Genetic Recombination in Crosses Between Streptomyces aureofaciens and Streptomyces rimosus

Genetics of Streptomyces rimosus, the oxytetracycline producer

From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.

Composition and mass of the bacteriophage phi29 prohead and virion

The protein composition of the Bacillus subtilis bacteriophage phi29 prohead and virion was determined by combustion of gel bands of (3)H-labeled proteins. Copy numbers of individual proteins were calculated relative to the 12 copies of the head-tail connector protein. The mean numbers of copies of the major capsid protein in the prohead and virion were 241 and 218, respectively, approaching the 235 copies determined previously by cryoelectron microscopy. The mean numbers of copies of the dimeric head fiber on the prohead and virion were 24 and 31, respectively, demonstrating partial occupancy of the 55 fiber binding sites. Measured copies of neck and tail proteins in the virion included 11 of the lower collar, 58 of the appendage, and 9 of the tail; if the true copies of these proteins are 12, 60, and 9, respectively, the entire neck and tail of phi29 has quasi-sixfold symmetry. The mass of the fiberless prohead with pRNA was about 14.2 MDa, and the mass of the prohead determined by scanning transmission electron microscopy was consistent with the biochemical data. The mass of the fiberless virion containing the 12.8-MDa DNA genome was about 30.4 MDa. A full complement of dimeric fibers on the prohead or virion would increase the mass of the particle by about 3.2 MDa. The data complement studies relating the structure of phi29 components to dynamic functions in morphogenesis and infection.

Thermostable, alkalophilic and cellulase free xylanase production by Thermoactinomyces thalophilus subgroup C

Thermoactinomyces thalophilus produced cellulase free extracellular endo-1,4-beta-xylanase (EC 3.2.1.8) at 50 degrees C and pH 8.5. Maximum xylanase production was achieved in fermentation medium using birchwood xylan as substrate after 96 h of growth at 50 degrees C. Other agricultural substrates such as wheat bran, wheat straw, sugarcane bagasse and cornstover produced less xylanase. The crude enzyme preparation from mutant T. thalophilus P2 grown under optimised fermentation conditions showed no cellulase contamination and maximum xylanase activity of 42 U/ml at 65%deg;C and pH 8.5-9.0. This enzyme with initial xylanase activity of 42 U/ml was found thermostable up to 65 degrees C and retaining 50% of its activity after its incubation for 125 min at 65 degrees C.

The 1-kb-repeat-encoded DNA-binding protein as repressor of an alpha-glucosidase operon flanking the amplifiable sequence AUD1 of Streptomyces lividans

High-copy-number amplification of the AUD1 element is frequently associated with the large chromosomal deletions responsible for genetic instability in Streptomyces lividans TK64. Five ORFs were found in a 7 kb region directly adjacent to AUD1. The putative products of ORF1, ORF2 and ORF3 showed similarities to ATP-binding cassette (ABC) sugar transporters, the deduced protein sequence of ORF4 displayed similarities to alpha-glucosidases whilst no homology to proteins with known functions was found for ORF5. ORF4 (renamed aglA) was expressed in Escherichia coli and the protein purified and characterized. An alpha-glucosidase activity was detected using the synthetic alpha-glucoside p-nitrophenyl alpha-D-glucopyranoside. Of the many oligosaccharides tested, only sucrose was hydrolysed at a measurable rate [specific activity 32.4 units (mg protein)(-1)] but no growth of S. lividans TK64 on sucrose was observed. A strain in which aglA was disrupted showed the same low alpha-glucosidase activity as strain TK64 and in both strains no stimulation of activity was seen by sucrose, trehalose or maltose; dextrin increased alpha-glucosidase activity about 10-fold. This probably resulted from induction of a second alpha-glucosidase-encoding gene. The AUD1 element contains three 1 kb repeats which encode DNA-binding proteins necessary for high-frequency amplification. In strains with a unique 1 kb repeat, disruption of the repeat led to a significant increase in the alpha-glucosidase activity. These results strongly suggest that the 1-kb-repeat-encoded proteins of AUD1 have a dual function: they are the repressors of the agl genes and they promote amplification of AUD1.

A spectinomycin resistance determinant from the spectinomycin producer Streptomyces flavopersicus

The spectinomycin (sp) resistance determinant from Streptomyces flavopersicus was cloned into Streptomyces lividans using the plasmid vector pIJ699. A plasmid, pDGL15, with a 3.65 kb insert from S. flavopersicus conferring resistance to Sp was isolated. DNA sequence analysis of the 3651 1 bp DNA insert revealed four open reading frames (ORFs). The amino acid sequence deduced from one ORF (SpcN) showed a high degree of similarity to an aminoglycoside phosphotransferase (StrN) and from a second one (SpcR) to a regulatory protein (StrR) of the streptomycin biosynthesis gene cluster from S. griseus. The two other ORFs were incomplete and the deduced amino acid sequences showed similarities to an amidinotransferase encoded in the streptomycin biosynthesis gene cluster of S. griseus and to the transposase of IS112, respectively. Expression of the spcN gene in E. coli under the control of tac promoter conferred Sp resistance to the cells. An enzymic assay confirmed that the gene product of spcN is an ATP-dependent aminoglycoside phosphotransferase which phosphorylates Sp and actinamine, the aminocyclitol moiety of Sp.

DNA amplification affects protease production and sporulation in Streptomyces fradiae

Chloramphenicol resistance is an unstable character in Streptomyces fradiae, since spontaneous chloramphenicol-sensitive (Cmls) mutants arose at very high frequencies. One such Cmls mutant, DM14, showed DNA amplification as well. Extracellular protease activity was tenfold higher in DM14 when compared with its wild-type parent. Protease activity decreased considerably in DM14 when treated with spectinomycin, a treatment that reduces the copy number of amplified units of DNA. Sporulation in DM14 was delayed in the presence of spectinomycin at a concentration of 5 micrograms/ml, whereas the wild type was unaffected at that concentration. The results strongly indicated that the amplified DNA affected the two secondary metabolic functions, viz., protease production and the onset of sporulation in the mutant.

Cloning and DNA sequence analysis of the mercury resistance genes of Streptomyces lividans

A broad-spectrum mercury resistance locus (mer) from a spontaneous chloramphenicol-sensitive (Cms), arginine auxotrophic (Arg-) mutant of Streptomyces lividans 1326 was isolated on a 6 kb DNA fragment by shotgun cloning into the mercury-sensitive derivative S. lividans TK64 using the vector pIJ702. The mer genes form part of a very large amplifiable DNA sequence present in S. lividans 1326. This element was amplified to about 20 copies per chromosome in the Cms Arg- mutant and was missing from strains like S. lividans TK64, cured for the plasmid SLP3. DNA sequence analysis of a 5 kb region encompassing the whole region required for broad-spectrum mercury resistance revealed six open reading frames (ORFs) transcribed in opposite directions from a common intercistronic region. The protein sequences predicted from the two ORFs transcribed in one direction showed a high degree of similarity to mercuric reductase and organomercurial lyase from other gram-negative and gram-positive sources. Few, if any, similarities were found between the predicted polypeptide sequences of the other four ORFs and other known proteins.

RNA dependence of the bacteriophage phi 29 DNA packaging ATPase

The activity of the DNA packaging adenosine triphosphatase (ATPase) of the Bacillus subtilis bacteriophage phi 29 is dependent upon prohead RNA. The 174 nucleotide viral-encoded RNA is positioned on the head-tail connector at the portal vertex of the phi 29 precursor shell (prohead). Here, the RNA interacts with the ATP-binding gene 16 product (gp16) to constitute the DNA-packaging ATPase and initiate DNA packaging in vitro. Both the prohead connector (gene 10 product, gp10) and gp16 may utilize an RNA recognition motif characteristic of a number of RNA-associated proteins, and the binding of gp16 by proheads shields the prohead RNA from RNase A. The ATPase activity of gp16 is stimulated fourfold by RNA and tenfold by proheads with RNA. RNA is needed continuously for the gp16/RNA ATPase activity and is essential for the gp16/prohead ATPase activity. The prohead, with its connector, RNA and associated gp16 in an assembly-regulated configuration, hydrolyzes ATP and drives phi 29 DNA translocation.

Deamplification and deletion of amplified DNA in Streptomyces lividans and S. fradiae

Streptomyces lividans arginine auxotrophs which show amplification of a 5.7-kb DNA sequence, arose at a very high frequency, varying from 10% to 25% of Cmls spores. The amplifiable DNA sequence was shown to be stable over many generations. However, treatment of Cmls arg mutants with subinhibitory concentrations of antibiotics such as spectinomycin, streptomycin, chloramphenicol, thiostrepton and kanamycin, either during sporulation or during vegetative growth of mycelia, led to the deletion of the entire amplified DNA sequence, including the left and right junction sequences. Depending upon the method of antibiotic treatment a reduction in the copy number of the amplified DNA was also observed. This reduction in copy number apparently occurred without drastically affecting the basic structure of the amplifiable unit of DNA. This phenomenon appears to be universal since deamplification and deletion were observed also in S. fradiae. Further, spontaneous arg mutants arose at much lower frequency from spectinomycin-pretreated Cmls cells compared to untreated cells. These arg mutants isolated in the presence of spectinomycin did not show amplification of the 5.7-kb sequence. Southern blot analysis using the 5.7-kb probe showed that the entire DNA sequence homologous to the amplifiable DNA sequence had been deleted.

Physiology of a wild strain and high yielding mutants of Streptomyces rimosus, producing oxytetracycline

A wild-type Streptomyces strain, yielding 1 g/L of oxytetracycline was compared with mutants giving up to 7 g/L, using complex media in stirred and shaken culture. Increased production of oxytetracycline was associated with high specific production rates and a longer production period. The superiority of the mutants was associated with changes in morphological behaviour during growth in submerged culture, and in their patterns of growth and respiration, coupled with increased resistance to the product. The productivity of the mutants was sensitive to the rate of stirring, the type of calcium carbonate used in the medium and the type of inoculum. Careful control of these factors was necessary to obtain high yields of oxytetracycline. With the exception of acetyl-CoA carboxylase, the levels of enzymes measured and of amounts of adenylates in the mycelium did not appear to be related to the degree of antibiotic production.

Candida amidevorans sp. nov., a new ascomycetous anamorph yeast from soil

A strain of an undescribed Candida species was isolated from soil. A description of the new species Candida amidevorans is given and its distinction from the most closely resembling species of the genus is discussed.

DNA amplification and an unstable arginine gene in Streptomyces lividans 66

Streptomyces lividans 66 produced spontaneous chloramphenicol-sensitive mutants (CmlS) at a frequency of about 1% of spores. The CmlS mutant strains were very unstable, giving Arg- mutants at frequencies of about 25% of spores. All the Arg- mutants had amplified a particular 5.75 kb DNA fragment into tandem repeats of 250-500 copies per chromosome.

Mutagenesis of Micromonospora rosaria by using protoplasts and mycelial fragments

Both mycelial fragments and protoplasts were successfully employed for mutagenesis of Micromonospora rosaria NRRL 3718, and the results were compared. The optimal conditions and effective procedures for mutagenesis of M. rosaria by a chemical mutagen, N-methyl-N'-nitro-N-nitrosoguanidine, have been determined. Mutation was efficiently induced when mycelial fragments were treated with N-methyl-N'-nitro-N-nitrosoguanidine at a concentration of 0.3 to 0.5 mg/ml in the reaction buffer of pH 7.0. Optimal treatment time was 20 to 40 min. Ampicillin treatment was very effective for enrichment of auxotrophs. Protoplasts showed much higher sensitivity to the lethal effect of N-methyl-N'-nitro-N-nitrosoguanidine. Although protoplasts have some advantage of single cell characteristics, the frequency of auxotrophs obtained was somewhat lower. Up to 4% of the colonies were shown to be auxotrophs under the well-defined conditions. This mutagenesis method with protoplasts or fragmented mycelia (or both) should be applicable to other actinomycetes that have limited or no sporulation.

Genetic recombination in Micromonospora rosaria by protoplast fusion

Auxotrophic strains of Micromonospora rosaria were isolated by N-methyl-N'-nitro-N'-nitrosoguanidine mutagenesis and used in intraspecific recombination by protoplast fusion. High-frequency fusion of protoplasts of M. rosaria strains was induced by polyethylene glycol (molecular weight, 1,000) (PEG 1,000). The optimum concentration of PEG 1,000 for fusion of M. rosaria was 50% (wt/vol). PEG 4,000 was slightly better than PEG 1,000 at concentrations lower than 50% (wt/vol). The recombinant frequency did not increase after treatment with PEG 1,000 (50% [wt/vol]) for longer than 20 min. Under these conditions, fusion with many auxotrophic strains of M. rosaria resulted in a high frequency of formation of true recombinants (sometimes more than 10%). Additionally, when ros (rosamicin nonproducing) strains were crossed by protoplast fusion; about 5% of the resultant prototrophic recombinants were shown to have the ros+ (rosamicin producing) characteristic restored. Rosamicin production by M. rosaria colonies was clearly distinguished by the broth overlay method. The results of fusion experiments between ros and ros+ strains indicated that either the chromosomal mutation or pleiotrophic effect of some auxotrophic markers is involved.

Production of Rosamicin: Improvement of Synthetic Medium

Rosamicin is one of the important macrolide antibiotics that has clinical efficacy and broad-spectrum antibacterial activity. Using a mutant strain of Micromonospora rosaria (NRRL 3718), a chemically defined medium was developed, and some fermentation conditions that are important to rosamicin biosynthesis were optimized to achieve rosamicin productivity of 230 μg/ml. Soluble starch and l -asparagine were found to be the best carbon and nitrogen sources, and a stimulative effect of magnesium and zinc ions was also found. The medium developed contains: soluble starch, 4%; l -asparagine, 0.15%; K 2 HPO 4 , 0.075%; CaCO 3 , 0.6%; MgSO 4 · 7H 2 O, 0.05%; FeSO 4 · 7H 2 O, 10 −4 M; CuSO 4 · 5H 2 O, 10 −5 M; ZnSO 4 · 7H 2 O, 10 −5 M; and MnSO 4 · (4-6)H 2 O, 10 −6 M. The required air supply was about 40 mmol of O 2 liter −1 · h −1 · atm −1 , and the favorable culture temperature was 28 to 29°C.

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: mapping and functional analysis of the head fiber gene

A set of mutants of Bacillus subtilis bacteriophage phi29 unable to synthesize the head fiber protein has been identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Infectious phage are produced during restrictive infection. We have focused on mutant sus 8.5(900) because the mutation is suppressible by both the su(+3) and su(+44) hosts, and it can be mapped by three- and four-factor crosses. After restrictive infection with mutant sus 8.5(900), a fragment about 70% of the size of the normal fiber is produced as well as particles that are fast-sedimenting in sucrose gradients relative to phi29(+). These particles have the buoyant density of particles with the fibers removed and have the absolute plating efficiency of phi29(+). Fiber protein is absent from prohead as well as virion. A second set of mutants produces fiber protein with a slightly altered electrophoretic mobility. This type of fiber protein is either present or absent on both prohead and virion. A third class of mutants, typified by 914, produces a "normal" fiber, but a major head protein of altered electrophoretic mobility. After infection by this mutant, the fiber is absent from both prohead and virion, and the biological and physical properties of the 914(-) particle are similar to those of particles produced after infection of the su(-) host by sus8.5(900). These observations suggest that the head fiber is not an essential component of the prohead or virion and that the assembly process is efficient in the absence of fiber protein. Three- and four-factor genetic crosses have established the order sus8(769)-8(914)-sus8.5(900)-sus9(756) and indicate that cistrons 8 and 8.5 code for the major head protein and head fiber protein, respectively.

Morphogenesis of bacteriophage phi29 of Bacillus subtilis: cleavage and assembly of the neck appendage protein

Each of the 12 neck appendages of the Bacillus subtilis bacteriophage phi29 consists of a single protein molecule with a molecular weight of about 75,000, and on the mature virion the appendages are assembled to the lower of two collars. The appendage protein is cleaved from a precursor protein, P(J), with a molecular weight of about 88,000. This cleavage is independent of neck assembly, occurring during infection by mutants that cannot synthesize the proteins of the upper and lower collars of the neck. The cleaved form of the appendage protein is efficiently complemented in vitro to particles lacking appendages. Thus, cleavage of the appendage precursor protein apparently does not occur in situ on the maturing virus.

Genetic analysis of bacteriophage phi29 of Bacillus subtilis: mapping of the cistrons coding for structural proteins

Four phage phi29 suppressor-sensitive mutants of cistron O have been examined for production of 14C-labeled viral-specific proteins in restrictive infections of Bacillus subtilis and fail to produce the protein of the viral neck lower collar. Cistrons O and F have been placed on the genetic map, containing 12 cistrons, by three-factor crosses. The phenotypes of five cistron J mutants have been analyzed by sodium dodecyl sulfate gel electrophoresis and autoradiography, and in three instances fragments of the normal polypeptide were detected. Three factor crosses with these mutants and a virus with a clear plaque phenotype were used to initiate the mapping of cistron J and the determination of the orientation of transcription in this map region.

Analysis of bacteriophage phi 29 gene function: protein synthesis in suppressor-sensitive mutant infection of Bacillus subtilis

Phage phi29 suppressor-sensitive (sus) mutants of 14 cistrons have been examined for production of (14)C-labeled viral-specific proteins in restrictive infections of Bacillus subtilis. Proteins specified by four cistrons (H, J, L, and N) have been resolved and identified by sodium dodecyl sulfate gel electrophoresis and autoradiography, and fragments of the normal polypeptides were detected. Mutants of six cistrons (C, D, E, F, I, and M) demonstrated two or more missing bands in the gel profiles, and thus some of these gene products may have regulatory functions. Mutation was detected in at least five genes coding for low-molecular-weight proteins, but a conditionally lethal mutant in only one of these genes has been isolated. Preliminary evidence that a precursor protein is cleaved to generate the neck appendage structural protein and a low-molecular-weight product has been obtained.

Viral protein synthesis in bacteriophage phi 29-infected Bacillus subtilis

Twenty-three (14)C-labeled phage phi29-specific proteins in lysates of UV-irradiated Bacillus subtilis have been resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis and identified by autoradiography. Included in this group of proteins are the six major structural proteins of the virion. Analysis of the temporal sequence of viral protein synthesis indicates that three groups of proteins can be identified by time of appearance, beginning at 2 to 4, 4 to 6, or 8 to 10 min after infection, respectively. These proteins account for approximately 90% of the coding capacity of the phi29 genome.

Transcription after bacteriophage SPP1 infection in Bacillus subtilis

The role of the host polymerase in Bacillus subtilis infected with phage SPP1 was studied in vivo with regard to production of phage-specific and host-specific ribonucleic acid (RNA) and to phage yield. Evidence is presented that the subunit(s) of B. subtilis RNA polymerase which is sensitive to rifampin and streptolydigin is necessary at all times during infection for phage production. The synthesis of phage RNA and the phage yield in strains resistant to either antibiotic were unaffected by the drug. Host RNA synthesis continued throughout infection; phage-specific RNA never accounted for more than 20% of pulse-labeled RNA at any time during infection.

Genetic recombination in Micromonospora

Biochemical mutants were obtained from Micromonospora chalcea, M. purpurea, and M. echinospora by using ultraviolet radiation or nitrosoguanidine. Crosses carried out between complementary nutritional mutants of the same species showed positive genetic interaction. Data are reported which indicate that the interaction between the crossed strains is due to genetic recombination. No evidence for interspecific genetic recombination was found.

Genetic recombination in Streptomyces bikiniensis var. zorbonensis

A genetic recombination system in Streptomyces bikiniensis var. zorbonensis is described. This strain produces a mixture of antibiotics including zorbamycin and zorbonomycin B and C. A genetic map has been constructed from data obtained from an analysis of haploid recombinants which shows linkage relationships of 17 marker loci. Determination of map location has been made for three different loci affecting antibiotic biosynthesis in this strain.

Factors affecting infection of protoplasts with deoxyribonucleic acid of actinophage PK-66

To establish a method for transmission of genetic materials in the genus Streptomyces, the conditions of infection of protoplasts of S. kanamyceticus by actinophage PK-66 deoxyribonucleic acid (DNA) were studied. The protoplasts of Streptomyces were prepared by treatments with lysozyme and trypsin. The infectivity of the phage DNA was enhanced by the presence of NaCl in the medium. The optimal concentration of the protoplasts for infection with DNA was 7 x 10(7) to 4 x 10(8)/ml. A proportional relationship was found between the infectivity and the DNA concentration within a certain range. The maximal production of mature phage was achieved after 19 hr of incubation. The number of phage propagated in the infection mixture reached 10(4) plaque-forming units per ml under the appropriate conditions. The phage DNA infected not only protoplasts prepared from S. kanamyceticus but also those prepared from S. violaceoniger and S. acidomyceticus, which were resistant to intact phage PK-66.