Transcriptional Profiling of Cross Pathway Control in
            <i>Neurospora crassa</i>
            and Comparative Analysis of the Gcn4 and CPC1 Regulons

Tian, Chaoguang; Kasuga, Takao; Sachs, Matthew S.; Glass, N. Louise

doi:10.1128/ec.00078-07

Cited by 74 publications

(116 citation statements)

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“…S4A). Remarkably, inspection of transcriptional profiling data shows that in the N. crassa strain mutant for the gene encoding a global transcriptional regulator crosspathway control-1 (CPC1), a yeast GCN4 ortholog, the level of rvt transcription undergoes a 47-fold increase under conditions of amino acid starvation induced by 3-aminotriazole (3-AT), an inhibitor of histidine biosynthesis (21). This increase is higher than that for any other gene of 10,526 N. crassa genes.…”

Section: Resultsmentioning

confidence: 99%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn 2+ as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.D NA-dependent polymerases are essential for cellular function, as they mediate the flow of genetic information from DNA to RNA to proteins (1). In contrast, RNA-dependent polymerases have long been associated with replication of selfish and parasitic genetic elements, such as viruses or transposons. Although the discovery of reverse transcriptase (RT) challenged the concept of unidirectionality of the flow of genetic information, this reverse direction has been reserved for retroviruses, pararetroviruses (hepadna-and caulimoviruses), and other RT-containing multicopy entities such as non-LTR and LTR retrotransposons, group II introns, retrons, and retroplasmids, as well as occasional retro (pseudo)genes (2-4). Similarly, viral RNA-dependent RNA polymerases (RdRPs), enzymes structurally related to RTs, serve to replicate the genomes of viruses that use RNA as genetic material (5). These and certain other polymerases are unified by the architecture known as "right hand," composed of the three subdomains called fingers, palm, and thumb (6). Like all polymerases, they use two-metal-ion catalysis for phosphoryl transfer reactions resulting in nucleotide addition.In 1997, this diverse superfamily of enzymes was joined by the telomerase reverse transcriptase (TERT), a specialized RT that maintains the ends of eukaryotic linear chromosomes by addition of short G-rich repeated DNA sequences that are copied multiple times via reverse transcription of a specific region of the associated RNA template constituting part of the holoenzyme (...

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Section: Resultsmentioning

confidence: 99%

A widespread class of reverse transcriptase-related cellular genes

Gladyshev

Arkhipova

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Mycelia were harvested by filtration and flash frozen in liquid nitrogen. Total RNA was isolated using TRIzol (14,15). Microarray hybridization and data analysis were as described in ref.…”

Section: Methodsmentioning

confidence: 99%

“…N. crassa also grew rapidly on ground Miscanthus stems, suggesting functional cellulase and hemicellulase degradative capacity. To determine the transcriptome associated with plant cell wall deconstruction, we used full genome microarrays (13)(14)(15) to monitor gene expression profiles during growth of N. crassa on ground Miscanthus stems. RNA sampled from N. crassa grown for 16 h on sucrose was compared to RNA from N. crassa grown on Miscanthus medium at 16 h, 40 h, 5 days, and 10 days ( Fig.…”

Section: Transcriptome Analysis Of N Crassa Grown On Miscanthus and mentioning

confidence: 99%

Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa

Tian

Beeson

Iavarone

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The filamentous fungus Neurospora crassa is a model laboratory organism, but in nature is commonly found growing on dead plant material, particularly grasses. Using functional genomics resources available for N. crassa, which include a near-full genome deletion strain set and whole genome microarrays, we undertook a systemwide analysis of plant cell wall and cellulose degradation. We identified approximately 770 genes that showed expression differences when N. crassa was cultured on ground Miscanthus stems as a sole carbon source. An overlap set of 114 genes was identified from expression analysis of N. crassa grown on pure cellulose. Functional annotation of up-regulated genes showed enrichment for proteins predicted to be involved in plant cell wall degradation, but also many genes encoding proteins of unknown function. As a complement to expression data, the secretome associated with N. crassa growth on Miscanthus and cellulose was determined using a shotgun proteomics approach. Over 50 proteins were identified, including 10 of the 23 predicted N. crassa cellulases. Strains containing deletions in genes encoding 16 proteins detected in both the microarray and mass spectrometry experiments were analyzed for phenotypic changes during growth on crystalline cellulose and for cellulase activity. While growth of some of the deletion strains on cellulose was severely diminished, other deletion strains produced higher levels of extracellular proteins that showed increased cellulase activity. These results show that the powerful tools available in N. crassa allow for a comprehensive system level understanding of plant cell wall degradation mechanisms used by a ubiquitous filamentous fungus.cellulase ͉ secretome ͉ transcriptome

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“…This S. cerevisiae AA starvation response governed by Gcn4 appears globally conserved throughout the ascomycetes phylogeny [44 ,45]. However, transcriptional profiling of the amino-acid starvation response in Neurospora crassa suggested that in these cells AA biosynthesis genes and tRNA-aminoacyl-transferases are highly co-regulated [44 ] and a meta-analysis of expression co-regulation between S. cerevisiae and C. albicans identified distinctions in the mode of tRNA-aminoacyl-transferases co-regulation between the two species [4]. Consistently, phylogenetic analyses of the Gcn4 element (TGASTCA) enrichment showed that it is conserved in the amino-acid biosynthesis regulon in most ascomycetes and that it is found upstream of genes encoding tRNA-aminoacyltransferases in many species but excluded from the S. cerevisiae branch (Figure 1c) [16,44] ( Figure 1).…”

Section: Amino-acid Biosynthesismentioning

confidence: 99%