Posttranscriptional control of gene expression in filamentous fungi

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.

The APSES transcription factor LmStuA is required for sporulation, pathogenic development and effector gene expression in Leptosphaeria maculans

Leptosphaeria maculans causes stem canker of oilseed rape (Brassica napus). The APSES transcription factor StuA is a key developmental regulator of fungi, involved in morphogenesis, conidia production and also more recently described as required for secondary metabolite production and for effector gene expression in phytopathogenic fungi. We investigated the involvement of the orthologue of StuA in L. maculans, LmStuA, in morphogenesis, pathogenicity and effector gene expression. LmStuA is induced during mycelial growth and at 14 days after infection, corresponding to the development of pycnidia on oilseed rape leaves, consistent with the function of StuA described so far. We set up the functional characterization of LmStuA using an RNA interference approach. Silenced LmStuA transformants showed typical phenotypic defects of StuA mutants with altered growth in axenic culture and impaired conidia production and perithecia formation. Silencing of LmStuA abolished the pathogenicity of L. maculans on oilseed rape leaves and also resulted in a drastic decrease in expression of at least three effector genes during in planta infection, suggesting either that LmStuA regulates, directly or indirectly, the expression of several effector genes in L. maculans or that the infection stage in which effectors are expressed is not reached when LmStuA expression is silenced.

Real-time PCR investigation of the dynamic expression of three "RNA processing and modification" genes of Phanerochaete chrysosporium exposed to lead

The expression of three ribosome binding proteins namely; polyadenylate-binding protein, splicing factor RNPS1 and ATP-dependent RNA helicase of Phanerochaete chrysosporium exposed to lead were analyzed by real-time PCR. The mRNA level of splicing factor RNPS1 showed 2.7 (p < 0.05), 2.6 (p < 0.05) and 4.9-fold (p < 0.001) increase when the cells were exposed to 25, 50 and 100 μM lead, respectively. 50 and 100 μM lead exposure resulted in almost 2-fold (p < 0.01and p < 0.05, respectively) increase in the expression of ATP-dependent RNA helicase. Polyadenylate-binding protein mRNA levels did not reveal any significant increase when cells exposed to the concentrations of lead employed. However, the mRNA level of polyadenylate-binding protein and splicing factor RNPS1 within a period of 1 and 2 h temporal exposure to 100 μM lead showed 2.5 (p < 0.001) and 3.4-fold (p < 0.001) increase, respectively. Expression level of ATP-dependent RNA helicase was not affected from the period of exposure to this metal.

Comparative assessment of fungal cellobiohydrolase I richness and composition in cDNA generated using oligo(dT) primers or random hexamers

Understanding soil fungal distribution and activities, particularly at the level of gene expression, is important in unveiling mechanisms regulating their activities in situ. Recent identification of fungal genes involved in carbon cycling has provided the foundation for developing reverse-transcriptase PCR assays to monitor spatiotemporal gene expression patterns in soils and other complex microbial systems. The polyadenylated 3' ends of eukaryotic mRNA transcripts enables the use of oligo(dT) primers for cDNA synthesis, but this can result in the overrepresentation of the 3' end of transcripts in cDNA pools. In an effort to increase the uniformity of transcripts represented in cDNA pools, random hexamers have been used. The use of both priming methods is abundant in the literature, but we do not know how these methods perform relative to each other. We performed comparative richness and compositional analyses of the fungal glycosyl hydrolase family 7 cellobiohydrolase I gene cbhI amplified from soil cDNAs that had been generated using either oligo(dT) primers or random hexamers. Our results demonstrate that similar cbhI richness and composition were recovered using both approaches. Richness estimates and compositional profiles of cbhI sequence libraries generated from random hexamer-primed cDNA were more variable than from libraries generated from oligo(dT) primed cDNA. However, our overall results indicate that, on average, comparable richness and composition were recovered from soil cDNAs when either priming method was used.

A Candida albicans early stage biofilm detachment event in rich medium

BACKGROUND

Dispersal from Candida albicans biofilms that colonize catheters is implicated as a primary factor in the link between contaminated catheters and life threatening blood stream infections (BSI). Appropriate in vitro C. albicans biofilm models are needed to probe factors that induce detachment events.

RESULTS

Using a flow through system to culture C. albicans biofilms we characterized a detachment process which culminates in dissociation of an entire early stage biofilm from a silicone elastomer surface. We analyzed the transcriptome response at time points that bracketed an abrupt transition in which a strong adhesive association with the surface is weakened in the initial stages of the process, and also compared batch and biofilm cultures at relevant time points. K means analysis of the time course array data revealed categories of genes with similar patterns of expression that were associated with adhesion, biofilm formation and glycoprotein biosynthesis. Compared to batch cultures the biofilm showed a pattern of expression of metabolic genes that was similar to the C. albicans response to hypoxia. However, the loss of strong adhesion was not obviously influenced by either the availability of oxygen in the medium or at the silicone elastomer surface. The detachment phenotype of mutant strains in which selected genes were either deleted or overexpressed was characterized. The microarray data indicated that changes associated with the detachment process were complex and, consistent with this assessment, we were unable to demonstrate that transcriptional regulation of any single gene was essential for loss of the strong adhesive association.

CONCLUSION

The massive dispersal of the early stage biofilm from a biomaterial surface that we observed is not orchestrated at the level of transcriptional regulation in an obvious manner, or is only regulated at this level by a small subpopulation of cells that mediate adhesion to the surface.

Tetracycline-regulated gene expression in the pathogen Ustilago maydis

A powerful approach to explore gene function is the use of tetracycline-regulated expression. Here, we report the establishment of this titratable gene expression system for Ustilago maydis. Obstacles of premature polyadenylation of the native tetR gene, high basal activity of the tetracycline-responsive promoter, and toxicity of the viral activation domain were overcome by designing a synthetic tetR* gene according to context-dependent codon usage, removing cryptic enhancer elements from the promoter, and using an acidic minimal activation domain, respectively. We verified tetracycline-dependent dose-response using optimised components and applied a straightforward single-step promoter replacement cassette to regulate expression of pheromone response factor, a key transcription factor regulating mating. Pheromone response in liquid culture and mating on solid media was abolished in the presence of tetracycline and doxycycline. Thus, functionality of this versatile new tool for the plant pathogen was proven in a biological context.

A two-component histidine kinase of the rice blast fungus is involved in osmotic stress response and fungicide action

We isolated and characterized a histidine kinase gene (HIK1) from the rice blast fungus, Pyricularia oryzae (Magnaporthe grisea). The deduced amino acid sequence of HIK1 showed highest similarity (85.7%) to a hybrid-type histidine kinase, Os-1/Nik-1 of Neurospora crassa. Disruption of HIK1 caused no defect in cell growth on normal media and in pathogenicity to rice plants. The Deltahik1 strain acquired resistance to three groups of fungicides (phenylpyrroles, dicarboximides, and aromatic hydrocarbons) similar to os-1 mutants of N. crassa. The Deltahik1 strain showed increased sensitivity to high concentrations of sugars although its salt sensitivity was not elevated, suggesting that the rice blast fungus can distinguish osmostresses caused by high sugar concentrations and high salt concentrations. In contrast, os-1 mutants of N. crassa are sensitive to high concentrations of both salts and sugars. These findings suggest that P. oryzae and N. crassa partially differ in their os (osmosensitive) signal transduction pathway.

Role for RNA-binding proteins implicated in pathogenic development of Ustilago maydis

Ustilago maydis causes smut disease on corn. Successful infection depends on a number of morphological transitions, such as pheromone-dependent formation of conjugation tubes and the switch to filamentous dikaryotic growth, as well as different types of mycelial structures during growth within the host plant. In order to address the involvement of RNA-binding proteins during this developmental program, we identified 27 open reading frames from the genome sequence encoding potential RNA-binding proteins. They exhibit similarities to RNA-binding proteins with Pumilio homology domains (PUM), the K homology domain (KHD), the double-stranded RNA binding motif (DSRM), and the RNA recognition motif (RRM). For 18 of these genes, we generated replacement mutants in compatible haploid strains. Through analysis of growth behavior, morphology, cyclic AMP response, mating, and pathogenicity, we identified three candidates with aberrant phenotypes. Loss of Khd1, a K homology protein containing three KHDs, resulted in a cold-sensitive growth phenotype. Deletion of khd4 encoding a protein with five KHDs led to abnormal cell morphology, reduced mating, and virulence. rrm4Delta strains were affected in filamentous growth and pathogenicity. Rrm4 is an RRM protein with a so far unique domain organization consisting of three N-terminal RRMs as well as a domain found in the C terminus of poly(A)-binding proteins. These results indicate a role for RNA-binding proteins in regulation of morphology as well as in pathogenic development in U. maydis.

Alternative splicing of transcripts of the transposon Restless is maintained in the foreign host Neurospora crassa and can be modified by introducing mutations at the 5' and 3' splice sites

The primary transcript of the transposon Restless from Tolypocladium inflatum undergoes an unusual mechanism of alternative splicing by employing either of two 3' "CAG" splice sites. These are separated by only four nucleotides, thus generating two different splice products, which differ in their coding capacity. To analyse whether this alternative splicing occurs in its natural host exclusively, we introduced the transposon into the heterologous host Neurospora crassa. In addition to the wild -type transposon sequence, transposon sequences mutagenised in vitro with modified 5' and 3' intron splice sites were generated. RNA was isolated from transformants and RT-PCR was performed with specific oligonucleotides flanking the intron sequence. Alternative splicing was analysed, employing a simple test procedure based on the convenient presence of a BamHI restriction site between both splice sites. The ratio of alternative splicing seems to be influenced by both the 5' and the 3' splice site, as mutations at either position influence the ratio of alternative splice products. At the 5' splice site, mutating the first "C" has a strong effect on the ratio of alternative splicing, while mutating the second "C" has little or no effect. Similarly, at the 3' splice site, only mutations at the first 3' "CAG" change the ratio of alternative splicing. It appears that alternative splicing of the Restless intron is not host-specific, but is influenced by the intron splice site sequences themselves.

Characterization and expression of the Neurospora crassa nmt-1 gene

The Neurospora crassa homologue of the yeast no message in thiamine ( nmt-1) gene was characterized. The deduced 342-amino-acid gene product has more than 60% identity with other fungal homologues and 42% similarity to a putative bacterial permease. In addition to three introns disrupting the coding sequence, a differentially spliced intron in the 5' untranslated region was also detected. Unlike other fungi, the N. crassa nmt-1 gene is repressed only 6- to 8-fold by exogenous thiamine concentrations above 0.5 microM; and a high basal level of nmt-1 mRNA persists even at 5 microM thiamine. Immuno-blotting with purified antibodies detected two variants of NMT-1 which differ in size and charge. The more abundant 39-kDa form is more strongly repressed by thiamine than the 37-kDa protein. NMT-1 abundance modulates slowly in response to changes in the concentration of exogenous thiamine, suggesting that N. crassa maintains thiamine reserves in excess of immediate needs. Disruption of the nmt-1 gene demonstrated that it is essential for growth in the absence of exogenous thiamine. NMT-1-deficient strains had a growth rate and colony density which was about 70% of the wild type, despite supplementation with a wide range of exogenous thiamine. These results suggest that the nmt-1 gene plays some other role in addition to thiamine biosynthesis.

The bacterial transposon Tn7 causes premature polyadenylation of mRNA in eukaryotic organisms: TAGKO mutagenesis in filamentous fungi

TAGKO is a Tn7-based transposition system for genome wide mutagenesis in filamentous fungi. The effects of transposon insertion on the expression of TAGKO alleles were examined in Magnaporthe grisea and Mycosphaerella graminicola. Northern analysis showed that stable, truncated transcripts were expressed in the TAGKO mutants. Mapping of the 3'-ends of TAGKO cDNAs revealed that they all contain Tn7 end sequences, regardless of the transposon orientation. Polyadenylation signals characteristic of eukaryotic genes, preceded by stop codons in all frames, are located in both ends of the bacterial transposon. Thus, TAGKO transcripts are prematurely polyadenylated, and truncated proteins are predicted to be translated in the fungal mutants. Depending on the extent of protein truncation, TAGKO mutations in HPD4 (encoding p-hydroxyphenylpyruvate dioxygenase) resulted in tyrosine sensitivity in the two fungi. Similarly, a particular M.grisea CBS1 (encoding cystathionine beta-synthase) TAGKO cDNA failed to complement cysteine auxotrophy in a yeast CBS mutant. TAGKO, therefore, represents a useful tool for in vivo study of truncated gene products in filamentous fungi.

The isolation of FOS-1, a gene encoding a putative two-component histidine kinase from Aspergillus fumigatus

In fungi, two-component histidine kinases are involved in response mechanisms to extracellular changes in osmolarity, resistance to dicarboximide fungicides, and cell-wall assembly. In the human opportunistic fungus, Candida albicans, each of the three histidine kinases plays a role in virulence. Here, we identify, for the first time, a gene, FOS-1, from the human pathogenic fungus Aspergillus fumigatus that predicts a protein with homology to two-component histidine kinases. The predicted FOS-1 protein is highly homologous to bacterial and other fungal histidine kinases in several functional domains, but is divergent at the amino- and carboxy-termini. A mutant lacking the FOS-1 locus, DeltaFOS-1, did not exhibit a detectable defect in either hyphal growth or morphology when grown on solid or liquid medium. However, in liquid medium, conidiophore development of the DeltaFOS-1 mutant was delayed. Compared to wild type, the DeltaFOS-1 strain was neither osmotically sensitive nor sensitive or resistant to a number of nondicarboximide antifungal drugs, but was highly resistant to dicarboximide fungicides and resistant to novozym 234, suggesting that FOS-1p may play a role in the regulation of cell-wall assembly.

Molecular characterization of actin genes from homobasidiomycetes: two different actin genes from Schizophyllum commune and Suillus bovinus

The actin-encoding genes Scact1 and Scact2 of the homobasidiomycete Schizophyllum commune are the first actin genes isolated from higher filamentous fungi. Their isolation shows that homobasidiomycetes have two actin encoding genes instead of one typical to yeasts and filamentous ascomycetes. This result was further confirmed by cloning two actin encoding genes, Sbact1 and Sbact2, from another homobasidiomycete Suillus bovinus. The comparison of the genomic and cDNA sequences of the actin genes showed that Scact1 and Scact2 genes of S. commune contain seven introns, five of which are at the same position in the two genes while S. bovinus actin genes contain nine similarly positioned introns. In the four genes, five intron positions are shared, which indicates a close relationship between the actin encoding genes from S. commune and S. bovinus. Northern hybridization and analysis of two-dimensional immunoblots showed a difference in the expression levels between the two actin genes in each fungus. No actin protein could be detected from S. commune Scact2. The deduced amino acid sequence of the Scact2 gene also differs considerably from any other known actin protein. These data suggest that the Scact2 gene either has a special as yet unidentified function in S. commune life cycle or is a transcribed but no longer translated pseudogene. Scact2 gene has a putative microORF (short open reading frame) and Scact1 gene an intron in the 5'-untranslated region, which could reduce the translational efficiency and increase the transcriptional efficiency of the Scact2 and Scact1 genes, respectively. During mating in S. commune or at formation of ectomycorrhiza in S. bovinus, the expression of actin genes was similar to that in vegetative hyphae. This result suggests that the reorganization of actin cytoskeleton in response to extra- and intracellular signals in higher filamentous fungi could be directly regulated by members of signalling pathways well characterized in yeast and mammalian cells.