A rapid and efficient method for multiple-site mutagenesis with a modified overlap extension PCR

A rapid and efficient method to perform site-directed mutagenesis based on an improved version of overlap extension by polymerase chain reaction (OE-PCR) is demonstrated in this paper. For this method, which we name modified (M)OE-PCR, there are five steps: (1) synthesis of individual DNA fragments of interest (with average 20-bp overlap between adjacent fragments) by PCR with high-fidelity pfu DNA polymerase, (2) double-mixing (every two adjacent fragments are mixed to implement OE-PCR without primers), (3) pre-extension (the teams above are mixed to obtain full-length reassembled DNA by OE-PCR without primers), (4) synthesis of the entire DNA of interest by PCR with outermost primers and template DNA from step 3, (5) post-extension (ten cycles of PCR at 72°C for annealing and extension are implemented). The method is rapid, simple and error-free. It provides an efficient choice, especially for multiple-site mutagenesis of DNAs; and it can theoretically be applied to the modification of any DNA fragment. Using the MOE-PCR method, we have successfully obtained a modified sam1 gene with eight rare codons optimized simultaneously. Electronic Supplementary Material Supplementary material is available for this article at .     

Improved PCR-based gene synthesis method and its application to the Citrobacter freundii phytase gene codon modification

Gene synthesis technologies provide a powerful tool for increasing protein expression through codon optimization and gene modification. Here we describe an improved PCR-based gene synthesis technology, which is accurate, simple and cheap. The improved PCR-based gene synthesis (IPS) method consists of two steps. The first one is the synthesis of 300-400 bp fragments by PCR reaction with Pfu DNA polymerase from 60-mer and 30-mer oligonucleotides with a 15 bp overlap. The second one is assembling of fragments from the first step into the full-length gene by PCR reaction. Using this approach, we have successfully synthesized a modified phytase gene with 1256 bp in length with optimal codons for expression in Pichia pastoris. P. pastoris strain that expressed the modified phytase gene (phyA-mod) showed a 50% increase in phytase activity level. In addition, we propose an inexpensive method for error correction, based on overlap-extension PCR (OE-PCR).     

A PCR method for the detection and differentiation of Lentinus edodes and Trametes versicolor in defined-mixed cultures used for wastewater treatment

A PCR-based method for the quantitative detection of Lentinus edodes and Trametes versicolor, two ligninolytic fungi applied for wastewater treatment and bioremediation, was developed. Genomic DNA was used to optimize a PCR method targeting the conserved copper-binding sequence of laccase genes. The method allowed the quantitative detection and differentiation of these fungi in single and defined-mixed cultures after fractionation of the PCR products by electrophoresis in agarose gels. Amplified products of about 150 bp for L. edodes, and about 200 bp for T. versicolor were purified and cloned. The PCR method showed a linear detection response in the 1.0 g–1 ng range. The same method was tested with genomic DNA from a third fungus (Phanerochaete chrysosporium), yielding a fragment of about 400 bp. Southern-blot and DNA sequence analysis indicated that a specific PCR product was amplified from each genome, and that these corresponded to sequences of laccase genes. This PCR protocol permits the detection and differentiation of three ligninolytic fungi by amplifying DNA fragments of different sizes using a single pair of primers, without further enzymatic restriction of the PCR products. This method has potential use in the monitoring, evaluation, and improvement of fungal cultures used in wastewater treatment processes.     

Comparison of ligninolytic activities of selected white-rot fungi

Summary Six fast growing ligninolytic white-rot fungi were compared with Phanerochaete chrysosporium. The results showed that the fungi have similar ligninolytic systems, although minor differences exist. Like in P. chrysosporium the ligninolytic system could be induced by veratryl alcohol in Coriolus versicolor and Chrysosporium pruinosum. These three lignin peroxidase producing fungi were the fastest lignin degraders in stationary cultures, whereas in agitated cultures Bjerkandera adusta showed highest lignin degradation rates. Metabolites accumulating during the degradation of veratryl alcohol were analyzed and compared. Peroxidase production seems to be a common feature of all the tested fungi. Polyclonal antibodies against the lignin peroxidase with pl of 4.65 from P. chrysosporium reacted with the extracellular peroxidases of C. pruinosum, C. versicolor and B. adusta, but not with those of Pleurotus ostreatus.Dedicated to Professor Dr. Hans-Jürgen Rehm on the occasion of his 60th birthday     

Enhanced ligninolytic enzyme production and degrading capability of Phanerochaete chrysosporium and Trametes versicolor

Ligninolytic enzyme production by the white-rot fungi Phanerochaete chrysosporium and Trametes versicolor precultivated with different insoluble lignocellulosic materials (grape seeds, barley bran and wood shavings) was investigated. Cultures of Phanerochaete chrysosporium precultivated with grape seeds and barley bran showed maximum lignin peroxidase (LiP) and manganese-dependent peroxidase (MnP) activities (1000 and 1232 U/l, respectively). Trametes versicolor precultivated with the same lignocellulosic residues showed the maximum laccase activity (around 250 U/l). For both fungi, the ligninolytic activities were about two-fold higher than those attained in the control cultures. In vitro decolorization of the polymeric dye Poly R-478 by the extracellular liquid obtained in the above-mentioned cultures was monitored in order to determine the respective capabilities of laccase, LiP and MnP. It is noteworthy that the degrading capability of LiP when P. chrysosporium was precultivated with barley bran gave a percentage of Poly R-478 decolorization of about 80% in 100 s, whereas control cultures showed a lower percentage, around 20%, after 2 min of the decolorization reaction.     

Targeted transformation in Coprinus cinereus

Summary We examined the influence of DNA form and size on the arrangement and genomic location of transforming DNA sequences in the basidiomycete Coprinus cinereus. Protoplasts with either single or double mutations in the tryptophan synthetase (TRPI) gene were transformed with cloned copies of this gene which contained only a single DNA strand, contained a specific single nick within the C. cinereus sequences (4.8 kb), contained a specific double-strand break, or contained an additional 35 kb of flanking genomic sequences. Gene replacement events were recovered when each DNA type was used. However, none of these substrates offers a substantial improvement in transformation or targeting frequency when compared to supercoiled circular DNA, which has allowed recovery of both gene replacements as well as homologous insertions in 5 % of the transformants analyzed. The frequency of transformants carrying tandem insertions with multiple copies of the transforming DNA was reduced when single-stranded DNA was used, and increased when DNA containing double-strand breaks was used. These results have important implications for the efficient design of targeted transformation and co-transformation experiments.     

Ligninolytic enzymes of selected white rot fungi cultivated on wheat straw

Ligninolytic enzymes of the white rot fungiCoriolopsis polyzona, Phanerochaete chrysosporium, andTrametes versicolor growing on wheat straw under nearly natural conditions were investigated. Manganese peroxidase (MnP), secreted as early as on day 3, was dominant over other activities during the initial phase (the first 10 days). Its activity profile was similar in all the three fungi. Lignin peroxidase (LIP) was not detected in the extracellular enzyme extracts ofC. polyzona andP. chrysosporium cultures.T. versicolor secreted LIP after 10 d of growth. Another, recently described, enzyme activity of manganese-independent peroxidase (MIP) was detected in all the three fungi tested and it appeared on about day 5 (later than MnP and earlier than LIP); it was the dominant activity after day 10. Laccase activity appeared at basal levels without any significant changes. Pyranose 2-oxidase was probably the major extracellular H₂O₂-generating activity (with all the three fungi) that appeared contemporarily with MnP, increased with time, peaking on day 17–18. Glyoxal oxidase could not be detected with any of the fungi.     

PCR amplification of lignin peroxidase genes in white rot fungi

Summary Degenerate oligonucleotides encoding the two conserved histidine regions of the Phanerochaete chrysosporium BKM-F-1767 lignin peroxidase gene have been used as PCR primers to clone lignin peroxidase genes from the genomic DMA of four different white rot fungi.     

Effect of culture conditions on manganese peroxidase production and activity by some white rot fungi

The ligninolytic system of white rot fungi is primarily composed of lignin peroxidase, manganese peroxidase (MnP) and laccase. The present work was carried out to determine the best culture conditions for production of MnP and its activity in the relatively little-explored cultures of Dichomitus squalens, Irpex flavus and Polyporus sanguineus, as compared with conditions for Phanerochaete chrysosporium and Coriolus versicolor. Studies on enzyme production under different nutritional conditions revealed veratryl alcohol, guaiacol, Reax 80 and Polyfon H to be excellent MnP inducers. Electronic Publication     

Hierarchical gene synthesis using DNA microchip oligonucleotides

High-cost of oligonucleotides is one of the major problems to low-cost gene synthesis. Although DNA oligonucleotides from cleavable DNA microchips has been adopted for the low-cost gene synthesis, construction of DNA molecules larger than 1 kb has been largely hampered due to the difficulties of DNA assembly associated with the negligible quantity of chip oligonucleotides. Here we report a hierarchical method for the synthesis of large genes using oligonucleotides from programmable DNA microchips. Using this hierarchical method, we successfully synthesized 1056 bp Dpo4 and 2325 bp Pfu DNA polymerase genes as models. This hierarchical strategy can be further expanded for the syntheses of multiple large genes in a scalable manner.     

Construction of a bacterial artificial chromosome (BAC) library of Coprinus cinereus

A bacterial artificial chromosome (BAC) library of the genomic DNA of Coprinus cinereus strain MP#2 was constructed using the BAC vector pBACTZ, which carries the C. cinereus trp1 gene. The library consists of 1536 clones. Analysis of inserts in some of the clones suggested that the library covers five times the C. cinereus genome. Screening of the BAC clones using ten markers mapped on nine different chromosomes also indicated that the library is likely to cover the whole length of the genomic DNA. We show an example of transformation of C. cinereus with BACs containing inserts of longer than 170kb.     

Nitrogen and carbon regulation of lignin peroxidase and enzymes of nitrogen metabolism inPhanerochaete chrysosporium

The regulation of nitrogen metabolism pathways was examined inPhanerochaete chrysosporium in relation to the repression of lignin peroxidase by nitrogen or carbon in this fungus. Under conditions of nitrogen derepression,P. chrysosporium synthesizes the amidohydrolases, formamidase (EC 3.5.1.9) and acetamidase (EC 3.5.1.4) and the enzymes of purine catabolism uricase (EC 1.7.3.3), allantoinase (EC 3.5.2.5), and allantoicase (EC 3.5.3.4). Formamidase is repressed to low levels in the presence of ammonium and there is no apparent control of this enzyme by carbon catabolite repression. Although formamide is a nitrogen source, it is not a carbon source forP. chrysosporium. Glutamate totally represses formamidase. Uricase, allantoinase, and allantoicase are also regulated by nitrogen repression but not carbon catabolite repression. Urease is synthesized at similar levels irrespective of the nitrogen or carbon conditions. The sensitivity of uricase, allantoinase, and allantoicase to nitrogen repression is less than that of formamidase. In contrast to formamidase, glutamate is not a more powerful repressor of uricase, allantoinase, and allantoicase compared with ammonium. No pathway-specific induction is required for the synthesis of formamidase, uricase, allantoinase, and allantoicase. Altogether these features indicate that nitrogen metabolism inP. chrysosporium is similar to that inAspergillus nidulans in its regulation, despite the absence of pathway-specific induction of the enzymes examined. These results are consistent with the existence of a regulatory gene mediating nitrogen catabolite repression similar to theA. nidulans areA gene inP. chrysosporium. Although glycerol acts as a nonrepressive carbon source for lignin peroxidase production (except when used at high concentrations), glutamate totally represses lignin peroxidase even in cultures with glycerol. This indicates that carbon regulation and nitrogen regulation of lignin peroxidase may not be separated inP. chrysosporium.     

The ability of white-rot fungi to degrade the endocrine-disrupting compound nonylphenol

Phanerochaete chrysosporium, Pleurotus ostreatus, Trametes versicolor and Bjerkandera sp. BOL13 were tested for their ability to degrade the endocrine-disrupting compound nonylphenol at an initial concentration of 100 mg l^–1. The highest removals were achieved with T. versicolor and Bjerkandera sp. BOL13, which were able to degrade 97 mg l^–1 and 99 mg l^–1 of nonylphenol in 25 days of incubation, respectively. Nonylphenol removal was associated with the production of laccase by T. versicolor, but the levels of laccase, manganese peroxidase and lignin peroxidase produced by Bjerkandera sp. BOL13 were very low. At 14°C, T. versicolor and Bjerkandera sp. BOL13 sustained the removal of 88 mg l^–1 and 79 mg l^–1 of nonylphenol, respectively. No pollutant removal was recorded at 4°C, although both fungi could grow at this temperature in the absence of nonylphenol. A microtoxicity assay showed that the fungi produced compounds that were toxic to Vibrio fischerii; and thus a reduction in toxicity could not be correlated with nonylphenol metabolism. T. versicolor and Bjerkandera sp. BOL13 were capable of colonizing soil artificially contaminated with 430 mg kg^–1 of nonylphenol. Only 1.3±0.1% of nonylphenol remained in the soil after 5 weeks of incubation.     

Comparison of abilities of white-rot fungi to mineralize selected xenobiotic compounds

Summary The abilities of the white-rot fungi Chrysosporium lignorum, Trametes versicolor, Phanerochaete chrysosporium and Stereum hirsutum to mineralize 3,4-dichloroaniline, dieldrin and phenanthrene were investigated. S. hirsutum did not mineralize any of the test compounds but the other strains partly mineralized them all to varying degrees. The relative degradation rates per unit biomass were T. versicolor > C. lignorum > P. chrysosporium. Evidence was obtained for the production of water-soluble metabolic intermediates but no attempt was made to characterize these. It was found that mineral salts-glucose medium supplemented with trace mineral nutrients, vitamins and 1.5 mm 3,4-dimethoxybenzyl alcohol (veratryl alcohol) resulted in the highest mineralization rate. At no time in these experiments was there detectable extracellular ligninase (lignin peroxidase) activity. Offprint requests to: P. Morgan     

Biological potential of fungal inocula for bioaugmentation of contaminated soils

The suitability of the fluorescein diacetate hydrolyzing activity (FDA) assay for determining the biological potential (ie fungal biomass produced per unit of substrate) of solid pelleted fungal inoculum intended for use in the bioaugmentation of contaminated soils with white-rot fungi, was evaluated. FDA activity of the white-rot fungusPhanerochaete chrysosporium grown on pelleted substrates and on agar was found to be proportional to quantities of fungal ergesterol and fungal dry matter, respectively. Inoculum biological potential was found to be greatly influenced by substrate formulation and structure, and temperature. Biological potential and the type of carrier influenced the ability ofP. chrysosporium to tolerate pentachlorophenol (PCP).Phanerochaete chrysosporium andTrametes versicolor introduced into PCP-contaminated soil on pellets with higher biological potential and higher nitrogen content (C:N ratio of 501), did not remove PCP more efficiently than when the fungi were introduced on pellets with a lower biological potential (C:N ratio of 3091). However, under the latter conditions most of the PCP was transformed to pentachloroanisole (PCA). In soil inoculated withT. versicolor on pellets with high biological potential, higher manganese peroxidase activity was detected compared to soil inoculated with pellets with a lower biological potential.     

Identification of new GH 10 and GH 11 xylanase genes from Aspergillus versicolor MKU3 by genome-walking PCR

Xylanases randomly clear the backbone of xylans, which are hemicelluloses representing a considerable source of fixed carbon in nature. Consequently, these enzymes have important industrial applications. To characterize the genes responsible for producing these enzymes, we cloned xylanase genes belonging to the GH11 and GH10 families from Aspergillus versicolor MKU3 using a 2-step polymerase chain reaction (PCR) protocol involving degenerate PCR and genome-walking PCR (GWPCR). We amplified a family 10 xylanase consensus fragment using degenerate PCR primers exhibiting specificity for conserved motifs within fungal family 10 xylanase genes. We identified a single family 10 xylanase gene (xynv10) and determined its entire gene sequence during the second step of GWPCR, which was used to amplify genomic DNA fragments upstream and downstream of xynv10. The xynv10 sequence contains a 1,378-bp open reading frame separated by 8 introns with an average size of 49 bp. We also amplified a partial GH11 xylanase gene sequence (xynv11) using degenerate PCR and genome-walking methods. Amplification of the C-terminal region of xynv11 using a degenerate primer designed from sequences revealed strong homology with the partial GH11 xylanase gene of A. versicolor MKU3. The structural region in xynv11 was approximately 680 bp and has one intron that is approximately 64 bp in length. Further expression and characterization of these genes will give better understanding of the role of these genes in xylan degradation by A. versicolor.     

Ultrastructural aspects of wheat straw degradation by Phanerochaete chrysosporium and Trametes versicolor

The ultrastructural patterns characterizing wheat straw degradation by the ligninolytic fungi Phanerochaete chrysosporium and Trametes versicolor were studied. During fungal attack, the less lignified tissues were degraded first, whereas the xylematic and sclerenchymatic fibers underwent a delayed attack. In straw samples degraded by T. versicolor, partial delignification, defibrillation and swelling of cell walls, often causing separation between primary and secondary walls, were observed. By contrast, the formation of erosions and fissures, with minor lignin removal, characterized the attack to the cell wall by P. chrysosporium. At an advanced stage of decay, KMnO₄ staining demonstrated abundant electron-dense material around hyphae and in the proximity of the cell-wall surface. In the case of P. chrysosporium, spherical black bodies were found in the erosions and fissures produced during fungal attack.     

Nested Inverse Polymerase Chain Reactions: An Effective Method for Cloning of Full-Length Sequences of Chalcone Synthase

Chalcone synthase is the key enzyme in biosynthesis of flavonoids, which play roles in pigmentation of flowers and protection against ultraviolet and pathogens. Inverse polymerase chain reaction (IPCR) is a method for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. In this study, IPCR united with nested PCR was successfully applied in cloning full-length sequences of three Phalaenopsis chalcone synthase genes (phchs3, phchs4, and phchs5, respectively). Firstly, routine PCR with homologous primers were performed, and gene fragments of phchs3 (1 kb), phchs4 (1.2 kb), and phchs5 (800 bp) were obtained and then sequenced. Then, inverse PCR were carried out for cloning full-length sequence of each gene. Because products were not unique in single round inverse PCR, nested PCR were performed, and the specificity was much enhanced. At last, full-length sequences of 2,499 bp for phchs3, 2,502 bp for phchs4, and 1,855 bp for phchs5 were obtained. This study proved that IPCR could be more efficient if being united with nested PCR.