Methods for electrophoretic karyotyping of filamentous fungi in the genus Trichoderma

Methods for electrophoretic karyotyping of filamentous fungi in the genus Trichoderma were developed. These techniques permitted the separation and visualization of intact chromosomes from viable protoplasts. Three strains were analyzed: Trichoderma harzianum strains T12 his-2 and T95 lys-1, and a prototrophic strain (1295-22) produced by protoplast fusion of T12 his-2 with T95 lys-1. Four chromosome bands ranging in size from 2.2 Mb (megabase pairs) to 5.4 Mb were visualized with strain T95 lys-1, whereas two chromosome bands were visualized for strains T12 his-2 and 1295-22. The largest chromosome of all three strains seems to be similar in size and has been estimated to be approximately 5.4 Mb. All remaining chromosomes observed were dissimilar in size. Methods for protoplast isolation, protoplast embedding, and electrophoretic conditions useful for separation of intact chromosomes ranging in size from 50 kb (kilobase pairs) up to approximately 6.0 Mb utilizing transverse alternating field electrophoresis (TAFE) will be discussed. The techniques provided should be applicable to a variety of lower eukaryotic organisms when using the TAFE system.     

Intrauterine 5-aminolevulinic acid induces selective fluorescence and photodynamic ablation of the rat endometrium

Electrophoretic karyotyping of the two most widely studied strains of Phanerochaete chrysosporium, BKMF-1767 and ME-446, has been determined using transverse alternating field electrophoresis. The genomic DNA of BKMF-1767 was resolved into 10 chromosomes ranging in size from 1.8-5.0 Mb, amounting to a total genome size of about 29 Mb. The genomic DNA of strain ME-446, on the other hand, was resolved into 11 chromosomes, amounting to a total genome size of about 32 Mb. Lignin peroxidase genes have been localized to five chromosomes in strain BKMF-1767 and to four chromosomes in strain ME-446.     

Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats

In order to determine primary genetic events which occur during the diversification of a Pseudomonas aeruginosa clone in natural habitats, comparative genome analysis of 21 isolates of a predominant clone, called clone C, derived mainly from patients with cystic fibrosis (CF) and the aquatic environment, was carried out. Physical chromosome maps were constructed for the restriction enzymes SpeI, PacI, SwaI and I-CeuI by one and two-dimensional pulsed-field gel electrophoresis and by comparison with the existing strain C map. The positioning of 26 genes generated the genetic maps. Chromosome size varied between 6345 and 6606 kilobase-pairs (kb). A plasmid of 95 kb was detected in the strains of non-CF origin and, in addition, was found to be integrated into the chromosome of all strains but one CF isolate. Four subgroups of clone C strains were discriminated by the acquisition and loss of large blocks of DNA that could cover more than 10% of the chromosome size. The exchange of DNA blocks which ranged in size from 1 kb to 214 kb occurred preferentially around the terminus of replication region which is poor in biosynthetic genes. Genetic material which was additionally introduced into strain C in comparison with strain PAO seems to be a target of mutational processes in clone C strains. Within and among subgroups CF isolates frequently exhibited large inversions affecting the whole chromosomal structure. We concluded that the exchange of DNA blocks by mechanisms of horizontal transfer and large chromosomal inversions are major factors leading to the divergence of a clone in the species P. aeruginosa.     

Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis

Sequence heterogeneities in 16S rRNA genes from individual strains of Paenibacillus polymyxa were detected by sequence-dependent separation of PCR products by temperature gradient gel electrophoresis (TGGE). A fragment of the 16S rRNA genes, comprising variable regions V6 to V8, was used as a target sequence for amplifications. PCR products from P. polymyxa (type strain) emerged as a well-defined pattern of bands in the gradient gel. Six plasmids with different inserts, individually demonstrating the migration characteristics of single bands of the pattern, were obtained by cloning the PCR products. Their sequences were analyzed as a representative sample of the total heterogeneity. An amount of 10 variant nucleotide positions in the fragment of 347 bp was observed, with all substitutions conserving the relevant secondary structures of the V6 and V8 regions in the RNA molecules. Hybridizations with specifically designed probes demonstrated different chromosomal locations of the respective rRNA genes. Amplifications of reverse-transcribed rRNA from ribosome preparations, as well as whole-cell hybridizations, revealed a predominant representation of particular sequences in ribosomes of exponentially growing laboratory cultures. Different strains of P. polymyxa showed not only remarkably differing patterns of PCR products in TGGE analysis but also discriminative whole-cell labeling with the designed oligonucleotide probes, indicating the different representation of individual sequences in active ribosomes. Our results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts.     

Extrachromosomal elements in a variety of strains representing the Bacteroides fragilis group of organisms

Previous nucleic acid association studies have identified at least nine deoxyribonucleic acid (DNA) homology classes of the Bacteroides fragilis group of organisms. Using these classes as a taxonomic framework, we have screened representative strains of the B. fragilis group for the presence of extrachromosomal (plasmid) DNA. [3H]thymidine-labeled cell lysates were subjected to sodium dodecyl sulfate-salt precipitation, and supernatant fractions from such preparations were analyzed using cesium chloride-ethidium bromide equilibrium centrifugation. One strain from each group was examined in this fashion. Five of the strains were judged to contain no detectable plasmid DNA; however, four strains were observed to yield satellite bands corresponding to covalently closed circular plasmid DNA. Plasmid DNA from such gradients was subjected to velocity sedimentation through both neutral and alkaline sucrose gradients to determine molecular size. A 23 X 10(6)-molecular-weight plasmid was found in a B. fragilis strain representing one DNA homology group of this species, whereas a 3 X 10(6)-molecular-weight plasmid was found in a B. fragilis strain representing a second homology group. Similarly, a 31 X 10(6)-molecular-weight plasmid was found in a Bacteroides thetaiotaomicron strain representing one DNA homology group of this species, whereas a 3 X 10(6)-molecular-weight plasmid was found in a B. thetaiotaomicron strain representing a second homology group. In all instances, the small-molecular weight plasmids were present to the extent of about 15 copies per chromosomal equivalent, whereas the large plasmids were present to the extent of approximately 1 copy per chromosomal equivalent. The biological function of these plasmids is unknown.     

Revised estimates of enterococcal chromosomal sizes

We previously reported that the chromosomal sizes of four strains of enterococci ranged from 2,045 to 2,761 kb. Extensive analysis and mapping subsequently confirmed the size of Enterococcus faecalis strain OG1 as 2,825 kb (prior size estimate range, 2,750-2,761 kb) (Murray et al., J. Bacteriol. 175, 5216, 1993). However, using variable conditions of electrophoresis and additional digestions, revised size estimates for the other strains are 2,852-3,093 kb for E. faecalis strain JH2-2 (prior range, 2,008-2,135 kb), 2,910-3,065 kb for E. faecalis strain HH67 (prior range, 2,170-2,288 kb), and 2,334-2,558 for E. faecium strain GE-1 (prior range, 2,045-2,155 kb). The earlier underestimations of the chromosomal sizes were due to the inconsistent presence of a large fragment, likely caused by shearing of the DNA during handling, causing it to be considered a partial digestion product, and failure to resolve multiple fragments of the same approximate size.     

The number of direct repeats in hagA is variable among Porphyromonas gingivalis strains

The coding sequence for the surface protein hemagglutinin A (HagA) of Porphyromonas gingivalis 381 has previously been shown to contain four direct 1.35-kb repeats, designated repHA. This study was performed to determine if the number of repHA units in hagA is consistently 4 or if allelic polymorphism exists among strains and/or upon multiple passage of P. gingivalis. To this end, primers which were homologous to the regions directly 5' and 3' of the repeat domain in hagA were synthesized. PCR conditions which allowed amplification of the 8.4-kb repeat region between the primers in P. gingivalis 381 were established. Genomic DNA templates from 13 other P. gingivalis strains and 9 fresh clinical isolates from patients were analyzed under the same conditions as used above. Analysis of these PCR products demonstrated that the strains tested had different numbers (two to four) of repHA units in the respective hagA genes. The PCR products of 8.4, 7.0, and 5.7 kb represent four, three, and two repeats, respectively. One strain from each group (381, four repeats; W83, three repeats; and AJW4, two repeats) was also tested to determine if the number of repeats remained invariant upon passaging onto solid medium. No variability in the number of repeats in hagA within a strain was detected after 18 passages. P. gingivalis 381 was chosen for further testing in a mouse abscess model to determine if conditions of in vivo growth would select for deletions or duplications of the repeated sequences. Five days after infection, no change in the number of repeats was detected in cells recovered from either nonimmunized or preimmunized mice. This data indicates an interstrain variability of the number of repeat units and hence a size variability of the HagA protein of P. gingivalis, but unlike some surface antigens of other pathogenic species, the number of repeats remains relatively stable given the conditions of growth tested here.     

Further molecular characterization and stability of the live oral attenuated cholera vaccine strain CVD103-HgR

Vibrio cholerae CVD103-HgR, the first live attenuated vaccine licensed for human use produced by recombinant DNA technology, was genetically compared to its parent strains 569B and CVD103. The genetic stability for both lyophilized vaccine in final container form and for viable organisms shed from vaccinees was determined. Results obtained lead us to conclude: (i) the genetic composition of the examined genes in CVD103-HgR is identical to that of the parent strains except for the alterations induced; (ii) the level of mercury resistance depends on the orientation of the mer operon within hlyA, with the highest level being observed for the orientation found in CVD103-HgR; (iii) no DNA sequences from plasmids used in construction remain in the genome; (iv) the strain is genetically stable; and (v) both CVD103-HgR and its parent strains contain defective lysogenic prophages. We have further confirmed that a certain amount of restriction fragment length polymorphism (RFLP) exists around the chromosomal ctx locus within V. cholerae strains of the classical biotype (detectable on chromosomal DNA restricted by either HindIII or EcoRI, but not PstI).     

Chromosomal polymorphism of the yeast Yarrowia lipolytica and related species: electrophoretic karyotyping and hybridization with cloned genes

Significant differences in electrophoretic karyotyping patterns were found among 27 strains of Y. lipolytica. Twenty-one of these strains were classified into four groups of similar karyotypes while six strains showed unique karyotypes. Chromosomal DNAs of different strains were hybridized with cloned genes of Y. lipolytica (URA3, LEU2, ARS18 and ARS68), which revealed four different bands in most strains. We conclude that the haploid chromosome number of Y. lipolytica is at least four, and possibly five or six. Electrophoretic karyotyping and hybridization with cloned genes of Y. lipolytica provided evidence of a large divergence between Y. lipolytica and related species of Saccharomycopsis, Endomycopsella and Endomyces.     

Lipase specificity toward some acetylenic and olefinic alcohols in the esterification of pentanoic and stearic acids

The Pichia pastoris TRP1 and HIS3 genes were cloned by complementation of the Saccharomyces cerevisiae trip1 and his3 mutants, respectively, and their nucleotide sequence was determined. The P. pastoris TRP1 gene includes an open reading frame (ORF) of 714 nucleotides corresponding to a polypeptide of 237 amino acids whose sequence shares about 40% identity with that of TRP1 encoding proteins in other yeast species. DNA sequencing showed that an ORF of 858 nucleotides, encoding a protein of 285 amino acids with high homology to inorganic pyrophosphatases (IPP1), is located downstream of the P. pastoris TRP1 gene. Both genes converge in this chromosomal region, showing a genetic organization analogous to that found in the Kluyveromyces lactis genome. The P. pastoris HIS3 gene possesses an ORF of 675 nucleotides, encoding a polypeptide of 224 amino acids which shows 74.1% identity to the homologous S. cerevisiae protein. The hexameric consensus GCN4 binding sequence (TGACTC), characteristic of many amino acid biosynthetic genes, is present in the promoter region.     

Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39

Three strains of Comamonas testosteroni were isolated from river sediment for the ability to degrade phenanthrene; two of the strains also grew on naphthalene, and one strain also grew on anthracene. The homology of the genes for polycyclic aromatic hydrocarbon degradation in these strains to the classical genes (nah) for naphthalene degradation from Pseudomonas putida NCIB 9816-4 was determined. The three C. testosteroni strains showed no homology to the nah gene probe even under low-stringency conditions. The genes for naphthalene and phenanthrene degradation were cloned from one of the three C. testosteroni strains. Two cosmid clones expressing polycyclic aromatic hydrocarbon dioxygenase activity were identified from a library prepared with genomic DNA from C. testosteroni GZ39. The genes coding for the first two enzymes in the catabolic pathway, phenanthrene dioxygenase and cis-phenanthrene dihydrodiol dehydrogenase, were localized to a 5.4-kb NcoI-PstI fragment by subcloning and gene expression experiments. Further subcloning and analysis revealed a novel organization of the genes, with the gene for cis-phenanthrene dihydrodiol dehydrogenase located between the genes for the individual phenanthrene dioxygenase components. A Southern blot with the cloned genes from C. testosteroni GZ39 confirmed that these genes are distinct from those found in P. putida NCIB 9816-4. Southern blots also demonstrated that C. testosteroni GZ38A possesses genes for phenanthrene degradation that are similar to those cloned from C. testosteroni GZ39. However, C. testosteroni GZ42 possesses genes for phenanthrene degradation that are not homologous to those cloned from C. testosteroni GZ39. This suggests that there are at least two different sets of genes for the degradation of phenanthrene among the three C. testosteroni strains.     

Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution

We studied the ancestry of virulence-associated genes in Escherichia coli by examining chromosomal regions specific to pathogenic isolates. The four virulence determinants examined were the alpha-hemolysin (hly) loci hlyI and hlyII, the type II capsule gene cluster kps, and the P (pap) and S (sfa) fimbria gene clusters. All four loci were shown previously to be associated with pathogenicity islands of uropathogenic E. coli isolates. The hly, kps, sfa, and pap regions each have an unexpected clustered distribution among the E. coli collection of reference (ECOR) strains, but all these regions were absent from a collection of diarrheagenic E. coli isolates. Strains in the ECOR subgroup B2 typically had a combination of at least three of the four loci, and all strains in subgroup D had a copy of the kps and pap clusters. In contrast, only four strains in subgroup A had either hly, kps, sfa, or pap, and no subgroup A strains had all four together. Strains of subgroup B1 were devoid of all four virulence regions, with the exception of one isolate that had a copy of the sfa gene cluster. This phylogenetic distribution of strain-specific sequences corresponds to the ECOR groups with the largest genome size, namely, B2 and D. We propose that the pathogenicity islands are ancestral to subgroups B2 and D and were acquired after speciation, with subsequent horizontal transfer into some group A, B1, and E lineages. These results suggest that the hly, kps, sfa, and pap pathogenicity determinants may play a role in the evolution of enteric bacteria quite apart from, and perhaps with precedence over, their ability to cause disease.     

Hyperlactatemia during acute severe asthma

The prevalence of the four human malaria parasites was investigated among malaria patients at northern, central and southern towns in Thailand along the border with Myanmar between September 1995 and May 1996. Thin smears obtained from 548 Thai and Burmese patients were reviewed by an acridine orange staining method, and many mixed infections with two to four species, including P. malariae and P. ovale, were detected. These diagnostic results were compared with those by two PCR-based diagnoses, microtitre plate hybridization (MPH) and a nested PCR method, both of which targets the same, species-specific regions in the 18S rRNA genes. In both PCR diagnoses, many P. malariae and P. ovale infections were also detected. Detection sensitivity of P. malariae infection was higher in nested PCR than MPH, and a total prevalence of P. malariae infection estimated by nested PCR reached 24.3% (133/548). In 16 of them, the size of PCR products amplified by the P. malariae-specific primer was about 20-bp shorter than the expected size of 115-bp. Four of 16 possessed two different bands with normal and shorter sizes, suggesting that P. malariae isolates may be separated into two types, and that those with shorter products may be new variant form (s) with a nucleotide deletion in the target region. On the other hand, 21 P. ovale infections (3.8%) were detected by nested PCR, but four of them were MPH-negative because of the sequence variation at the probe region. These results indicated that the prevalence of P. malariae and P. ovale along the Thai-Myanmar border may be substantially higher than previously reported.     

Mechanism of bacteriophage SfII-mediated serotype conversion in Shigella flexneri

We have isolated the lysogenic bacteriophage SfII, which mediates glucosylation of Shigella flexneri O-antigen, resulting in expression of the type II antigen. SfII belongs to group A of the Bradley classification and has a genome size of 42.3kb. DNA sequencing of a 4 kb BamHI subclone identified four open reading frames (ORFs), of which only two were found to be necessary for serotype conversion. These genes were named bgt, which encodes a putative bactoprenol glucosyl transferase, and gtrII, encoding the putative type II antigen determining glucosyl transferase. These genes are adjacent to the integrase gene (int) and attachment site (attP), which are highly homologous to those of Salmonella bacteriophage P22. Another ORF encoded a highly hydrophobic protein of 120 amino acids with homologues in Escherichia coli, Salmonella bacteriophage P22 and S. flexneri. Previous studies identified gtrX, the glucosyl transferase gene, of bacteriophage SfX, which also glucosylates the O-antigen specifically. We determined that gtrX-mediated expression of the group 7,8 antigen also requires bgt. This allowed us to identify gtrII as being the serotype antigen II determining glucosyl transferase. Southern hybridization and polymerase chain reaction (PCR) analyses indicated that bgt homologues exist in the genomes of all S. flexneri serotypes and in E. coli K-12, whereas gtrII was only detected in strains of serotype 2. Transposon TnphoA-derived chromosomal mutations of bgt and gtrII in S. flexneri serotype 2a were isolated and characterized. [35S]-methionine labelling and the use of a T7 RNA polymerase expression system identified a protein of 34kDa corresponding to Bgt. However, GtrII, which has a predicted molecular weight of 55 kDa, was not detected. We propose that the function of Bgt is to transfer the glucose residues from the UDP-glucose onto bactoprenol and GtrII then transfers the glucose onto the O-antigen repeat unit at the rhamnose III position. The chromosomal organization of these serotype-converting genes, when compared with their homologues in E. coli K-12 chromosome and the P22 bacteriophage genome, were very similar. This suggests that the regions encode similar functions in these organisms and have a similar evolutionary origin.     

Leishmania major: histone H1 gene expression from the sw3 locus

Histone H1 in the parasitic protozoan Leishmania is a developmentally regulated protein encoded by the sw3 gene. Here we report that histone H1 variants exist in different Leishmania species and strains of L. major and that they are encoded by polymorphic genes. Amplification of the sw3 gene from the genome of three strains of L. major gave rise to different products in each strain, suggesting the presence of a multicopy gene family. In L. major, these genes were all restricted to a 50-kb Bg/II fragment found on a chromosomal band of 1.3 Mb (chromosome 27). The detection of RFLPs in this locus demonstrated its heterogeneity within several species and strains of Leishmania. Two different copies of sw3 (sw3.0 and sw3.1) were identified after screening a cosmid library containing L. major strain Friedlin genomic DNA. They were identical in their 5' UTRs and open reading frames, but differed in their 3' UTRs. With respect to the originally cloned copy of sw3 from L. major strain LV39, their open reading frames lacked a repeat unit of 9 amino acids. Immunoblots of L. guyanensis parasites transfected with these cosmids revealed that both copies could give rise to the histone H1 protein. The characterization of this locus will now make possible a detailed analysis of the function of histone H1 in Leishmania, as well as permit the dissection of the molecular mechanisms governing the developmental regulation of the sw3 gene.     

Microstructure and properties of copper and aluminum alloy 3003 heavily worked by equal channel angular extrusion

A technique invented in the former Soviet Union and recently introduced in the United States, called equal channel angular extrusion (ECAE), produces intense and uniform deformation by simple shear and is applied to 25 × 25 × 152-mm billets of Cu 101 and Al 3003. Microcrystalline structures with a grain size of 0.2 to 0.4 μm are created during room-temperature multipass ECAE deformation for true strains lying in the range ε=2.31 to 9.24. Evidence shows that intense simple shear deformation promotes dynamic or continuous recrystallization by subgrain rotation. The effects of the number of extrusion passes and deformation route for Cu 101, and the deformation route after four passes for Al 3003, are studied. Increasing the number of ECAE passes in Cu 101 causes strength to reach saturation and grain refinement stabilization after four passes (true strain of 4.68), and subgrain misorientation to increase as the number of passes increases. For multipass ECAE with billet orientation constant (route A) or rotated 90 deg between all passes (route B), two levels of structures are created inside the original grains: shear bands (first level) and very fine subgrains (second level) within the shear bands. For a billet rotation of 180 deg between passes (route C), an unusual event is observed. At each even numbered pass, shear bands nearly disappear and only subgrains are present inside the original grains. Route B gives the highest strength, whereas route C produces a more equiaxed and stable microstructure. Subsequent static recrystallization increases the average grain size to 5 to 10 μm.     

The molecular karyotype of the megabase chromosomes of Trypanosoma brucei and the assignment of chromosome markers

We present the molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock TREU927/4 (927). We have identified 11 diploid chromosomes ranging in size from 1 to 5.2 Mb approximately and pairs of homologues differ in size by up to 15%. A total of 401 cDNA probes were hybridised to T. brucei stock 927 chromosomes and 168 chromosome-specific markers were defined. Most of these markers were hybridised to the separated chromosomal DNA of two other cloned field isolates and four F1 progeny clones from a laboratory cross. The chromosomes vary in size by up to two and a half times between stocks and the DNA content of the 11 pairs of homologues varies by up to 33% in different stocks. Stock 927 contains the smallest chromosomes and the least nuclear genomic DNA. Nevertheless, all 11 syntenic groups of cDNA probes are maintained in all stocks. In the F1 hybrids only we have identified one extra PFG band to which none of our probes hybridise. We have shown that probes thought to be specific for the bloodstream-form variant surface glycoprotein expression sites hybridise to different chromosomes in different stocks and may hybridise to either one or both of a homologous pair of chromosomes. We have also determined the chromosomal location of the ribosomal RNA gene arrays.     

Repressor titration: a novel system for selection and stable maintenance of recombinant plasmids

The propagation of recombinant plasmids in bacterial hosts, particularly in Escherichia coli, is essential for the amplification and manipulation of cloned DNA and the production of recombinant proteins. The isolation of bacterial transformants and subsequent stable plasmid maintenance have traditionally been accomplished using plasmid-borne selectable marker genes. Here we describe a novel system that employs plasmid-mediated repressor titration to activate a chromosomal selectable marker, removing the requirement for a plasmid-borne marker gene. A modified E.coli host strain containing a conditionally essential chromosomal gene (kan) under the control of the lac operator/promoter, lac O/P, has been constructed. In the absence of an inducer (allolactose or IPTG) this strain, DH1 lackan , cannot grow on kanamycin-containing media due to the repression of kan expression by LacI protein binding to lac O/P. Transformation with a high copy-number plasmid containing the lac operator, lac O, effectively induces kan expression by titrating LacI from the operator. This strain thus allows the selection of plasmids without antibiotic resistance genes (they need only contain lac O and an origin of replication) which have clear advantages for use as gene therapy vectors. Regulation in the same way of an essential, endogenous bacterial gene will allow the production of recombinant therapeutics devoid of residual antibiotic contamination.     

Expression of var genes located within polymorphic subtelomeric domains of Plasmodium falciparum chromosomes

Plasmodium falciparum var genes encode a diverse family of proteins, located on the surfaces of infected erythrocytes, which are implicated in the pathology of human malaria through antigenic variation and adhesion of infected erythrocytes to the microvasculature. We have constructed a complete representative telomere-to-telomere yeast artificial chromosome (YAC) contig map of the P. falciparum chromosome 8 for studies on the chromosomal organization, distribution, and expression of var genes. Three var gene loci were identified on chromosome 8, two of which map close to the telomeres at either end of the chromosome. Analysis of the previously described chromosome 2 contig map and random P. falciparum telomeric YAC clones revealed that most, if not all, 14 P. falciparum chromosomes contain var genes in a subtelomeric location. Mapping the chromosomal location of var genes expressed in a long-term culture of the P. falciparum isolate Dd2 revealed that four of the five different expressed var genes identified map within subtelomeric locations. Expression of var genes from a chromosomal domain known for frequent rearrangements has important implications for the mechanism of var gene switching and the generation of novel antigenic and adhesive phenotypes.