the precursors of the adenosyl-B12 cofactor of ethanolamine ammonia-lyase; eutA mutants could use ethanolamine as the nitrogen source only when adenosyl-B12 was provided. No function has been assigned to the eutD gene, which is required for use of ethanolamine as a carbon source. Ethanolamine uptake assays of eut mutants suggest that no ethanolamine permease is encoded in the eut operon.
Alp, a suppressor of lon protease mutants in Escherichia coli
Authors: Trempy J E , Gottesman S
Published: November 2016

Escherichia coli lon mutants lack a major ATP-dependent protease, are sensitive to UV light and methylmethane sulfonate (MMS), and overproduce capsular polysaccharide. Evidence is presented that an activity (Alp), cloned on a multicopy plasmid, can suppress the phenotypes of lon mutants. The sensitivity to UV and MMS is a reflection of the stabilization of the cell division inhibitor SulA, while the capsule overproduction arises through the stabilization of a transcriptional activator of capsule biosynthetic genes, RcsA. Multicopy alp (pAlp) suppressed capsule formation in delta lon cells, and delta lon cells containing the pAlp plasmid were resistant to MMS treatment. The MMS resistance of delta lon pAlp+ cells correlates with an increase in the degradation of SulA to that found in lon+ cells. Lon-directed degradation of SulA was energy dependent, as was the increase in degradation of SulA in delta lon pAlp+ cells. alp maps close to pheA, at 57 min on the E. coli chromosome. Although pAlp can substitute for Lon, cells lacking alp activity did not have the phenotype on a lon mutant. This study demonstrates that at least one activity, when overproduced in the cell, can substitute for Lon protease.
Recruitment of a chromosomally encoded maleylacetate reductase for degradation of 2,4-dichlorophenoxyacetic acid by plasmid pJP4
Authors: Kukor J J , Olsen R H , Siak J S
Published: November 2016

When Pseudomonas aeruginosa PAO1c or P. putida PPO200 or PPO300 carry plasmid pJP4, which encodes enzymes for the degradation of 2,4-dichlorophenoxyacetic acid (TFD) to 2-chloromaleylacetate, cells do not grow on TFD and UV-absorbing material with spectral characteristics of chloromaleylacetate accumulates in the culture medium. Using plasmid pRO1727, we cloned from the chromosome of a nonfluorescent pseudomonad, Pseudomonas sp. strain PKO1, 6- and 0.5-kilobase BamHI DNA fragments which contain the gene for maleylacetate reductase. When carrying either of the recombinant plasmids, pRO1944 or pRO1945, together with pJP4, cells of P. aeruginosa or P. putida were able to utilize TFD as a sole carbon source for growth. A novel polypeptide with an estimated molecular weight of 18,000 was detected in cell extracts of P. aeruginosa carrying either plasmid pRO1944 or plasmid pRO1945. Maleylacetate reductase activity was induced in cells of P. aeruginosa or P. putida carrying plasmid pRO1945, as well as in cells of Pseudomonas strain PKO1, when grown on L-tyrosine, suggesting that the tyrosine catabolic pathway might be the source from which maleylacetate reductase is recruited for the degradation of TFD in pJP4-bearing cells of Pseudomonas sp. strain PKO1.
Localization and regulation of bacteriophage Mu promoters
Authors: Stoddard S F , Howe M M
Published: November 2016

Mu promoters active during the lytic cycle were located by isolating RNA at various times after induction of Mu prophages, radiolabeling it by capping in vitro, and hybridizing it to Mu DNA fragments on Southern blots. Signals were detected from four new promoters in addition to the previously characterized Pe (early), PcM (repressor), and Pmom (late) promoters. A major signal upstream of C was first observed at 12 min and intensified thereafter with RNA from cts and C amber but not replication-defective prophages; these characteristics indicate that this signal arises from a middle promoter, which we designate Pm. With 20- and 40-min RNA, four additional major signals originated in the C-lys, F-G-I, N-P, and com-mom regions. These signals were missing with RNA from C amber and replication-defective prophages and therefore reflected the activity of late promoters, one of which we presume was Pmom. Uninduced lysogens showed weak signals from five regions, one from the early regulatory region, three between genes B and lys, and one near the late genes K, L, and M. The first of these probably resulted from PcM activity; the others remain to be identified.
Requirement for autoinducer in transcriptional negative autoregulation of the Vibrio fischeri luxR gene in Escherichia coli
Authors: Dunlap P V , Ray J M
Published: November 2016

The effect of a mutation in luxI (autoinducer synthetase gene) on transcription of luxR in the cloned Vibrio fischeri lux system (luxR, luxICDABE) was examined in Escherichia coli. For the luxI mutant, transcription from the luxR promoter (monitored with beta-galactosidase levels from a luxR::lacZ fusion, with LuxR supplied in trans) decreased fivefold, to levels of the luxI+ strain, only in the presence of added autoinducer. The results demonstrate that, as has been shown at the translational level, autoinducer is required for negative autoregulation of luxR at the transcriptional level.
Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome
Authors: Nakata A , Amemura M , Makino K
Published: November 2016

Between 59 and 60 min on the Escherichia coli genetic map, there is a highly conserved sequence of 29 base pairs, containing an inverted repeat of seven base pairs that appears 14 times, 32 or 33 base pairs apart, downstream of the iap gene coding region. About 24 kilobase pairs downstream of the 14 repeats, a similar 29-base-pair sequence with a spacing of 32 base pairs appears seven times. Nucleotide sequences hybridizing with the 29-base-pair fragment were also detected in Shigella dysenteriae and Salmonella typhimurium but not in Klebsiella pneumoniae or Pseudomonas aeruginosa.
Intergeneric conjugation between Escherichia coli and Streptomyces species
Authors: Mazodier P , Petter R , Thompson C
Published: November 2016

We have constructed Escherichia coli-Streptomyces shuttle plasmids which are capable of conjugal transfer from E. coli to Streptomyces spp. These plasmids contained the pBR322 and pIJ101 origins of replication and the RK2 (IncP) origin of transfer. The transfer of plasmid was specifically dependent the presence of a 760-base-pair, cis-acting, oriT-containing fragment and on RP4 (IncP) functions supplied in trans. Conditions of mating and selection of exconjugants were analyzed with Streptomyces lividans as recipient. Plasmid transfer to other Streptomyces species was also demonstrated.
Isolation and characterization of isoprene mutants of Escherichia coli
Authors: Sherman M M , Petersen L A , Poulter C D
Published: November 2016

Isoprenoid compounds are found in all organisms. In Escherichia coli the isoprene pathway has three distinct branches: the modification of tRNA; the respiratory quinones ubiquinone and menaquinone; and the dolichols, which are long-chain alcohols involved in cell wall biosynthesis. Very little is known about procaryotic isoprene biosynthesis compared with what is known about eucaryote isoprene biosynthesis. This study approached some of the questions about isoprenoid biosynthesis and regulation in procaryotes by isolating and characterizing mutants in E. coli. Mutants were selected by determining their resistance to low levels of aminoglycoside antibiotics, which require an electron transport chain for uptake into bacterial cells. The mutants were characterized with regard to their phenotypes, map positions, enzymatic activities, and total ubiquinone content. In particular, the enzymes studied were isopentenyldiphosphate delta-isomerase (EC 5.3.3.2), farnesyldiphosphate synthetase (EC 2.5.1.1), and higher prenyl transferases.
Localization of the ribosome-releasing factor gene in the Escherichia coli chromosome
Authors: Ichikawa S , Ryoji M , Siegfried Z , Kaji A
Published: November 2016

The ribosome-releasing factor (RRF) gene was localized at a position between 2 and 6 min on the Escherichia coli chromosome by measuring the gene-dosage-dependent production of RRF in various E. coli F' merozygotes. This position was confirmed and refined by using a nucleotide probe corresponding to a 16-amino-acid sequence in RRF. It was found that the RRF gene was contained in pLC 6-32 of the Clark-Carbon Gene Bank. Restriction enzyme mapping of E. coli genomic DNA with the above probe led us to conclude that the RRF gene is situated in the 4-min region, somewhere downstream (clockwise) of the elongation factor Ts gene, tsf. A pLC 6-32-derived DNA fragment which carries the RRF gene was found to contain a partial sequence of tsf. The exact location of the translational initiation site of the RRF gene was determined to be 1.1 kilobases downstream from the translational termination site of tsf. The RRF gene is designated frr.
Multiple defects in Escherichia coli mutants lacking HU protein
Authors: Huisman O , Faelen M , Girard D , Jaffé A , Toussaint A , Rouvière-Yaniv J
Published: November 2016

The HU protein isolated from Escherichia coli, composed of two partially homologous subunits, alpha and beta, shares some of the properties of eucaryotic histones and is a major constituent of the bacterial nucleoid. We report here the construction of double mutants totally lacking both subunits of HU protein. These mutants exhibited poor growth and a perturbation of cell division, resulting in the formation of anucleate cells. In the absence of HU, phage Mu was unable to grow, to lysogenize, or to carry out transposition.
Cloning and sequencing of the gltX gene, encoding the glutamyl-tRNA synthetase of Rhizobium meliloti A2
Authors: Laberge S , Gagnon Y , Bordeleau L M , Lapointe J
Published: November 2016

The gltX gene, coding for the glutamyl-tRNA synthetase of Rhizobium meliloti A2, was cloned by using as probe a synthetic oligonucleotide corresponding to the amino acid sequence of a segment of the glutamyl-tRNA synthetase. The codons chosen for this 42-mer were those most frequently used in a set of R. meliloti genes. DNA sequence analysis revealed an open reading frame of 484 codons, encoding a polypeptide of Mr 54,166 containing the amino acid sequences of an NH2-terminal and various internal fragments of the enzyme. Compared with the amino acid sequence of the glutamyl-tRNA synthetase of Escherichia coli, the N-terminal third of the R. meliloti enzyme was strongly conserved (52% identity); the second third was moderately conserved (38% identity) and included a few highly conserved segments, whereas no significant similarity was found in the C-terminal third. These results suggest that the C-terminal part of the protein is probably not involved in the recognition of substrates, a feature shared with other aminoacyl-tRNA synthetases.
Genetic analysis of transcriptional activation and repression in the Tn21 mer operon
Authors: Ross W , Park S J , Summers A O
Published: November 2016

Transcription of the Tn21 mercury resistance operon (mer) is controlled by the toxic metal cation Hg(II). This control is mediated by the product of the merR gene, a 144-amino-acid protein which represses transcription of the structural genes (merTPCAD) in the absence of Hg(II) and activates transcription in the presence of Hg(II). We have used a mer-lac transcriptional fusion to obtain regulatory mutants in this metal-responsive system. Some mutants were defective in Hg(II)-induced activation while retaining repression function (a- r+), others were defective in repression but not activation (a+ r-), and some had lost both functions (a- r-). Mutations in three of the four cysteine residues of merR resulted in complete loss of Hg(II)-inducible activation but retention of the repressor function, suggesting that these residues serve as ligands for Hg(II) in the activation process. Other lesions adjacent to or very near these cysteines exhibited severely reduced activation and also retained repressor function. There were two putative helix-turn-helix (HTH) domains in merR, and mutants in each had very different phenotypes. A partially dominant mutation in the more amino-terminal region of the two putative HTH regions resulted in loss of both activation and repression (a- r-), consistent with a role for this region in DNA binding. Mutations in the more centrally located HTH region resulted only in loss of Hg(II)-induced activation (a- r+). Lesions in the central and in the carboxy-terminal regions of merR exhibited both Hg(II)-independent and Hg(II)-dependent transcriptional activation, suggesting that elements important in the activation mechanism may be widely distributed in this relatively small protein. The sole cis-acting mutant obtained with this operon fusion strategy, a down-promoter mutation, lies in a highly conserved base in the -35 region of the merTPCAD promoter.
Isolation of nit-4, the minor nitrogen regulatory gene which mediates nitrate induction in Neurospora crassa
Authors: Fu Y H , Kneesi J Y , Marzluf G A
Published: November 2016

Expression of nitrate reductase in Neurospora crassa requires the positive action of nit-4, a pathway-specific regulatory gene, which mediates nitrate induction. We report the molecular cloning of the nit-4 gene and present results which suggest that the nit-4 gene is constitutively expressed to yield a low-abundance 2.2-kilobase transcript. These results indicate that the nit-2 major control gene and the nit-4 pathway-specific control gene independently regulate the expression of the nitrate assimilatory structural genes.
Temperature inhibition of siderophore production in Azospirillum brasilense
Authors: Bachhawat A K , Ghosh S
Published: November 2016

The effect of growth at 42 degrees C on the different components of the siderophore-mediated iron transport that are induced by iron limitation in Azospirillum brasilense was examined. Biosynthesis of the siderophore spirilobactin was strongly inhibited (20-fold) by growth at 42 degrees C, whereas the transport of iron by the ferric-spirilobactin transport system and the induction of the iron-regulated outer membrane proteins were unaffected.
Characterization of two mutant metJ proteins with reduced, temperature-dependent capacity to regulate Escherichia coli K-12 met regulon elements
Authors: Bala G A , Collier C D , Emmett M R , Johnson J R
Published: November 2016

At 28 degrees C, but not at 34 or 42 degrees C, strains with the metJ193 allele repressed chromosomal met genes but not a plasmid-borne met promoter. Increasing the metJ193 gene dosage to two copies resulted in overrepression of chromosomal and plasmid-borne met promoters at 28 degrees C. Suppressing the metJ185 amber mutation with supF (tRNATyr) produced the MetJ185F protein. Strains producing MetJ185F repressed chromosomal met promoters but not a plasmid-borne met promoter at 42 degrees C. These are the first known defective MetJ proteins with documented temperature-dependent function.
Mutagenesis of the Tra1 core region of RK2 by using Tn5: identification of plasmid-specific transfer genes
Authors: Guiney D G , Deiss C , Simnad V , Yee L , Pansegrau W , Lanka E
Published: November 2016

The conjugation system of the IncP alpha plasmid RK2/RP4 is encoded by transfer regions designated Tra1, Tra2, and Tra3. The Tra1 core region, cloned on plasmid pDG4 delta 22, consists of the origin of transfer (oriT) and 2.6 kilobases of flanking DNA providing IncP alpha plasmid-specific functions that allow pDG4 delta 22 to be mobilized by the heterologous IncP beta plasmid R751. Tn5 insertions in pDG4 delta 22 define a minimal 2.2-kilobase region required for plasmid-specific transfer of oriT. The Tra1 core contains the traJ and traK genes as well as an 18-kilodalton open reading frame downstream of traJ. The traJ and traK genes were shown to be required for transfer by complementation of inserts within these genes. Genetic evidence for the role of the 18-kilodalton open reading frame in transfer was obtained, although this protein has not been detected in cell lysates. These studies indicate that at least three transfer proteins are involved in plasmid-specific interactions at oriT.
Developmental regulation of a Rhizobium cell surface antigen during growth of pea root nodules
Authors: VandenBosch K A , Brewin N J , Kannenberg E L
Published: November 2016

A monoclonal antibody, AFRC MAC 203, was used to examine the expression of a nodule-induced cell surface antigen associated with lipopolysaccharide in Rhizobium leguminosarum bv. viciae 3841. Silver-enhanced immunogold-labeled tissue sections revealed that, in very young tissues of pea root nodules, the nodule-induced form of lipopolysaccharide antigen was not expressed either by rhizobia in the infection thread or by bacteria recently released into the plant cell cytoplasm. In the more mature regions of the nodule, the antigen was expressed by membrane-enclosed bacteroids, including immature forms that had not yet expressed the enzyme nitrogenase and were not yet Y shaped. Immunogold labeling of thin sections revealed that the MAC 203 antigen, but not the nitrogenase, was also expressed by bacteria in infection threads situated in and between bacteroid-containing plant cells in mature nodule tissue.
Cell length, nucleoid separation, and cell division of rod-shaped and spherical cells of Escherichia coli
Authors: Donachie W D , Begg K J
Published: November 2016

By comparing the dimensions and DNA contents of normal rod-shaped Escherichia coli with those of mutants that grow as spheres or ellipsoids, we have determined that two parameters remain unchanged: the DNA/mass ratio and the average cell length (diameter, for spherical cells). In consequence, the average volumes and DNA contents of the spherical mutant cells are about four to six times greater than those of rod-shaped cells growing at a similar rate. In addition, it was found that cells of both rod and sphere forms had approximately the same number of nucleoids (as seen when the DNA was condensed after inhibition of protein synthesis). The nucleoids of the spherical cells therefore consist of four to six completed chromosomes each (polytene nucleoids). We suggest that the attainment of a minimum cell length is necessary for nucleoid separation after chromosome replication and that such a separation is itself a prerequisite for septum formation.
Nucleotide sequence of the transcriptional control region of the osmotically regulated proU operon of Salmonella typhimurium and identification of the 5' endpoint of the proU mRNA
Authors: Overdier D G , Olson E R , Erickson B D , Ederer M M , Csonka L N
Published: November 2016

Southern blot analysis of 15 proU transposon insertions in Salmonella typhimurium indicated that this operon is at least 3 kilobase pairs in length. The nucleotide sequence of 1.5-kilobase-pair fragment that contains the transcriptional control region of the proU operon and the coding sequences specifying 290 amino acids of the first structural gene of the operon was determined. The predicted amino acid sequence of the product of this gene shows extensive similarity to the HisP, MalK, and other proteins that are inner membrane-associated components of binding protein-dependent transport systems. S1 mapping and primer extension analysis of the proU mRNAs revealed several species with different 5' ends. Two of these endpoints are sufficiently close to sequences that have weak similarities to the consensus -35 and -10 promoter sequences that they are likely to define two transcription start sites. However, we cannot rule out the possibility that some or all of the 5' endpoints detected arose as a result of the degradation of a longer mRNA. The expression of proU-lacZ operon fusions located on plasmids was normal in S. typhimurium regardless of the plasmid copy number. The sequences mediating normal, osmoregulated expression of the proU operon were shown by subcloning to be contained on an 815-base-pair fragment. A 350-base-pair subclone of this fragment placed onto a lacZ expression vector directed a high-level constitutive expression of beta-galactosidase, suggesting that there is a site for negative regulation in the proU transcriptional control region which has been deleted in the construction of this plasmid.
Structure and expression of the cytochrome aa3 regulatory gene ctaA of Bacillus subtilis
Authors: Mueller J P , Taber H W
Published: November 2016

Mutations that define the ctaA gene of Bacillus subtilis block cytochrome aa3 formation and sporulation. We have recently described the isolation and initial characterization of the ctaA locus. Analysis of in vivo mRNA transcripts by RNase protection experiments located the 5' and 3' termini of the ctaA transcript, confirming a monocistronic structure. By using a nuclease protection assay, an increase in the abundance of steady-state ctaA mRNA was observed during the initiation of sporulation, followed by a decrease during subsequent stages. Transcripts originating from the ctaA gene were most abundant 2.0 h after the end of exponential growth. This pattern of ctaA mRNA accumulation was confirmed by coupling the transcription of the ctaA gene to lacZ in an integrative plasmid vector. Expression of ctaA was not repressed by glucose and was independent of the spoOA and spoOH (sigH) gene products. Postexponential expression was found to be dependent on the product of the strC gene. The expression of ctaA appears to be regulated in a growth stage-specific manner. The transcriptional start site, identified by high-resolution S1 nuclease protection experiments, was preceded by a single sigma A-dependent promoter sequence.