Cooperative action of the NIT2 and NIT4 transcription factors upon gene expression in Neurospora crassa

Developing a Temperature-Inducible Transcriptional Rheostat in Neurospora crassa

Heat shock protein (HSP)-encoding genes (hsp), part of the highly conserved heat shock response (HSR), are known to be induced by thermal stress in several organisms. In Neurospora crassa, three hsp genes, hsp30, hsp70, and hsp80, have been characterized; however, the role of defined cis elements in their responses to discrete changes in temperature remains largely unexplored. To fill this gap, while also aiming to obtain a reliable fungal heat shock-inducible system, we analyzed different sections of each hsp promoter by assessing the expression of real-time transcriptional reporters. Whereas all three promoters and their resected versions were acutely induced by high temperatures, only hsp30 displayed a broad range of expression and high tunability, amply exceeding other inducible promoter systems existing in Neurospora, such as quinic acid- or light-inducible ones. As proof of concept, we employed one of these promoters to control the expression of clr-2, which encodes the master regulator of Neurospora cellulolytic capabilities. The resulting strain fails to grow on cellulose at 25°C, whereas it grows robustly if heat shock pulses are delivered daily. Additionally, we designed two hsp30 synthetic promoters and characterized them, as well as the native promoters, using a gradient of high temperatures, yielding a wide range of responses to thermal stimuli. Thus, Neurospora hsp30-based promoters represent a new set of modular elements that can be used as transcriptional rheostats to adjust the expression of a gene of interest or for the implementation of regulated circuitries for synthetic biology and biotechnological strategies. IMPORTANCE A timely and dynamic response to strong temperature fluctuations is paramount for organismal biology. At the same time, inducible promoters are a powerful tool for fungal biotechnological and synthetic biology endeavors. In this work, we analyzed the activity of several N. crassa heat shock protein (hsp) promoters at a wide range of temperatures, observing that hsp30 exhibits remarkable sensitivity and a dynamic range of expression as we charted the response of this promoter to subtle increases in temperature, and also as we built and analyzed synthetic promoters based on hsp30 cis elements. As proof of concept, we tested the ability of hsp30 to provide tight control of a central process, cellulose degradation. While this study provides an unprecedented description of the regulation of the N. crassa hsp genes, it also contributes a noteworthy addition to the molecular toolset of transcriptional controllers in filamentous fungi.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

Interaction of Yna1 and Yna2 Is Required for Nuclear Accumulation and Transcriptional Activation of the Nitrate Assimilation Pathway in the Yeast Hansenula polymorpha

A few yeasts, including Hansenula polymorpha are able to assimilate nitrate and use it as nitrogen source. The genes necessary for nitrate assimilation are organised in this organism as a cluster comprising those encoding nitrate reductase (YNR1), nitrite reductase (YNI1), a high affinity transporter (YNT1), as well as the two pathway specific Zn(II)2Cys2 transcriptional activators (YNA1, YNA2). Yna1p and Yna2p mediate induction of the system and here we show that their functions are interdependent. Yna1p activates YNA2 as well as its own (YNA1) transcription thus forming a nitrate-dependent autoactivation loop. Using a split-YFP approach we demonstrate here that Yna1p and Yna2p form a heterodimer independently of the inducer and despite both Yna1p and Yna2p can occupy the target promoter as mono- or homodimer individually, these proteins are transcriptionally incompetent. Subsequently, the transcription factors target genes containing a conserved DNA motif (termed nitrate-UAS) determined in this work by in vitro and in vivo protein-DNA interaction studies. These events lead to a rearrangement of the chromatin landscape on the target promoters and are associated with the onset of transcription of these target genes. In contrast to other fungi and plants, in which nuclear accumulation of the pathway-specific transcription factors only occur in the presence of nitrate, Yna1p and Yna2p are constitutively nuclear in H. polymorpha. Yna2p is needed for this nuclear accumulation and Yna1p is incapable of strictly positioning in the nucleus without Yna2p. In vivo DNA footprinting and ChIP analyses revealed that the permanently nuclear Yna1p/Yna2p heterodimer only binds to the nitrate-UAS when the inducer is present. The nitrate-dependent up-regulation of one partner protein in the heterodimeric complex is functionally similar to the nitrate-dependent activation of nuclear accumulation in other systems.

Fungal biology in the post-genomic era

In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick’s central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The “next generation” sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.

LbNrt RNA silencing in the mycorrhizal symbiont Laccaria bicolor reveals a nitrate-independent regulatory role for a eukaryotic NRT2-type nitrate transporter

Fungal nitrogen metabolism plays a fundamental role in function of mycorrhizal symbiosis and consequently in nutrient cycling of terrestrial ecosystems. Despite its global ecological relevance the information on control and molecular regulation of nitrogen utilization in mycorrhizal fungi is very limited. We have extended the nitrate utilization RNA silencing studies of the model mycorrhizal basidiomycete, Laccaria bicolor, by altering the expression of LbNrt, the sole nitrate transporter-encoding gene of the fungus. Here we report the first nutrient transporter mutants for mycorrhizal fungi. Silencing of LbNrt results in fungal strains with minimal detectable LbNrt transcript levels, significantly reduced growth capacity on nitrate and altered symbiotic interaction with poplar. Transporter silencing also creates marked co-downregulation of whole Laccaria fHANT-AC (fungal high-affinity nitrate assimilation cluster). Most importantly, this effect on the nitrate utilization pathway appears independent of extracellular nitrate or nitrogen status of the fungus. Our results indicate a novel and central nitrate uptake-independent regulatory role for a eukaryotic nitrate transporter. The possible cellular mechanisms behind this regulation mode are discussed in the light of current knowledge on NRT2-type nitrate transporters in different eukaryotes.

Hansenula polymorpha NMR2 and NMR4, two new loci involved in nitrogen metabolite repression

In the yeast Hansenula polymorpha (Pichia angusta) nitrate assimilation is tightly regulated and subject to a dual control: nitrogen metabolite repression (NMR), triggered by reduced nitrogen compounds, and induction, elicited by nitrate itself. In a previous paper [Serrani, F., Rossi, B. and Berardi, E (2001) Nitrogen metabolite repression in Hansenula polymorpha: the nmrl-l mutation. Curr. Genet. 40, 243-250], we identified five loci (NMR1-NMR5) involved in NMR, and characterised one of them (NMR1), which likely identifies a regulatory factor. Here, we describe two more mutants, namely nmr2-1 and nmr4-1. The first one possibly identifies a regulatory factor involved in nitrogen metabolite repression by various nitrogen sources alternative to ammonium. The second one, apparently involved in ammonium assimilation, probably has sensor functions.