Distant upstream regulatory sequences control the level of expression of the am (GDH) locus of Neurospora crassa

Regulation of the amylolytic and (hemi-)cellulolytic genes in aspergilli

Filamentous fungi produce high levels of polysaccharide-degrading enzymes and are frequently used for the production of industrial enzymes. Because of the high secretory capacity for enzymes, filamentous fungi are effective hosts for the production of foreign proteins. Genetic studies with Aspergillus nidulans have shown pathway-specific regulatory systems that control a set of genes that must be expressed to catabolize particular substrates. Besides the pathway-specific regulation, wide domain regulatory systems exist that affect a great many individual genes in different pathways. A molecular analysis of various regulated systems has confirmed the formal models derived from purely genetic data. In general, many genes are subject to more than one regulatory system. In this article, we describe two transcriptional activators, AmyR and XlnR, and an enhancer, Hap complex, in view of their regulatory roles in the expression of the amylolytic and (hemi-)cellulolytic genes mainly in aspergilli. The amyR gene has been isolated as a transcriptional activator involved in the expression of amylolytic genes from A. oryzae, A. niger, and A. nidulans, and the xlnR gene, which has been isolated from A. niger and A. oryzae, activates the expression of xylanolytic genes as well as some cellulolytic genes in aspergilli. Both AmyR and XlnR have a typical zinc binuclear cluster DNA-binding domain at their N-terminal regions. Hap complex, a CCAAT-binding complex, enhances the overall promoter activity and increases the expression levels of many fungal genes, including the Taka-amylase A gene. Hap complex comprises three subunits, HapB, HapC, and HapE, in A. nidulans and A. oryzae as well as higher eukaryotes, whereas HAP complex in Saccharomyces cerevisiae and Kluyveromyces lactis has the additional subunit, Hap4p, which is responsible for the transcriptional activation. Hap complex is suggested to enhance transcription by remodeling the chromatin structure. The regulation of gene expression in filamentous fungi of industrial interest could follow basically the same general principles as those discovered in A. nidulans. The knowledge of regulation of gene expression in combination with traditional genetic techniques is expected to be increasingly utilized for strain breeding. Furthermore, this knowledge provides a basis for the rational application of transcriptional regulators for biotechnological processes in filamentous fungi.

HAP-Like CCAAT-binding complexes in filamentous fungi: implications for biotechnology

Regulatory CCAAT boxes are found frequently in eukaryotic promoter regions. They are bound by different CCAAT-binding factors. Until now, a single CCAAT-binding complex has been reported in fungi. It is also found in higher eukaryotes and is highly conserved among eukaryotic organisms. This multimeric protein complex is designated HAP, AnCF, CBF, or NF-Y. The complex consists of at least three subunits. In fungi, only the HAP complex of Saccharomyces cerevisiae had been known for a long time. The recent cloning of genes encoding the components of the corresponding complex (AnCF/PENR1) of Aspergillus nidulans and characterization of CCAAT-regulated genes in A. nidulans, as well as other filamentous fungi, led to a deeper insight into the role of this transcription complex, in particular in aerobically growing fungi. An overview of the function of HAP-like complexes in gene regulation in filamentous fungi is presented. Some of the genes that have been found to be regulated by HAP-like complexes encode enzymes of biotechnological interest, like taka-amylase, xylanases, cellobiohydrolase, and penicillin biosynthesis enzymes. The importance of HAP-like complexes in controlling the expression of biotechnologically important genes is discussed.

The Neurospora aab-1 gene encodes a CCAAT binding protein homologous to yeast HAP5

The expression of the am (glutamate dehydrogenase) gene is dependent upon two upstream activating sequences, designated URSam(alpha) and URSam(beta). A heteromeric nuclear protein Am Alpha Binding protein (AAB) binds specifically to a CCAAT box within the URSam(alpha) element. AAB appears to be composed of three components. We used polyclonal antiserum raised against the highly purified AAB1 subunit to isolate a partial aab-1 cDNA clone, which was then used to isolate a full-length cDNA and a genomic clone. The full-length cDNA has the potential to encode a 272 amino acid protein with a calculated molecular weight of 30 kD. Amino acid sequence obtained by Edman analysis of the AAB1 protein confirmed that the aab-1 gene had been cloned. AAB-1 shows similarity to the HAP5 protein of yeast and the CBF-C protein of rat. Each of these proteins is an essential subunit of their respective heteromeric CCAAT binding proteins. The aab1 gene maps on linkage group III of Neurospora crassa near the trp-1 locus. Disruption of the aab-1 gene results in pleiotropic effects on growth and development as well as a 50% reduction in glutamate dehydrogenase levels. Transformation of the aab-1 disruption mutant strain with the cloned genomic copy of the aab-1 gene rescued all of the phenotypic alterations associated with the aab-1 mutation.

DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa

In plants, animals, and fungi, DNA methylation is frequently associated with gene silencing, yet little is known about the role of the methylation in silencing. In Neurospora crassa, repeated sequences are silenced by repeat-induced point mutation (RIP) and genes that have suffered numerous GC --> AT mutations by RIP are typically methylated at remaining cytosines. We investigated possible effects on transcription from methylation associated with RIP by taking advantage of 5-azacytidine, which prevents most methylation in Neurospora and a dim-2 mutation that abolishes all detectable methylation. Northern analyses revealed that methylation prevents the accumulation of transcripts from genes mutated by RIP. Measurements of transcription rates in vivo showed that methylation inhibits transcription severely but does not influence mRNA stability. Results of nuclear run-on experiments demonstrated that transcription initiation was not significantly inhibited by the dense methylation in the promoter sequences. In contrast, methylation blocked transcription elongation in vivo.

The orientation of gene maps by recombination of flanking markers for the am locus of Neurospora crassa

Fincham (1967), Smyth (1973 b) and Rambosek and Kinsey (1983) have each generated fine-structure maps of the am gene of Neurospora crassa. Each map had a consistent linear order of alleles but the assignment of an orientation with respect to other linkage group-V loci differed. Fincham found the end marked by the am6 allele to be at the distal end of the locus, Smyth found am6 to be at the proximal end while the data of Rambosek and Kinsey did not suggest an orientation. Smyth s orientation has been adopted as the standard, but not unreservedly. We have aligned the genetic and physical maps of the am gene, showing that am6 is at the distal end, supporting Fincham's orientation. However, we suggest that an assumption used to orient fine structure genetic maps is flawed and that the conflicting orientation between these three studies follows from the different choice of flanking markers.

Purification of a heteromeric CCAAT binding protein from Neurospora crassa

Expression of the Neurospora crassa am (NADP-specific glutamate dehydrogenase) gene is controlled by two upstream enhancer-like elements designated URSam alpha and URSam beta. URSam alpha is localized between - 1.3 and - 1.4 kb with respect to the major transcriptional start site. Deletion of a 90 bp sequence containing this element resulted in the loss of approximately 50% of normal glutamate dehydrogenase expression. Gel mobility shift analysis indicated that a nuclear protein from Neurospora binds in a specific manner to sequences within the 90 bp fragment. We have now used a combination of ion-exchange and affinity chromatography to purify this nuclear protein, which we call Am Alpha Binding protein (AAB). The activity was monitored by gel shift analysis. The protein was purified more than 14,000-fold with a yield of approximately 7%. The purified protein appears as a heteromer on denaturing polyacrylamide gel electrophoresis, with only two strong bands visible in silver-stained preparations. One band has an apparent molecular mass of 40 kDa, the other appears as a doublet with an apparent molecular mass of 30 kDa. DNAse I protection analysis indicated a protected region consisting of 30 bp, which contains a CCAAT pentanucleotide motif. Mutagenesis of the CCAAT motif abolished the binding of AAB to the DNA fragment.

Molecular characterization of upstream regulatory sequences controlling the photoinduced expression of the albino-3 gene of Neurospora crassa

In the filamentous fungus Neurospora crassa the biosynthesis of carotenoids is regulated by blue light, principally through transcriptional activation of some key genes in the carotenogenic enzymatic pathway. Here we report the characterization of the photoinducible promoter of the albino-3 (al-3) gene, encoding GGPP synthase. We have modified the 5' non-coding sequence of the cloned al-3 gene by deletion and site-directed mutagenesis, and we have tested the residual photoinducibility of the different constructs by transformation and subsequent analysis of gene expression in dark-grown and light-induced mycelia. The results indicate that a promoter region between positions -226 and -55 contains all the necessary information for blue light photoinduction. Multiple regulatory elements are involved in the regulated expression of the al-3 gene. One (termed the APE element) is important for the light-induction switch on of the gene and a second belongs to the CCAAT boxes family. The putative APE element is also found in the promoter of other N. crassa photoinducible genes.

Yeast exo-beta-glucanases can be used as efficient and readily detectable reporter genes in Saccharomyces cerevisiae

Yeast exo-1,3-beta-glucanases are secretable proteins whose function is basically trophic and may also be involved in cell wall glucan hydrolytic processes. Since fluorescein di(beta-D-glucopyranoside) is a fluorogenic substrate detectable and quantifiable by flow cytometry, it was used for testing the ability of the EXG1 gene product of Saccharomyces cerevisiae and its homologous gene in Candida albicans to function as reporter genes. These open reading frames were coupled to different promoters in multicopy plasmids, and exoglucanase activity quantified at flow cytometry. Exoglucanases were found to be useful tools for the study of promoter regions in S. cerevisiae. This technique has the advantage over other reporter gene systems--such as beta-galactosidase fusions--that it does not require permeabilization of yeast cells and therefore it allows the recovery of viable cells--by sorting--after flow cytometry analysis.

A simple and efficient system for targeting DNA to the am locus of Neurospora crassa

We have developed a system of recipient strains and donor plasmids that allows targeting of DNA sequences to the am locus of Neurospora crassa. A recipient strain was constructed that contains the 3' two-thirds of the bacterial Hygromycin B (Hy) phosphotransferase-encoding gene (hph) in single copy downstream from the am structural gene encoding NADP-specific glutamate dehydrogenase. Plasmids have been constructed that contain am, but with the 5' end of hph downstream from am. Resistance to Hy can occur during transformation only if recombination occurs within the region of overlap of the hph sequences from the transforming DNA and of the chromosomal hph sequences. A lacZ alpha gene with a multiple cloning site has been inserted into the region between the am and hph sequences to facilitate subcloning into the targeting vector. Additionally, unique sites at the junctions of the vector and targeting DNA allow easy removal of vector sequences prior to transformation. A second recipient strain has been constructed that has had the am structural gene deleted. This strain may be used to provide a double selection for homologous integration. Additionally, this strain facilitates replacement of am with heterologous constructs, including constructs that drive transcription of am with different promoters. The insertion of hph downstream from am has no apparent effect on am expression, and the resistance segregates as a Mendelian factor in crosses. Transformation efficiency is reduced two to three orders of magnitude, but interestingly, nearly all of the resistant strains have only a single copy of the transforming DNA.

Sequential gel mobility shift scanning of 5' upstream sequences of the Neurospora crassa am (GDH) gene

We have used gel mobility shift assays to scan 1.7 kb of 5' non-coding sequence of the am (glutamate dehydrogenase) gene of Neurospora crassa for binding by partially fractionated Neurospora proteins. Using genetic analysis this region had been shown to play an important role in the control of glutamate dehydrogenase (GDH) expression. Gel mobility shift analysis identified three regions to which Neurospora proteins bind specifically. Two of these corresponded to the two elements previously defined by genetic analysis (URSam alpha and URSam beta). The third protein binding site appears to be unrelated to am gene expression. Competition experiments showed that the proteins that bind to the URSam alpha and URSam beta elements are different. The URSam alpha element was shown to contain two independent binding sites for the URSam alpha binding protein(s). Both fragments contain a CCAAT motif, suggesting that URSam alpha binding protein(s) may be members of one of the CCAAT-binding protein families. The effect of deletion of either the URSam alpha or URSam beta elements on catabolite induction of am expression was also determined. Both elements appear to act as constitutive enhancers of gene expression.

Promoter analysis of the bli-7/eas gene

Expression of the Neurospora crassa gene bli-7, (identical with eas, and ccg-2), is induced by blue light, as well as glucose- or nitrogen-starvation. A promoter analysis was performed by an assay that does not involve promoter-reporter constructs but rather the insertion of foreign DNA into the transcribed sequence. To detect regulatory elements a series of deletions in the upstream region was generated. The inducibility of the gene, in response to the three inducing conditions mentioned, is lost by eliminating the region between -1498 bp and -1017 bp upstream of the transcription start point. A segment with an apparently negative effect was found between -595 bp and -429 bp, as well as a stretch of DNA from -429 bp to -380 bp which may exert a positive influence after light induction.

Chromosome rearrangements recovered following transformation of Neurospora crassa

New chromosome rearrangements were found in 10% or more of mitotically stable transformants. This was shown for transformations involving a variety of different markers, vectors and recipient strains. Breakpoints were randomly distributed among the seven linkage groups. Controls using untransformed protoplasts of the same strains contained almost no rearrangements. A study of molecularly characterized Am+ transformants showed that rearrangements are frequent when multiple ectopic integration events have occurred. In contrast, rearrangements are absent or infrequent when only the resident locus is restored to am+ by a homologous event. Sequences of the transforming vector were genetically linked to breakpoints in 6 of 10 translocations that were examined using Southern hybridization or colony blots.

Cloning and characterisation of pepC, a gene encoding a serine protease from Aspergillus niger

We have cloned a gene, pepC, encoding a serine proteinase, PEPC, from Aspergillus niger by screening a phage lambda genomic DNA library with a gene (PRB1) from Saccharomyces cerevisiae which codes for proteinase YscB. The nucleotide (nt) sequence of pepC revealed that the gene is composed of two exons of 369 nt and 1230 nt separated by a single 70-nt intron. The deduced protein of 533 amino acids (aa) has a putative signal sequence for transport into the endoplasmic reticulum. Based on the extensive homology shown with serine proteinases (SerP) of the subtilisin family, which includes the active site triad, we hypothesise that the protein is made as a larger precursor which is matured by the cleavage of 130-140 aa from its N terminus and possibly by the removal of approx. 70 aa from its C terminus.

Regulatory sequences for expressing genes in oomycete fungi

Promoter and terminator sequences from a range of species were tested for activity in the oomycetes, a group of lower fungi that bear an uncertain taxonomic affinity to other organisms and in which little is known of the sequences required for transcription. Transient assays, using the reporter gene beta-glucuronidase (GUS), were used to examine the function of these promoters and terminators in the plant pathogens Phytophthora infestans and P. megasperma f. sp. glycinea, and in the saprophytic water mold, Achlya ambisexualis. Oomycete promoters, isolated from the ham34 and hsp70 genes of Bremia lactucae and the actin gene of P. megasperma f. sp. glycinea, resulted in high levels of GUS accumulation in each of the three oomycetes. In contrast, little or no activity was detected when promoters from higher fungi (four ascomycetes and one basidiomycete), plants, and animals were tested. The terminator from the ham34 gene resulted in much higher levels of GUS accumulation than did others, although an oomycete terminator was not absolutely required for expression. Transcript mapping of RNA from stable transformants confirmed accurate initiation from the B. lactucae hsp70 promoter and termination within 3' ham34 sequences in P. infestans. Our results indicate that the transcriptional machinery of the oomycetes differs significantly from that of the higher fungi, but that enough conservation exists within the class to allow vectors developed from one oomycete species to be used for others.

Comparative studies of the quinic acid (qa) cluster in several Neurospora species with special emphasis on the qa-x-qa-2 intergenic region

The organization of the quinic acid (qa) genes in Neurospora crassa has been compared to that in several other Neurospora species. This gene cluster was found to be highly conserved in all species examined. However, there are numberous restriction fragment length polymorphisms that distinguish the heterothallic and homothallic species. Catabolic dehydroquinase assays indicated that qa-2 gene expression in the homothallic species is subject to induction by quinic acid, as is the case in N. crassa. The qa-x-qa-2 intergenic region of the homothallic species N. africana was cloned and sequenced. Conserved qa activator (qa-1F) binding sites have been identified in this region. When the qa-x-qa-2 intergenic region of N. crassa was replaced with its N. africana counterpart, qa-2 gene expression was reduced; however repression by glucose appeared normal. Furthermore, the N. africana start site for qa-2 transcription (which differs from the N. crassa start site) was utilized in the transformant. The overall evidence suggests that a weakening of the -120 activator binding site in the qa-x-qa-2 intergenic region may be responsible for these differences.

The initiation site for recombination cog is at the 3' end of the his-3 gene in Neurospora crassa

Recombination at his-3 in Neurospora crassa is thought to be initiated through a site designated cog which lies in the his-3 to ad-3 interval of linkage group I. Fragments of the his-3 gene were used to transform various his-3 mutant alleles to prototrophy in order to link the genetic map to the nucleotide sequence. It was established that cog is at the 3' end of his-3 and is therefore not the his-3 promoter. This suggests that cog may be dissimilar to a number of yeast recombinators which are associated with promoters of transcription.

Nucleotide sequence and nuclear protein binding of the two regulatory sequences upstream of the am (GDH) gene in Neurospora

We have constructed a series of deletions in the 5' non-coding sequences of the cloned Neurospora crassa am gene which specifies NADP specific glutamate dehydrogenase. All of the deletions begin at -4.4 kb with respect to the am transcription start site and extend for various distances toward the am gene. Using vectors with a truncated fragment of the am gene, we introduced these deletions into the chromosome upstream of am by transformation. Analysis of glutamate dehydrogenase expression in strains with the deletion mutations confirmed that there are two upstream regulatory sequences (URS) that control the expression of the am gene. The more distal of these elements (URSam beta) has been limited to the 157 bp between -1924 and -2081 with respect to the start of am transcription. The proximal element (URSam alpha) was limited to the 97 bp between -1296 and -1393. The DNA sequence of the entire region was determined. Within the sequences that contain the URS elements several regions of homology with yeast UAS sequences were found. Gel mobility assays with DNA fragments containing the URS elements indicated that sequences in both elements are bound by nuclear proteins from Neurospora. The interaction of these proteins and the DNA fragments was found to be specific.