Prototrophic Isolates Research Articles

Enhancing the chemical transformation of Candida parapsilosis

ABSTRACT Candida parapsilosis is a leading cause of invasive mycoses and the major cause of nosocomial fungaemia amongst low and very low birth weight neonates. However, the molecular and physiological characteristics of this fungus remain understudied. To advance our knowledge about the pathobiology of this pathogen, we sought to develop and validate an effective method for chemical transformation of C. parapsilosis. Chemical transformation is the primary procedure for introducing foreign DNA into Candida yeast as it requires no special equipment, although its performance efficacy drops rapidly when the size of the transforming DNA increases. To define optimal conditions for chemical transformation in C. parapsilosis, we selected a leucine auxotroph laboratory strain. We identified optimal cell density for transformation, incubation times, inclusion of specific enhancing chemicals, and size and amounts of DNA fragments that resulted in maximized transformation efficiency. We determined that the inclusion of dimethyl sulfoxide was beneficial, but dithiothreitol pretreatment reduced colony recovery. As a result, the modified protocol led to a 20–55-fold increase in transformation efficiency, depending on the size of the transforming fragment. We validated the modified methodology with prototrophic isolates and demonstrated that the new approach resulted in the recovery of significantly more transformants in 5 of 6 isolates. Additionally, we identified a medium in which transformation competent yeast cells could safely be maintained at −80°C for up to 6 weeks that reduces laboratory work and shortens the overall procedure. These modifications will significantly aid further investigations into the genetic basis for virulence in C. parapsilosis.

Inhibition of Non-Homologous End Joining and integration of DNA upon transformation of Rhizopus oryzae

Site-directed integration of DNA in the fungus Rhizopus has long been problematic because linearized plasmids used for transformation tend to replicate in high-molecular-weight concatenated structures, and rarely integrate into the chromosome. This work examines the methods that might interfere with the multimerization process, select against plasmids that had recircularized, and encourage strand invasion, hopefully leading to plasmid integration. In vitro methods were used to determine if the structure of the double-strand break had any effect on the ability to rejoin plasmid ends. In cell-free extracts, little difference in end-joining activity was found between linearized plasmids with 5' overhangs, 3' overhangs, or blunt ends. In addition, dephosphorylation of ends had no effect. Transformation of plasmids prepared in the same ways confirmed that they were easily religated in vivo, with almost all prototrophic isolates retaining autonomously replicated plasmids. It was possible to block religation by modifying the free ends of the linearized plasmids using oligonucleotide adapters which were blocked at the 3'-OH position and contained phosphorothioate nucleotides to make them nuclease-resistant. However, gene replacement, with repair of the auxotrophic mutation in the host chromosome, was the predominant event observed upon the transformation of these plasmids. The highest rates of integration were obtained with a plasmid containing a truncated, non-functional pyrG gene. Autonomous replication of this plasmid did not support prototrophic growth, but homologous recombination into the chromosome restored the function of the endogenous pyrG gene. All of the transformants obtained with this selective construct were found to have integrated the plasmid, with multicopy insertion being common.

Antimicrobial resistance of Neisseria gonorrhoeae in Japan, 1993–2002: continuous increasing of ciprofloxacin-resistant isolates

Susceptibility testing was conducted on 1357 isolates of Neisseria gonorrhoeae isolated from 1993 through 2002 in Japan to assess the antimicrobial resistance. Selected isolates were characterised by auxotype and analysis was done for mutations within the quinolone resistance-determining region (QRDR) in the gyrA and parC genes, which confer fluoroquinolone resistance to the organism. Isolates with ciprofloxacin resistance increased significantly from 6.6% (1993–1994) to 73.5% (2002). The proportion of plasmid-mediated penicillin-resistant isolates (PPNG) decreased significantly from 7.9% (1993–1994) to 0.9% (2002). The percentage of chromosomal-mediated resistance to penicillin decreased from 27.4% in 2000 to 12.0% in 2001 but increased to 28.9% in 2002. The proportion of isolates with any type of resistance to tetracycline decreased from 24.7% in 2000 to 13.9% in 2001 and then increased to 22.3% in 2002. The proportion of prototrophic isolates significantly decreased from 84.4% in 1992–1993 to 7.7% in 2001, while that of the proline-requiring isolates significantly increased from 4.4% in 1992–1993 and 80.8% in 1998. The proline-requiring isolates were less susceptible to ciprofloxacin than the prototrophic or arginine-requiring isolates. Of 87 isolates resistant to ciprofloxacin, 2 (2.3%) contained five amino acid substitutions within the GyrA and ParC proteins, 76 (87.4%) contained three or four amino acid substitutions and 9 (10.3%) contained one or two amino acid substitutions.

Association between proline-requiring auxotype and fluoroquinolone resistance in Neisseria gonorrhoeae isolated in Japan.

We examined the association between auxotype and fluoroquinolone resistance in Neisseria gonorrhoeae isolated in Fukuoka, Japan, and investigated whether the prevalence of fluoroquinolone-resistant N. gonorrhoeae isolates was caused by the dissemination of the same clone in the community. We examined the antimicrobial susceptibility of 294 N. gonorrhoeae, isolates obtained during three different periods in Fukuoka, Japan, and 89 isolates of N. gonorrhoeae, classified by the presence of amino-acid substitutions in the quinolone resistance-determining regions (QRDRs) of GyrA and ParC proteins, to various agents, and we examined the auxotypes of the isolates. In 22 isolates with amino-acid substitutions within QRDRs in GyrA and ParC, pulsed-field gel electrophoresis analysis was performed. The proportion of fluoroquinolone-resistant isolates (ciprofloxacin, minimum inhibitory concentration [MIC] > or = 1 microg/ml) in 1998 (23.9%) was significantly higher than that in 1992-1993 (0%). The proportion of proline-requiring isolates increased significantly, from 4.4% in 1992-1993 to 54.5% in 1998. The ciprofloxacin MIC90 for the proline-requiring isolates were 32- and 128-fold, respectively, higher than those for the prototrophic isolates and the arginine-requiring isolates. The proportion of isolates with amino-acid substitutions within the QRDRs in GyrA and ParC in the proline-requiring group (55.5%) was significantly higher than that in the prototrophic group (0%). Of the 22 isolates with amino-acid substitutions within the QRDRs in GyrA and ParC, 16 showed the same pulsed-field gel electrophoresis pattern. These results suggest that a close association exists between the increase in the proline-requiring isolates and the increase in the fluoroquinolone-resistant isolates in the gonococci isolated in Fukuoka, and that the prevalence of fluoroquinolone-resistant N. gonorrhoeae isolates with GyrA and ParC substitutions may be mainly caused by the dissemination of a single clone in the community.

Auxotrophy of Burkholderia (Pseudomonas) cepacia from cystic fibrosis patients

The nutritional status of 89 isolates of Burkholderia cepacia from 81 cystic fibrosis (CF) patients was evaluated. Forty of the isolates, from 38 patients, were not able to grow in a minimal medium containing glucose and mineral salts only and were thus auxotrophs. In contrast, all of 29 isolates from non-CF (clinical and environmental) sources were prototrophic. Addition of a pool of amino acids to the minimal medium was sufficient to promote growth of all tested CF auxotrophic isolates. Indeed, phenylalanine, tyrosine, cysteine, methionine, and histidine alone or in combination were required for growth by the majority of the nutritionally deficient B. cepacia isolates. Furthermore, extracts of sputum from CF patients, when added to minimal medium, promoted growth of 29 auxotrophic B. cepacia isolates regardless of their amino acid requirements. Finally, auxotrophic and prototrophic isolates from the same patient exhibited a conserved genotype, as determined by macrorestriction analysis of chromosomal DNA. These results suggest that the auxotrophic mutants are selected from the prototrophic population and maintained by the nutritionally rich environment of the CF airways.

Strain improvement of Claviceps purpurea by protoplast fusion without introducing auxotrophic markers

Protoplasts of morphologically and biochemically different Claviceps purpurea strains producing ergotoxins were fused without introducing selective auxotrophic markers. Fused strains thus obtained differed significantly in biosynthetic activity and morphology from the prototrophic isolates obtained after fusion of the same parent strains marked by auxotrophy. Comparison of the two types of fused strains showed about tenfold higher alkaloid production in fusants obtained from prototrophic strains. Selected stable prototrophic isolates also showed a significant productivity improvement in comparison with the original parent strains.

Activation of ergot alkaloid biosynthesis in prototrophic isolates by Claviceps purpurea protoplast fusion

Intraspecific protoplast fusions were carried out with active ergocornine-ergokryptine and inactive ergocristine Claviceps purpurea strains and vice versa. The isolated prototrophic strains from both types of crossings produced all three alkaloid types, showing that biosynthesis of distinct alkaloid was activated in an inactive partner strain. The prototrophic isolates were stable on minimal medium but they segregated by subculturing on complete medium. In comparison with the original partner strains, differences in morphological and cytological characteristics were also established.

Spheroplast fusion and heterokaryon formation in Mucor racemosus.

Heterokaryons of Mucor racemosus were produced by fusion of spheroplasts from two auxotrophic strains of the fungus. Germinated sporangiospores were converted to spheroplasts by using commercial chitinase and Myxobacter AL-1 chitosanase. Spheroplasts from the auxotrophic strains were mixed in a buffered Ca(NO3)2 solution and fusion occurred. After cell wall regeneration, prototrophs were isolated. The frequency of heterokaryon formation was 1.45 X 10(-4). Prototrophic isolates segregated parental nuclei at a high frequency, indicating that heterokaryons had formed.

GENETIC EVIDENCE FOR ZYGOTIC MEIOSIS IN PHYTOPHTHORA CAPSICI

Variation of several traits among single‐oospore isolates of the heterothallic oomycete, Phytophthora capsici, was studied to determine genetically the place of meiosis in the life cycle. Low percentages of met– offspring were recovered from two crosses of met– X prototrophic isolates. Arg– cultures were also recovered from the crosses indicating the possible presence of a suppressed arg– gene in one of the parental cultures. Three arg– X met– crosses yielded all four of the possible classes of offspring. Thus meiosis was either zygotic or, if gametangial, the original parental cultures must have been heterozygous at both the arg and met loci. However, when these parental cultures were crossed, only prototrophic offspring were recovered. A ratio of 3 prototrophs: 1 met– was obtained from cross R in which two prototrophic offspring from a previous arg– X met– cross were mated. This indicated the presence of a suppressor of met– and may explain the low recovery of met– offspring from earlier crosses. From backcrosses of met– offspring from this cross to the A2 prototrophic parent, ratios close to the expected 1:1 were obtained. When the A1 prototrophic parent of cross R (K‐10) was crossed to an A2 prototrophic isolate, met– offspring were again recovered, which indicated that K‐10 carried a suppressed met deficiency. In two crosses of streptomycin‐resistant (Sr) X sensitive (Ss) isolates, ratio of 108 Ss: 14 Sr and 84 Ss:14 Sr were obtained. Although 1:1 ratios would have been expected if meiosis were zygotic, segregation of Ss and Sr in the F1 generation indicated that gametangial meiosis was unlikely. Segregation of the A1 and A2 mating types in all crosses also indicated that meiosis was zygotic in P. capsici. Possible control of mating type by a single pair of alleles, by plasmids, and by more complex mechanisms is discussed in relation to the mating type ratios obtained.