Host-controlled Restriction of T-even Bacteriophages: Relation of Four Bacterial Deoxyribonucleases to Restriction

Escherichia coli strains B and K-12, which restrict growth of nonglucosylated T- even phage (T(*) phage), and nonrestricting strains (Shigella sonnei and mutants of E. coli B) were tested for levels of endonuclease I and exonucleases I, II, and III, by means of in vitro assyas. Cell-free extracts freed from deoxyribonucleic acid (DNA) were examined with three substrates: E. coli DNA, T(*)2 DNA, and T2 DNA. Both restricting and nonrestricting strains had comparable levels of the four nuclease activities and had similar patterns of preference for the three substrates. In addition, mutants of E. coli B and K-12 that lack endonuclease I were as effective as their respective wild types in restricting T(*) phage.     

Efficient plasmid transformation of Streptomyces ambofaciens and Streptomyces fradiae protoplasts.

A procedure for efficient transformation of Streptomyces ambofaciens and Streptomyces fradiae protoplasts with plasmid DNA was developed. Transformation frequencies with S. fradiae protoplasts were strongly influenced by the temperatures for cell growth, protoplast formation, and protoplast regeneration. Transformation frequencies for both species were also influenced by the culture age before protoplast formation, the source and concentration of polyethylene glycol, the transformation-inducing agent, the concentration of protoplasts used in the transformation procedure, and the number of protoplasts added to regeneration plates. Transformation frequencies were substantially higher for both species when calf thymus DNA and protamine sulfate were added to the transformation mix. With S. fradiae, transformation frequencies were much lower with plasmid DNA prepared from other species than with the same plasmids prepared from S. fradiae, suggesting that S. fradiae expresses restriction and modification. With the modified transformation procedures using DNA prepared from homologous hosts, S. ambofaciens and S. fradiae are now transformed routinely at frequencies of 10(6) to 10(7) transformants per micrograms of plasmid DNA.     

High-frequency transduction of pBR322 by cytosine-substituted T4 bacteriophage: evidence for encapsulation and transfer of head-to-tail plasmid concatemers

Transduction of plasmid pBR322 by cytosine-substituted T4 phages has been studied. Three T4 phage mutants which substitute cytosine for all of hydroxymethylcytosine residues in the DNA, were shown to transduce pBR322 at frequencies of 2 × 10^?2 to 4 × 10^?3 transductants per singly infected cell. Also, three T4 phage strains which partially substitute cytosine for hydroxymethylcytosine, transduced pBR322 at frequencies of 2 × 10^?3 to 2 × 10^?4. The transduction frequencies of pBR322 we attained are at least 10-fold higher than those reported by G. G. Wilson, K. Young, and G. J. Edlin (1979, Nature (London)280, 80–82). We found that multiplicity of infection in preparation of the transducing phage is the most important factor affecting the frequency of pBR322 transduction. When a lysate made at a multiplicity of infection ranging from 0.5 to 0.05 was used as the donor phage, transduction frequency of pBR322 was 10- to 40-fold higher than that of high-m.o.i. lysate. The transduction frequency was not affected by either restriction systems or amber suppressors of the recipient cells. However, no pBR322-containing transductant was obtained when either recA or polA mutants were used as the recipients. DNA from T4dC phage containing pBR322-transducing particles was analyzed on agarose gel electrophoresis after cleavage with restriction endonucleases. It was suggested that the pBR322 DNA in the T4dC phage particles exists as head-to-tail concatemers.     

Transformation of Salmonella typhimurium with plasmid DNA: differences between rough and smooth strains.

Lipopolysaccharide-defective mutants of Salmonella typhimurium were transformed by plasmid DNA with a Ca2+ treatment method. Only those mutants with an Rc or Rd2 chemotype, due to galE or rfaF mutations, respectively, gave efficiencies greater than 10(5) transformants per microgram of DNA, frequencies 8- to 630-fold higher than with smooth strains or other rough mutants.     

High efficiencies of gene transfer with immobilized recombinant retrovirus: kinetics and optimization

We used a combination of mathematical modeling and experiments to investigate the rate-limiting steps of retroviral transduction on surface-bound fibronectin (FN) and identify the conditions that maximize the efficiency of gene transfer. Our results show that fibronectin-assisted gene transfer (FAGT) is a strong function of the time and temperature of virus incubation in FN-coated plates. Gene transfer increases sharply at short times, reaches a maximum at intermediate times, and eventually declines as a result of loss of retroviral activity. The maximum transduction efficiency and the time at which this is attained increase with decreasing temperature of virus incubation. Depending on the temperature and the type of target cells, the initial rate of gene transfer increases by 3- to 10-fold and the maximum transduction efficiency increases by 2- to 4-fold as compared to traditional transduction (TT). Interestingly, Polybrene (PB) inhibits FAGT in a dose-dependent manner by inhibiting binding of retrovirus to FN. In contrast to traditional transduction, FAGT yields higher than 10-fold transduction efficiencies with concentrated retrovirus stocks. Gene transfer is directly proportional to the concentration of the virus-containing medium with no sign of saturation for the range of concentrations tested. These results suggest that immobilization of recombinant retrovirus can be rationally optimized to yield high efficiency of gene transfer to primary cells and improve the prospect of gene therapy for the treatment of human disease.     

Beta-lactamase genes of Streptomyces badius, Streptomyces cacaoi and Streptomyces fradiae: cloning and expression in Streptomyces lividans

Genes encoding extracellular beta-lactamases (EC 3.5.2.6) of Gram-positive Streptomyces badius, Streptomyces cacaoi and Streptomyces fradiae have been cloned into Streptomyces lividans. The beta-lactamase gene of S. badius was initially isolated on a 7 kb BamHI fragment and further located on a 1300 bp DNA segment. An 11 kb BamHI fragment was isolated encompassing the S. cacaoi beta-lactamase gene, which was subcloned to a 1250 bp DNA fragment. The beta-lactamase gene of S. fradiae was cloned on an 8 kb BamHI fragment and mapped to a 4 kb DNA segment. Each of the three BamHI fragments encompassing the beta-lactamase genes hybridized to a BamHI fragment of the corresponding size in chromosomal DNA from the respective strain used for cloning. The activities of the three beta-lactamases were predominantly found to be extracellular in the S. lividans recombinants. The S. badius and S. cacaoi beta-lactamases exhibited a 10-100-times lower activity in S. lividans, whereas the S. fradiae beta-lactamase showed an approximately 10-fold higher activity in the cloned state, compared with the activities found in the original strains.     

Transformation of Acidiphilium by electroporation and conjugation.

Two techniques, electroporation and conjugation, have been used to introduce the RK2-based broad-host-range plasmids pRK415 and pLAFR3 into strains of the bacterial genus Acidiphilium. Using electroporation, cells were also transformed with a series of chimeric plasmids constructed by cloning cryptic Acidiphilium plasmids into the Escherichia coli vector pBR328. Various parameters affecting electroporation were investigated. Transformation efficiency varied widely with different recipient strains. Growth at an elevated temperature (37 degrees C) prior to electroporation increased transformation efficiency 10-fold compared with growth at 32 degrees C. For three strains tested, optimum transformation efficiency was obtained with field strengths of 10-15 kV/cm. Transformation efficiency increased linearly with increasing DNA concentration up to 10 micrograms/mL. Transformation efficiencies in these experiments ranged up to 10(4) transformants/micrograms DNA. Mobilization of pRK415 and pLAFR3 from E. coli strain S17.1 into several Acidiphilium strains was achieved following incubation for 3 h on nutrient agar medium (pH 7.0). Conjugation frequencies in the range of 10(-5)-10(-9) per recipient cell were obtained. Conjugation frequency was also dependent on recipient strain.     

Transduction of concatemeric plasmids containing the cos site of Lactococcus lactis bacteriophage sk1

Lactococcus lactis bacteriophage sk1 can transduce plasmids containing the phage cos site and surrounding DNA sequences at frequencies as high as 2x10(-3) transductants per PFU. Deletion analysis demonstrated that the presence of phage DNA spanning cos and putative R sites were the most important for efficient plasmid transduction. Inserts of 440 bp containing cos and the R sites were sufficient to induce transduction frequencies of 10(-4) transductants per PFU. The role of the R1 site was investigated by altering 14 of the 19 bases in the site. This resulted in a two-fold decrease in transduction frequency compared to a 26-fold decrease in transduction following deletion of the entire site. It was demonstrated that transducing plasmids were packaged as linear trimeric concatemers commencing at the cos site.     

Transduction of linked chromosomal genes between Pseudomonas aeruginosa strains during incubation in situ in a freshwater habitat

Both transduction of single chromosomal loci and cotransduction of closely linked loci were observed between lysogenic and nonlysogenic strains of Pseudomonas aeruginosa in a freshwater habitat. Transductants were recovered at frequencies of 10(-6) to 10(-5) transductants per CFU. Transductants of lysogenized strains were recovered 10- to 100-fold more frequently than were transductants of nonlysogenic parents. Lysogens are thus capable of introducing phages which mediate generalized transduction into the natural microbial community and serving as recipients of transduced DNA. It would appear that lysogeny has the potential of increasing the size and flexibility of the gene pool available to natural populations of bacteria. The ability to generate and select new genetic combinations through phage-mediated exchange can be significant in the face of a continually changing environment and may contribute to the apparent fitness of the lysogenic state in natural ecosystems.     

Transduction of linked chromosomal genes between Pseudomonas aeruginosa strains during incubation in situ in a freshwater habitat.

Both transduction of single chromosomal loci and cotransduction of closely linked loci were observed between lysogenic and nonlysogenic strains of Pseudomonas aeruginosa in a freshwater habitat. Transductants were recovered at frequencies of 10(-6) to 10(-5) transductants per CFU. Transductants of lysogenized strains were recovered 10- to 100-fold more frequently than were transductants of nonlysogenic parents. Lysogens are thus capable of introducing phages which mediate generalized transduction into the natural microbial community and serving as recipients of transduced DNA. It would appear that lysogeny has the potential of increasing the size and flexibility of the gene pool available to natural populations of bacteria. The ability to generate and select new genetic combinations through phage-mediated exchange can be significant in the face of a continually changing environment and may contribute to the apparent fitness of the lysogenic state in natural ecosystems.     

Transformation and Transduction in Recombination-defective Mutants of Bacillus subtilis

The effects on transformation and transduction of an ultraviolet sensitivity (uvr(-)) and two ultraviolet sensitivity-recombination deficiency (rec-1(-) and rec-2(-)) mutations in isogenic strains of Bacillus subtilis were investigated. Transformation frequency in the rec-1(-) and rec-2(-) strains was reduced to approximately 5 and 25%, respectively, of the parental strains. Normal kinetics of deoxyribonucleic acid dose response in transformation were found for the rec-1(+) and rec-2(-) strains. Biphasic curves were obtained with the rec-1(-) strains. Transduction frequency with bacteriophage SP-10 decreased parallel to transformation frequency in the rec-1(-) and rec-2(-) strains. This result suggests that transformation and SP-10 transduction share a common mechanism for genetic recombination. It also indicates that the reduction in transformation frequency of these strains was not due to altered competence. Transduction frequency with bacteriophage PBS-1 or 3NT, on the contrary, was not diminished in rec-1(-) strains. This frequency was reduced in rec-2(-) strains but not as severely as that of transformation or SP-10 transduction. Several hypotheses to interpret these differences are presented. Recombination frequency between linked markers was reduced more than 50% in transformation by the presence of the rec-1(-) mutation. Linkage was unaffected in the rec-2(-) strains. Neither the rec-1(-) nor the rec-2(-) mutation had an effect on linkage in PBS-1 or 3NT transduction. The uvr(-) strains were transformed at a frequency equal to or greater than that of the parental strains. These strains were transduced by all bacteriophage systems at frequencies about twofold higher than those of parental strains.     

Conditional Temperature-sensitive Restriction of Pseudomonas Bacteriophage CB3

Restriction of Pseudomonas bacteriophage CB3 growth on some Pseudomonas aeruginosa hosts was studied. On restricting hosts, growth of this phage was severely inhibited below 32 C and hence was temperature-sensitive. Investigation of this phenomenon revealed that restricting hosts were not killed as a consequence of their infection under nonpermissive conditions. The ability of some hosts to restrict showed segregation in sexual crosses between restricting and nonrestricting hosts. However, the pattern of restriction among various hosts differed with the phage in question when other phages were compared with CB3. Temperature-shift experiments indicated that blockage of an early event in the phage lytic cycle occurred when restricting conditions were imposed on cells infected with CB3. This blockage could be eliminated by holding at permissive conditions until the cold-sensitive step was bypassed or by pulsing restricting cells for 5 min at 37 C.     

Improvement of tylosin fermentation by mutation and medium optimization

A tylosin-hyperproducing mutant of Streptomyces fradiae MNU20 was isolated from 3500 strains obtained from either MNNG- or u.v.-treated S. fradiae NRRL2702. With the optimal medium, S. fradiae MNU20 was able to produce 159 mg tylosin g biomass(-1), indicating the tylosin productivity in S. fradiae NRLL2702 was increased 14-fold by mutation and medium optimization. When the effect of valine, succinate and natural zeolite on tylosin production was investigated sing the optimal medium, these substances essentially enhanced tylosin production up to 349 mg g biomass(-1); their time addition during the culture period appeared to be critical for the increase.     

Epoxide hydrolase activity of Streptomyces strains

The discovery of epoxide hydrolases within a Streptomyces sp. strain collection is described. Screening was performed in 96 well microtiter plates using a modified 4-(p-nitrobenzyl)pyridine assay with styrene oxide, 1,2-epoxy-hexane or 3-phenyl ethylglycidate (3-PEG) as substrates. Out of 120 strains investigated, S. antibioticus Tü4, S. arenae Tü495 and S. fradiae Tü27 exhibited epoxide hydrolase activity. These strains were further investigated by performing laboratory-scale biotransformations utilizing styrene oxide, 1,2-epoxy-hexane and 3-PEG followed by subsequent quantitative analysis employing chiral gas chromatography. The highest conversions were achieved with whole cells from S. antibioticus Tü4 in the presence of 10% (v/v) DMSO. However, enantioselectivity was only satisfying (E = 31) in the presence of 5% (v/v) acetone, which allowed isolation of optically pure non-hydrolyzed (R)-styrene oxide (99% enantiomeric excess (ee)) and (S)-phenyl-1,2-ethandiol (72% ee) at 55% conversion after 24 h. The resolution of 3-PEG proceeded with slightly lower enantioselectivity albeit higher reaction rates. With S. fradiae Tü27 and S. arenae Tü495 enantioselectivity towards styrene oxide was only E = 3-4.     

Identification and application of plasmids suitable for transfer of foreign DNA to members of the genus Gordonia

Gene transfer systems for Gordonia polyisoprenivorans strains VH2 and Y2K based on electroporation and conjugation, respectively, were established. Several parameters were optimized, resulting in transformation efficiencies of >4 x 10(5) CFU/ micro g of plasmid DNA. In contrast to most previously described electroporation protocols, the highest efficiencies were obtained by applying a heat shock after the intrinsic electroporation. Under these conditions, transfer and autonomous replication of plasmid pNC9503 was also demonstrated to proceed in G. alkanivorans DSM44187, G. nitida DSM44499(T), G. rubropertincta DSM43197(T), G. rubropertincta DSM46038, and G. terrae DSM43249(T). Conjugational plasmid DNA transfer to G. polyisoprenivorans resulted in transfer frequencies of up to 5 x 10(-6) of the recipient cells. Recombinant strains capable of polyhydroxyalkanoate synthesis from alkanes were constructed.     

Restriction-modification systems in Streptomyces antibioticus

Several restriction systems were detected in different strains of Streptomyces antibioticus by using actinophages as biological indicators. Adsorption of phages to the bacteria, together with the study of the efficiency of plating gave an initial indication of restriction in three strains. The alternation of efficiency of plating values obtained from restricting and nonrestricting hosts, gave evidence for the presence of a restriction-modification system in another strain. No common modification systems were detected among the different strains tested. Two specific endonucleases with a possible role in restriction were detected in strains ATCC 11891 and ETH 7451, respectively.     

High efficiency transformation by electroporation of Pichia pastoris pretreated with lithium acetate and dithiothreitol

Transformation efficiencies for Pichia pastoris are usually several orders of magnitude below those for other yeast. We report here that pretreatment of P. pastoris with 0.1 M lithium acetate (LiAc) and 10 mM dithiothreitol (DTT) before electroporation increased transformation efficiency approximately 150-fold. DTT alone enhanced the transformation efficiency up to 20-fold, but LiAc alone had little effect. Cultures grown to 1.15-2.6 A at 600 nm had higher transformation efficiencies than younger or older cultures. A cell concentration of 10(10)/mL gave the highest efficiencies. Digestion of pPIC9K within the AOX1 gene with Sacl gave efficiencies approximately 30 times higher than digestion in other genes with other enzymes. Given the optimization of these factors, the highest transformation efficiency was obtained with instrument settings of 1.5 kV, 25 microF, and 186 omega. The transformation efficiency at optimal conditions reached 4 x 10(6) transformants/microgram DNA with pPIC9K. A maximum of 2.6 x 10(5) transformants was produced when 1 microgram of pPIC9K DNA was used.     

应用离心方法提高杆状病毒对哺乳动物细胞转导实验效率

重组杆状病毒作为一种对哺乳动物细胞的新型基因转移载体已获得了日益广泛的应用。为进一步提高转导实验的效率,本研究利用已构建的带有CMV启动子-增强型绿色荧光蛋白(eGFP)表达盒的重组杆状病毒BacV-CMV-EGFPA,在CV-1细胞中探索了应用离心方法提高转导实验效率的可行性。结果显示离心方法可显著提高单位时间内重组杆状病毒对哺乳动物细胞的转导效率,同时不会对靶细胞造成损伤。通过对离心时间、离心后孵育时间、病毒上清的稀释缓冲液的进一步摸索优化,结果显示病毒上清以PBS为稀释缓冲环境室温600g水平离心1h即可获得高水平的转导效率,优于在PBS环境中27℃孵育8h的效果。该方法可在获得高转导效率的同时显著缩短实验时间,具有快捷、高效、低损伤的特点,可作为一种常规操作方法用于日常实验。本研究进一步应用该方法对多种不同来源和类型的哺乳动物细胞株进行基因转导,结果显示该方法可适用于多数不同种属和组织来源的哺乳动物细胞,其中对贴壁细胞的效果最为显著。     

High-Frequency Plasmid Transduction by Lactobacillus gasseri Bacteriophage phiadh

The temperate bacteriophage phiadh mediates plasmid DNA transduction in Lactobacillus gasseri ADH at frequencies in the range of 10 to 10 transductants per PFU. BglII-generated DNA fragments from phage phiadh were cloned into the BclI site of the transducible plasmid vector pGK12 (4.4 kb). Phage phiadh lysates induced from Lactobacillus lysogens harboring pGK12 or the recombinant plasmids were used to transduce strain ADH to chloramphenicol resistance. The transduction frequencies of recombinant plasmids were 10- to 10-fold higher than that of native pGK12. The increase in frequency generally correlated with the extent of DNA-DNA homology between plasmid and phage DNAs. The highest transduction frequency was obtained with plasmid pTRK170 (6.6 kb), a pGK12 derivative containing the 1.4- and 0.8-kb BglII DNA fragments of phiadh. DNA hybridization analysis of pTRK170-transducing phage particles revealed that pTRK170 had integrated into the phiadh genome, suggesting that recombination between homologous sequences present in phage and plasmid DNAs was responsible for the formation of high-frequency transducing phage particles. Plasmid DNA analysis of 13 transductants containing pTRK170 showed that each had acquired intact plasmids, indicating that in the process of transduction a further recombination step was involved in the resolution of plasmid DNA monomers from the recombinant pTRK170::phiadh molecule. In addition to strain ADH, pTRK170 could be transduced via phiadh to eight different L. gasseri strains, including the neotype strain, F. Gasser 63 AM (ATCC 33323).