The oliC3 gene of Aspergillus niger: isolation, sequence and use as a selectable marker for transformation

Visualization of Three Sclerotiniaceae Species Pathogenic on Onion Reveals Distinct Biology and Infection Strategies

Botrytis squamosa, Botrytis aclada, and Sclerotium cepivorum are three fungal species of the family Sclerotiniaceae that are pathogenic on onion. Despite their close relatedness, these fungi cause very distinct diseases, respectively called leaf blight, neck rot, and white rot, which pose serious threats to onion cultivation. The infection biology of neck rot and white rot in particular is poorly understood. In this study, we used GFP-expressing transformants of all three fungi to visualize the early phases of infection. B. squamosa entered onion leaves by growing either through stomata or into anticlinal walls of onion epidermal cells. B. aclada, known to cause post-harvest rot and spoilage of onion bulbs, did not penetrate the leaf surface but instead formed superficial colonies which produced new conidia. S. cepivorum entered onion roots via infection cushions and appressorium-like structures. In the non-host tomato, S. cepivorum also produced appressorium-like structures and infection cushions, but upon prolonged contact with the non-host the infection structures died. With this study, we have gained understanding in the infection biology and strategy of each of these onion pathogens. Moreover, by comparing the infection mechanisms we were able to increase insight into how these closely related fungi can cause such different diseases.

Developing Aspergillus niger as a cell factory for food enzyme production

Aspergillus niger has become one of the most important hosts for food enzyme production due to its unique food safety characteristics and excellent protein secretion systems. A series of food enzymes such as glucoamylase have been commercially produced by A. niger strains, making this species a suitable platform for the engineered of strains with improved enzyme production. However, difficulties in genetic manipulations and shortage of expression strategies limit the progress in this regard. Moreover, several mycotoxins have recently been detected in some A. niger strains, which raises the necessity for a regulatory approval process for food enzyme production. With robust strains, processing engineering strategies are also needed for producing the enzymes on a large scale, which is also challenging for A. niger, since its culture is aerobic, and non-Newtonian fluid properties are developed during submerged culture, making mixing and aeration very energy-intensive. In this article, the progress and challenges of developing A. niger for the production of food enzymes are reviewed, including its genetic manipulations, strategies for more efficient production of food enzymes, and elimination of mycotoxins for product safety.

Identification of a minimal cre1 promoter sequence promoting glucose-dependent gene expression in the beta-lactam producer Acremonium chrysogenum

The promoter of the cre1 gene, encoding the glucose-dependent regulator CRE1 from the beta-lactam producer Acremonium chrysogenum, carries 15 putative CRE1 binding sites (BS1 to BS15). For a detailed analysis, we fused cre1 promoter deletion derivatives with the DsRed reporter gene to perform a comparative gene expression analysis. Plate assays, Northern hybridizations, and spectrofluorometric measurements of DsRed identified the minimal D4 promoter sequence that promoted glucose-dependent expression. Truncated recombinant CRE1 interacted with D4 in electromobility shift analysis and these binding studies were further extended with two oligonucleotides, carrying putative CRE1 binding sites BS14 and BS15. Surface plasmon resonance analysis was performed using BS14 and BS15, along with four derivatives containing 2 or 4 bp substitutions within BS14 and BS15, respectively. Substitutions within BS14 abolished the high affinity interaction with CRE1, while mutations in BS15 only marginally diminished the affinity with CRE1. In vivo analysis of a modified D4 sequence with substitutions in the two binding sites confirmed the in vitro binding results and still promoted glucose-dependent gene expression. Our results will contribute to the construction of versatile expression vectors carrying a minimal cre1 promoter sequence that still confers glucose-dependent induction of gene expression.

The development of gene expression systems for filamentous fungi

Filamentous fungi have been used for decades in the commercial production of enzymes, antibiotics, and specialty chemicals. Traditionally, improving the yields of these products has involved either mutagenesis and screening or modification of fermentation conditions. Generally, selective breeding of strains has not been successful, because most of the commercially important fungal species lack a sexual cycle. For a few species, strain improvements have been made possible by employing the parasexual cycle for genetic crosses (30). The recent development of DNA-mediated transformation systems for several industrially important fungal species has spawned a flurry of research activity directed toward the development of gene expression systems for these microorganisms. This technology is now a viable means for novel and more directed approaches to improving existing fungal strains which produce enzymes or antibiotics. In addition, fungal expression systems are now being tested for the production of heterologous gene products such as mammalian pharmaceutical proteins. The goal of this review is to present a summary of the gene expression systems which have recently been developed for some filamentous fungi of commercial importance. To insure that the most recent developments are presented we have included data from not only scientific papers, but also from personal communications, abstracts, symposia, and our own laboratory.

Purification and characterisation of an Aspergillus niger invertase and its DNA sequence

A secreted invertase was purified 23-fold by ultrafiltration, ion-exchange, and gel filtration chromatography from the culture supernatant of 18 h sucrose-grown cultures of Aspergillus niger. The purified enzyme hydrolysed sucrose and raffinose but there was no detectable hydrolysis of inulin, melezitose or PNPG. Invertase activity was optimal at pH 5.5 and 50 degrees C. The molecular mass of reduced invertase was 115 kDa, as determined by SDS gel electrophoresis. The native molecular weight of between 225 kDa and 250 kDa, estimated by electrophoresis under non-denaturing conditions, suggests that the protein is a dimer of identical subunits. The suc1 gene encoding this protein was completely-sequenced. The translated sequence yields a protein of 566 amino acids with a calculated molecular mass of 61 kDa, suggesting that carbohydrates represent about 50% of the mass of the protein.

Aspergillus nidulans nuclear proteins bind to a CCAAT element and the adjacent upstream sequence in the promoter region of the starch-inducible Taka-amylase A gene

Aspergillus nidulans was used as an intermediate host to investigate the regulation of the Taka-amylase A (TAA) gene from Aspergillus oryzae. The induction of Taa by starch was confirmed to be regulated at the transcriptional level by analyzing the transcripts specific for Taa synthesized in vitro in nuclei from starch- and glucose-grown cells. A 55 bp DNA fragment containing a consensus CCAAT sequence from the promoter region of the Taa gene was shown to confer starch inducibility on the gene. A nuclear extract from starch-grown cells was assayed for proteins which bind to the promoter region of the Taa gene. A protein designated AnCP1 bound to the CCAAT sequence. A nuclear extract from glucose-grown cells contained two DNA-binding proteins designated AnCP2 and AnNP1. AnCP2 bound to the same CCAAT sequence as AnCP1, while AnNP1 bound to the 25 bp region just upstream of the AnCP2 binding site. Occupancy of the two binding sites appeared to be mutually exclusive, which is suggestive of a negative regulatory mechanism for gene expression.

The Aspergillus niger niaD gene encoding nitrate reductase: upstream nucleotide and amino acid sequence comparisons

The Aspergillus niger niaD gene has been sequenced and the inferred nitrate reductase (NR) protein found to consist of 867 amino acid residues (97 kDa). The gene is interrupted by six small introns, as deduced by comparison with the niaD gene of Aspergillus nidulans. The positions of these putative introns are conserved between the two fungi, although the sequences are dissimilar. The niiA gene, encoding nitrite reductase, the second reductive step in the nitrate assimilation pathway, is tightly linked to niaD and divergently transcribed in A. niger, similar to the general organisation in the related fungi, Aspergillus oryzae and A. nidulans. The nucleotide (nt) sequences of the intergenic region between niiA and niaD (excluding the ATG translation start codon) of A. niger (1668 nt) and A. oryzae (1575 nt) were determined and compared with the previously determined A. nidulans (1262 nt) sequence. No striking extended nt regions of homology are observed in spite of the fact that transgenic strains with fungal niaD or the two control genes required for induction and repression show virtually normal regulation. Fungal NR shows considerable aa homology with higher plant NR, particularly within the co-factor domains for flavin adenoside dinucleotide, heme and molybdopterin cofactor.

Transformation frequencies are enhanced and vector DNA is targeted during retransformation of Leptosphaeria maculans, a fungal plant pathogen

Leptosphaeria maculans, a fungal pathogen of Brassica spp., was successfully transformed with the vector pAN8-1, encoding phleomycin resistance. Protoplasts of a vigorous Phleor transformant were then retransformed using the partially homologous vector, pAN7-1 which encodes hygromycin B resistance. Retransformation of this strain to hygromycin resistance occurred at frequencies that were consistently twofold higher than with the original recipient strain. Linearised pAN7-1 DNA transformed phleomycin-resistant protoplasts at higher frequencies still. All the transformants that were tested retained a phleomycin-resistant phenotype (20/20). Molecular analysis of five transformants generated with circular pAN7-1 DNA indicated that in four cases the pAN7-1 vector had integrated into pAN8-1 sequences. These results suggest that transformation frequencies in L. maculans are limited by the ability of vector DNA to integrate into the genome. Hence, construction of strains with target sites for integration may prove to be a generally useful method for improving transformation frequencies of poorly characterised filamentous fungi, particularly when using heterologous vectors. This would greatly facilitate the identification of genes by transfer of gene libraries and the standardisation of chromosomal location effects in studies of expression of nested promoter deletions.

Sequence of the nuclear ATP synthase subunit 9 gene of Podospora anserina: lack of similarity to the mitochondrial genome

The nuclear gene coding for the mitochondrial subunit 9 of the F0F1-ATP synthase complex was isolated from a genomic library of Podospora anserina. Nucleotide sequencing revealed an open reading frame capable to code for 144 amino acids including an amino-terminal pre-sequence of 63 amino acid residues for mitochondrial import of the pre-proteolipid. The P. anserina proteolipid shows extensive sequence identity with the corresponding gene products of the related filamentous fungi Neurospora crassa, Aspergillus nidulans and Aspergillus niger. In contrast to the situation in Saccharomyces cerevisiae, N. crassa and A. nidulans, no sequence similarity of the ATP synthase subunit 9 gene to the mitochondrial genome of P. anserina could be detected. Thus, in P. anserina this gene appears to be exclusively encoded by the nuclear genome.

Expression of heterologous proteins in Aspergillus

Filamentous fungi, in particular those of the genus Aspergillus have been well exploited for their ability to produce high levels of extracellular proteins in an inexpensive manner. Since many human proteins with the potential to be used therapeutically are secreted and require post-translational modification for biological activity, eukaryotic expression-secretion systems have been targeted for development. Recent developments in DNA-mediated transformation systems have allowed the utilization of Aspergillus as a host for the production of recombinant proteins. Several features such as well-characterized genetics and the availability of many mutants make Aspergillus nidulans the organism of choice for development of expression secretion systems. Recombinant strains contain integrated expression cassettes often in multiple copy, which are mitotically stable. In this review, we discuss the recent progress made in the use of Aspergillus as expression secretion hosts for the production of proteins of therapeutic significance.

Improved transformation frequency and heterologous promoter recognition in Aspergillus niger

Wild-type strains of Aspergillus niger were transformed with integrative vectors. The number of stable transformants varied from approximately 20-30/micrograms up to 17,000/micrograms using acetamide and hygromycin B selection, respectively. The introduction of deletions of 5' and 3' non-coding regions of the acetamidase gene (amdS+) revealed that these sequences influenced the number of transformants. The molecular characterization of A. niger transformants revealed that several copies of the vectors were tandemly integrated into the nuclear DNA. These oligomers were stably inherited, even after 100 days of growth on non-selective medium. The expression of the vector-encoded genes was confirmed by evidence from the mRNAs and corresponding proteins encoded by the selectable marker genes.

Regulation of the glaA gene of Aspergillus niger

The glucoamylase gene of Aspergillus niger, glaA, is expressed at high levels in the presence of starch. We have determined the nucleotide sequence of 1966 bp of the 5' flanking region of the glaA gene and have begun to identify sequences important for the control of glaA expression by deletion analysis. Constructs containing deletions extending into the glaA gene promoter were introduced into an A. niger host whose own glaA gene had been disrupted by a gene replacement event. Secreted levels of glucoamylase, expressed from each of the recombinant glaA genes, were measured by enzyme immunoassay. The effect of each deletion on the expression of glaA, when grown on differing carbon sources, was used to determine the limits of sequences upstream of glaA responsible for gene regulation. A region between -562 and -318 appears to direct high-level expression, whereas only 214 bp of 5' flanking sequence is required to initiate the start to transcription.

Improved production of chymosin in Aspergillus by expression as a glucoamylase-chymosin fusion

We have extended the work on chymosin production in Aspergillus by constructing an expression vector in which the cDNA encoding bovine prochymosin B was fused in frame immediately following the codon for the last amino acid of the A. awamori glucoamylase (glaA) gene. Transformation of A. awamori with this plasmid led to the secretion of considerably higher amounts of chymosin than obtained with previous chymosin expression vectors. We present evidence that mature chymosin is autocatalytically released from the glucoamylase-chymosin fusion protein after secretion.

Functional elements in the promoter region of the Aspergillus nidulans gpdA gene encoding glyceraldehyde-3-phosphate dehydrogenase

Analysis of the promoter region of the highly expressed Aspergillus nidulans gpdA gene is described. The nucleotide (nt) sequence of a 1.3-kb region upstream from the ATG was determined. Comparison with promoter regions of other Aspergillus and Neurospora genes revealed several regions of similar sequence. Both random and site-specific mutations were introduced into the promoter region of the gpdA gene, and the resulting mutant promoters were fused to the Escherichia coli lacZ gene. The constructed fusions were introduced into A. nidulans and transformants that contained one copy of these fusions at the argB locus were analysed. beta-Galactosidase assays and primer extension experiments were used to identify sequence elements involved in transcription activation and transcription initiation. Two elements, located around 650 and 250 nt upstream from the major transcription start point (tsp), were identified as transcription activation elements. These elements coincide with regions of putative secondary structure (direct or inverted repeats). A third element, a C + T-rich region directly upstream from the major tsp, was shown to be involved in correct initiation of transcription.

Screening of basidiomycetes for lignin peroxidase genes using a DNA probe

Basidiomycetes were screened for lignin peroxidase (LPO) genes using a DNA probe prepared from the LPO restriction fragment of Phanerochaete chrysosporium. Southern blot analysis showed restriction fragments of chromosomal DNA of Bjerkandera adusta and Coriolus consors hybridized with the probe. Bjerkandera adusta produced LPO in a glucose-peptone medium. Ion-exchange chromatography showed that this fungus produced multiple molecular forms of LPO. One of the enzymes, LPO-2, was purified and characterized. The molecular weight of LPO-2 was 41,000 with a pI of 4.2. Spectral analysis demonstrated that LPO-2 is a haem protein. The enzyme cleaved lignin model dimers mainly at the C alpha-C beta position of the side chain. The LPO-2 exhibited close similarity to LPOs of P. chrysosporium with respect to their basic properties.

Cloning of a new bidirectionally selectable marker for Aspergillus strains

Mutants that lack adenosine triphosphate sulfurylase (ATPsase; EC 2.7.7.4) are unable to use sulfate as sole source of sulfur and are also resistant to selenate. These mutants, denoted sC-, are readily obtained from any strain of Aspergillus niger or Aspergillus nidulans by the strong selection for selenate resistance. We have cloned the gene encoding ATPsase from A. nidulans by complementation of an sC mutant strain of A. nidulans with a gene library and show that plasmids containing this gene transform both A. niger and A. nidulans sC- strains, restoring their ability to grow on sulfate as sole sulfur source. The fact that strong selection for either sC+ or sC- can be applied provides a simple way of delivering genetically engineered constructs to any strain of A. niger including strains of industrial importance. In addition, this system is useful for gene replacements and other genomic DNA manipulations in Aspergillus species.

Physical characterization of the aldehyde-dehydrogenase-encoding gene of Aspergillus niger

To facilitate a better understanding of the regulation of aldA, the gene encoding aldehyde dehydrogenase (AldDH) in the ascomycete fungus, Aspergillus niger, the gene has been physically characterized. The complete nucleotide (nt) sequence of the gene and its flanking regions has been determined. Analysis of the gene has revealed the presence of three introns. The homologous gene in the related fungus, Aspergillus nidulans, contains only two introns. The coding regions of these genes, excluding the intron sequences, show 80% homology at the nt level and 82% homology at the amino acid (aa) level. The aa sequence of the A. niger enzyme is significantly homologous to mammalian sequences, particularly around one Cys residue, which is hypothesized to be adjacent to another Cys known to be at the active site of mammalian AldDHs. The 5' region of the gene shows one major and two minor transcription start points and a general structure common to highly expressed fungal genes. The 3' region shows four sites of polyadenylation. Sequence comparisons of the 5' region of the A. niger aldA gene to other Aspergillus genes has shown a common sequence in the 5' regions of several A. nidulans genes, all but one of which are subject to carbon catabolite repression. This sequence may be important for the regulatory mechanism.

Improved transformation efficiency of Aspergillus niger using the homologous niaD gene for nitrate reductase

Aspergillus niger transformation frequencies of up to 1,176 transformants per micrograms DNA were achieved using the plasmid vector pSTA10 containing the A. niger nitrate reductase structural gene. Analysis of genomic endonuclease cleaved DNA from nitrate utilising transformants by DNA hybridisation, showed that most integration events are as a result of homologous recombination. The niaD transformation system was used successfully for the introduction of the unselected Escherichia coli fusion genes lacZ, encoding beta-galactosidase, and uidA, for beta-glucuronidase, as well as the Neurospora crassa tub-2 gene, for beta-tubulin. pSTA10 was also capable of transforming niaD mutants of other filamentous fungi such as A.nidulans, A. oryzae and Penicillium chrysogenum.

Transformation in fungi

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater precision and efficiency than is possible in other species that show a high proportion of DNA integration events at nonhomologous (ectopic) sites. With a little more trouble, however, the methodology pioneered for S. cerevisiae can be applied to other fungi too. Transformation of fungi with DNA constructs designed for high gene expression and efficient secretion of gene products appears to have great commercial potential.