Efficient Transfer of the Pheromone-Independent Enterococcus faecium Plasmid pMG1 (Gmr) (65.1 Kilobases) to Enterococcus Strains during Broth Mating

Plasmid pMG1 (65.1 kb) was isolated from a gentamicin-resistant Enterococcus faecium clinical isolate and was found to encode gentamicin resistance. EcoRI restriction of pMG1 produced five fragments, A through E, with molecular sizes of 50.2, 11.5, 2.0, 0.7, and 0.7 kb, respectively. The clockwise order of the fragments was ACDEB. pMG1 transferred at high frequency to Enterococcus strains in broth mating. pMG1 transferred between Enterococcus faecalis strains, between E. faecium strains, and between E. faecium and E. faecalis strains at a frequency of approximately 10⁻⁴ per donor cell after 3 h of mating. The pMG1 transfers were not induced by the exposure of the donor cell to culture filtrates of plasmid-free E. faecalis FA2-2 or an E. faecium strain. Mating aggregates were not observed by the naked eye during broth mating. Small mating aggregates of several cells in the broth matings were observed by microscopy, while no aggregates of donor cells which had been exposed to a culture filtrate of E. faecalis FA2-2 or an E. faecium strain were observed, even by microscopy. pMG1 DNA did not show any homology in Southern hybridization with that of the pheromone-responsive plasmids and broad-host-range plasmids pAMβ1 and pIP501. These results indicate that there is another efficient transfer system in the conjugative plasmids of Enterococcus and that this system is different from the pheromone-induced transfer system of E. faecalis plasmids.     

pMG7-mediated restriction of Pseudomonas aeruginosa phage DNAs is determined by a class II restriction endonuclease.

A class II restriction endonuclease, PaeR7, has been isolated from a Pseudomonas aeruginosa strain containing the resistance plasmid pMG7. The activity cannot be isolated from an isogenic strain which does not contain this resistance plasmid. EndoR· PaeR7 requires Mg²⁺ for activity but does not require ATP or S-adenosyl-l-methionine. Specific digestion patterns are produced upon agarose gel electrophoresis of substrate DNAs which have been digested with the enzyme. The enzyme is the biochemical basis for the pMG7-mediated phage interference reported by Jacoby and Sutton (1977). DNAs isolated from restricted phages act as substrates for the enzyme while DNAs isolated from unrestricted phages and phages which have been modified by growth on strains containing pMG7 do not act as substrates for the enzyme.     

Transfer of IncP Plasmids to Extremely Acidophilic Thiobacillus thiooxidans

The broad-host-range IncP plasmids RP4, R68.45, RP1::Tn501, and and pUB307 were transferred directly to extremely acidophilic Thiobacillus thiooxidans from Escherichia coli by conjugation at frequencies of 10^-5 to 10^-7 per recipient. The ability of T. thiooxidans to receive and express the antibiotic resistance markers was examined. The plasmid RP4 was transferred back to E. coli from T. thiooxidans at a frequency of 1.0 × 10^-3 per recipient.     

Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes

The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7^Mtu and Rps7^Zma) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes.     

Isolation and Molecular Characterization of pMG160, a Mobilizable Cryptic Plasmid from Rhodobacter blasticus

A 3.4-kb cryptic plasmid was obtained from a new isolate of Rhodobacter blasticus. This plasmid, designated pMG160, was mobilizable by the conjugative strain Escherichia coli S17.1 into Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodopseudomonas palustris. It replicated in the latter strains but not in Rhodospirillum rubrum, Rhodocyclus gelatinosus, or Bradyrhizobium species. Plasmid pMG160 was stably maintained in R. sphaeroides for more than 100 generations in the absence of selection but showed segregational instability in R. palustris. Instability in R. palustris correlated with a decrease in plasmid copy number compared to the copy number in R. sphaeroides. The complete nucleotide sequence of plasmid pMG160 contained three open reading frames (ORFs). The deduced amino acid sequences encoded by ORF1 and ORF2 showed high degrees of homology to the MobS and MobL proteins that are involved in plasmid mobilization of certain plasmids. Based on homology with the Rep protein of several other plasmids, ORF3 encodes a putative rep gene initiator of plasmid replication. The functions of these sequences were demonstrated by deletion mapping, frameshift analysis, and analysis of point mutations. Two 6.1-kb pMG160-based E. coli-R. sphaeroides shuttle cloning vectors were constructed and designated pMG170 and pMG171. These two novel shuttle vectors were segregationally stable in R. sphaeroides growing under nonselective conditions.     

Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria.     

Detection of Plasmid Transfer from Pseudomonas fluorescens to Indigenous Bacteria in Soil by Using Bacteriophage φR2f for Donor Counterselection

The transfer of a genetically marked derivative of plasmid RP4, RP4p, from Pseudomonas fluorescens to members of the indigenous microflora of the wheat rhizosphere was studied by using a bacteriophage that specifically lyses the donor strain and a specific eukaryotic marker on the plasmid. Transfer of RP4p to the wheat rhizosphere microflora was observed, and the number of transconjugants detected was approximately 10³ transconjugants per g of soil when 10⁷ donor cells per g of soil were added; transfer in the corresponding bulk soil was slightly above the limit of detection. All of the indigenous transconjugants which we analyzed contained a 60-kb plasmid and were able to transfer this plasmid to a Nx^r Rp^rP. fluorescens recipient strain. The indigenous transconjugants were identified as belonging to Pseudomonas spp., Enterobacter spp., Comamonas spp., and Alcaligenes spp.     

Biochar Enhances Aspergillus niger Rock Phosphate Solubilization by Increasing Organic Acid Production and Alleviating Fluoride Toxicity

During fungal rock phosphate (RP) solubilization, a significant quantity of fluoride (F⁻) is released together with phosphorus (P), strongly inhibiting the process. In the present study, the effect of two F⁻ adsorbents [activated alumina (Al₂O₃) and biochar] on RP solubilization by Aspergillus niger was examined. Al₂O₃ adsorbed part of the F⁻ released but also adsorbed soluble P, which makes it inappropriate for microbial RP solubilization systems. In contrast, biochar adsorbed only F⁻ while enhancing phosphate solubilization 3-fold, leading to the accumulation of up to 160 mg of P per liter. By comparing the values of F⁻ measured in solution at the end of incubation and those from a predictive model, it was estimated that up to 19 mg of F⁻ per liter can be removed from solution by biochar when added at 3 g liter⁻¹ to the culture medium. Thus, biochar acted as an F⁻ sink during RP solubilization and led to an F⁻ concentration in solution that was less inhibitory to the process. In the presence of biochar, A. niger produced larger amounts of citric, gluconic, and oxalic acids, whether RP was present or not. Our results show that biochar enhances RP solubilization through two interrelated processes: partial removal of the released F⁻ and increased organic acid production. Given the importance of organic acids for P solubilization and that most of the RPs contain high concentrations of F⁻, the proposed solubilization system offers an important technological improvement for the microbial production of soluble P fertilizers from RP.     

Fungal rock phosphate solubilization using sugarcane bagasse

The effects of different doses of rock phosphate (RP), sucrose, and (NH₄)₂SO₄ on the solubilization of RP from Araxá and Catal?o (Brazil) by Aspergillus niger, Penicillium canescens, Eupenicillium ludwigii, and Penicillium islandicum were evaluated in a solid-state fermentation (SSF) system with sugarcane bagasse. The factors evaluated were combined following a 2³?+?1 factorial design to determine their optimum concentrations. The fitted response surfaces showed that higher doses of RP promoted higher phosphorus (P) solubilization. The addition of sucrose did not have effects on P solubilization in most treatments due to the presence of soluble sugars in the bagasse. Except for A. niger, all the fungi required high (NH₄)₂SO₄ doses to achieve the highest level of P solubilization. Inversely, addition of (NH₄)₂SO₄ was inhibitory to P solubilization by A. niger. Among the fungi tested, A. niger stood out, showing the highest solubilization capacity and for not requiring sucrose or (NH₄)₂SO₄ supplementation. An additional experiment with A. niger showed that the content of soluble P can be increased by adding higher RP doses in the medium. However, P yield decreases with increasing RP doses. In this experiment, the maximal P yield (approximately 60?%) was achieved with the lower RP dose (3?g?L^?1). Our results show that SSF can be used to obtain a low cost biofertilizer rich in P combining RP, sugarcane bagasse, and A. niger. Moreover, sugarcane bagasse is a suitable substrate for SSF aiming at RP solubilization, since this residue can supply the C and N necessary for the metabolism of A. niger within a range that favors RP solubilization.     

Chromosome transfer and R-prime formation by an RP4::mini-Mu derivative in Escherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, and Proteus mirabilis

We have introduced into the wide host range conjugative plasmid RP4, a mini-Mu derivative which was known to be able to transpose spontaneously in E. coli K-12, and to induce in such a host several kinds of chromosomal rearrangements including replicon fusions. Unlike RP4, RP4::mini-Mu can mediate the transfer of the host chromosome to a recipient bacterium and generate R primes at high frequencies (10^?4 for the transfer of a given marker, 10^?5 for the formation of R primes carrying a given marker). Two such RP4::mini-Mu plasmids were introduced into one Salmonella typhimurium strain, one Klebsiella pneumoniae strain, and one Proteus mirabilis strain. Each of these three strains were mated with an E. coli K-12 recipient and transconjugants carrying R primes were recovered in all three cases at frequencies ranging from 5 × 10^?6 to 10^?7.     

Restriction-modification systems determined by Pseudomonas plasmids

Four additional Pseudomonas R plasmids determining the PaeR7 restriction-modification system have been detected. All are transfer deficient and appear to belong to the same incompatibility group. The Pseudomonas fertility plasmid FP110 determines a different restriction-modification system and also inhibits the propagation of phage B39 by a separate mechanism. Pseudomonas R plasmid pMG73 has a third distinct restriction-modification specificity. PaeFP110 and PaeR73 are proposed as designations for these new plasmid-determined systems for restriction and modification.     

Rock phosphate solubilization by four yeast strains

The solubilization of rock phosphate (RP) by four yeast strains, Rhodotorula sp., Candida rugosa, Saccharomyces cerevisiae and Saccharomyces rouxii, which were isolated from wheat rhizospheric soils, was investigated in this study. The yeast isolates demonstrated diverse levels of soluble phosphate releasing abilities in modified Pikovskaya liquid medium containing RP as sole phosphate source. C. rugosa was the most effective solubilizer under different conditions, followed by Rhodotorula sp., S. rouxii and S. cerevisiae. Acidification of the broth seemed to be the major mechanism for RP solubilization by the yeast isolates, and the increase in soluble phosphate released was correlated significantly with an increase in titratable acidity and a drop in pH. The optimal composition for the solubilization of RP by the yeast isolates in the broth was 20 g L^?1 glucose, 1 g L^?1 yeast extract, 0.5 g L^?1 (NH₄)₂SO₄, and 5 g L^?1 RP, respectively. The yeast isolates were able to solubilize RP at wide range of temperature and initial pH, with the maximum percentage of soluble phosphate released being recorded at 30–35 °C and pH 5–6, respectively.     

IncP Plasmids Are Unusually Effective in Mediating Conjugation of Escherichia coli and Saccharomyces cerevisiae: Involvement of the Tra2 Mating System

Mobilizable shuttle plasmids containing the origin-of-transfer (oriT) region of plasmids F (IncFI), ColIb-P9 (IncI1), and RP4/RP1 (IncPα) were constructed to test the ability of the cognate conjugation system to mediate gene transfer from Escherichia coli to Saccharomyces cerevisiae. Only the Pα system caused detectable mobilization to yeast, giving peak values of 5 × 10⁻⁵ transconjugants per recipient cell in 30 min. Transfer of the shuttle plasmid required carriage of oriT in cis and the provision in trans of the Pα Tra1 core and Tra2 core regions. Genes outside the Tra1 core did not increase the mobilization efficiency. All 10 Tra2 core genes (trbB, -C, -D, -E, -F, -G, -H, -I, -J, and -L) required for plasmid transfer to E. coli K-12 were needed for transfer to yeast. To assess whether the mating-pair formation (Mpf) system or DNA-processing apparatus of the Pα conjugation system is critical in transkingdom transfer, an assay using an IncQ-based shuttle plasmid specifying its own DNA-processing system was devised. RP1 but not ColIb mobilized the construct to yeast, indicating that the Mpf complex determined by the Tra2 core genes plus traF is primarily responsible for the remarkable fertility of the Pα system in mediating gene transfer from bacteria to eukaryotes.     

Overexpression of SOD in retina: need for increase in H2O2-detoxifying enzyme in same cellular compartment

In retinitis pigmentosa (RP), various mutations cause rod photoreceptor cell death leading to increased oxygen levels in the outer retina, progressive oxidative damage to cones, and gradual loss of cone cell function. We have been exploring the potential of overexpressing components of the endogenous antioxidant defense system to preserve cone cell function in rd10^+/+ mice, a model of RP. rd10^+/+ mice deficient in superoxide dismutase 1 (SOD1) showed increased levels of superoxide radicals and carbonyl adducts (a marker of oxidative damage) in the retina and more rapid loss of cone function than rd10^+/+ mice with normal levels of SOD1. This suggests that SOD1 is an important component of the antioxidant defense system of cones, but increased expression of SOD1 in rd10^+/+ mice increased oxidative damage and accelerated the loss of cone function. Coexpression of SOD1 with glutathione peroxidase 4 (Gpx4), which like SOD1 is localized in the cytoplasm, but not with catalase targeted to the mitochondria, reduced oxidative damage in the retina and significantly slowed the loss of cone cell function in rd10^+/+ mice. Gene transfer resulting in increased expression of SOD2, but not coexpression of SOD2 and mitochondrial Gpx4, resulted in high levels of H₂O₂ in the retina. These data suggest that to provide benefit in RP, overexpression of an SOD must be combined with expression of a peroxide-detoxifying enzyme in the same cellular compartment.     

Conjugal Transfer of Megaplasmid 2 between Rhizobium meliloti Strains in Alfalfa Nodules

A DNA fragment containing the RP4 mob function, as well as the gentamicin and spectinomycin resistance genes, was inserted by gene replacement onto the megaplasmid 2 (pM2) of Rhizobium meliloti 0540 (Inf⁻ EPS⁻), resulting in PG101 (Inf⁻ EPS⁻). The self-transfer of pM2 and the mobilization of pM2 by plasmid RP4-4 were investigated during conjugation between PG101 and R. meliloti 2526 (Nod⁻). In filter conjugations, pM2 was readily mobilized by RP4-4. In addition to this, the self-transfer of one megaplasmid (pM) was detected at a frequency of 3 × 10⁻⁷. Bacteria isolated from the nodules of alfalfa and coinoculated with strains PG101 and 2526 showed that pM2 was mobilized at a frequency of approximately 7 × 10⁻⁵. Bacterial cell numbers were too low in the nodules for detection of the self-transfer of pM2 to occur. No pM2 transfer was detected in the inoculum. A comparison of the transfer frequencies for the various conjugation conditions revealed that pM2 transfer occurred as frequently in the nodules as in filter conjugations. These results indicate that the nodule creates conditions for gene transfer that are comparable to optimal laboratory conditions.     

Map of plasmid RP4 derived by insertion of transposon C.

We have determined the location of 36 sites on plasmid RP4 into which transposon C (an 8.5 × 10⁶ molecular weight DNA sequence conferring trimethoprim and streptomycin resistance) had spontaneously inserted itself. These were located by sucrose gradient analysis of EcoRI-generated and then, separately, the HindIII-generated DNA fragments from each RP4-TnC² plasmid. RP4 has a single EcoRI-susceptible site and, suitably displaced from this, a HindIII-susceptible site, whereas TnC has, respectively, one and two sites for these two enzymes. Thus the sizes of the restriction fragments depend on the location and orientation of the inserted TnC.Some of the RP4-TnC clones had lost one of the RP4 characters: transferability (Tra), tetracycline (Tc) or kanamycin (Km) resistances, but no ampicillin (Ap) sensitive clones were detected. Insertions giving each of these phenotypic changes cluster together at positions on the circular RP4 map that presumably locate the genes responsible for the Tra⁺, Km^r and Tc^r phenotypes. The Tra^? plasmids were grouped into four classes on the basis of their conferred phage sensitivities and plasmid copy numbers. The gene giving Ap^r was located by its known proximity to a BamHI-susceptible site. All the plasmids analysed had TnC inserted with one particular orientation. TnC insertions giving no detectable phenotypic change were not randomly placed around RP4, but clustered into certain regions. Two large regions, one containing TnA, had no TnC insertions. Ligation experiments with restriction fragments from various RP4-TnC plasmids led to the conclusion that both these regions contain genes essential to the replication and maintenance of RP4. The location of the HindIII site of RP4 within the gene giving Km^r should prove valuable to the use of this plasmid as a cloning vehicle.     

Transformation and Physical Properties of R-Factor RP4 Transferred from Escherichia coli to Rhizobium trifolii

Transformation of R-factor RP4 specifying resistance to ampicillin, kanamycin, and tetracycline from Escherichia coli to Rhizobium trifolii is reported. Partially purified RP4 deoxyribonucleic acid (DNA) of the donor strain E. coli J5-3 that carried the R-factor was prepared by the lysozyme-ethylenediaminetetraacetic acid-Triton X-100 procedure and was used in transformation experiments with R. trifolii as recipient. The frequency of transformation of the R-factor into R. trifolii was 1.3 × 10⁻⁴. Dye buoyant density and sucrose gradient centrifugation of R. trifolii DNA showed that the expression of the specified drug resistance of RP4 by R. trifolii was accompanied by the acquisition of an extrachromosomal, satellite DNA component which has indistinguishable physical properties from the R-factor in the donor strain. The significance of the transformation is discussed.