Unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in Neurospora crassa

<p>Abstract</p> <p>Background</p> <p>Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse <it>Trichoderma reesei </it>(<it>Hypocrea jecorina</it>) have revealed an interconnection between transcriptional regulation of cellulolytic enzymes and the light response. <it>Neurospora crassa </it>has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in <it>N. crassa</it>.</p> <p>Results</p> <p>We show that the <it>N. crassa </it>photoreceptor genes <it>wc-1, wc-2 </it>and <it>vvd </it>are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. The negative effect of VVD on production of cellulolytic enzymes is thereby accomplished by its role in photoadaptation and hence its function in White collar complex (WCC) formation. In contrast, the induction of <it>vvd </it>expression by the WCC does not seem to be crucial in this process. Additionally, we found that WC-1 and WC-2 not only act as a complex, but also have individual functions upon growth on cellulose.</p> <p>Conclusions</p> <p>Genome wide transcriptome analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression. Genes with functions in amino acid metabolism, glycogen metabolism, energy supply and protein folding are enriched among genes with decreased expression levels in the <it>wc-1 </it>and <it>wc-2 </it>mutants. The ability to properly respond to amino acid starvation, i. e. up-regulation of the cross pathway control protein <it>cpc-1</it>, was found to be beneficial for cellulase gene expression. Our results further suggest a contribution of oxidative depolymerization of cellulose to plant cell wall degradation in <it>N. crassa</it>.</p

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination

To test the inferences of spotted microarray technology against a biochemically well-studied process, we performed transcriptional profiling of conidial germination in the filamentous fungus, Neurospora crassa. We first constructed a 70 base oligomer microarray that assays 3366 predicted genes. To estimate the relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout a time course using a Bayesian analysis of gene expression level. Remarkable consistency of mRNA profiles with previously published northern data was observed. Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. A functional classification database was employed to characterize the global picture of gene expression. Consensus motif searches identified a putative regulatory component associated with genes involved in ribosomal biogenesis. Our transcriptional profiling data correlate well with biochemical and physiological processes associated with conidial germination and will facilitate functional predictions of novel genes in N.crassa and other filamentous ascomycete species. Furthermore, our dataset on conidial germination allowed comparisons to transcriptional mechanisms associated with germination processes of diverse propagules, such as teliospores of the phytopathogenic fungus Ustilago maydis and spores of the social amoeba Dictyostelium discoideum

Geometries for Possible Kinematics

The algebras for all possible Lorentzian and Euclidean kinematics with $\frak{so}(3)$ isotropy except static ones are re-classified. The geometries for algebras are presented by contraction approach. The relations among the geometries are revealed. Almost all geometries fall into pairs. There exists $t \leftrightarrow 1/(\nu^2t)$ correspondence in each pair. In the viewpoint of differential geometry, there are only 9 geometries, which have right signature and geometrical spatial isotropy. They are 3 relativistic geometries, 3 absolute-time geometries, and 3 absolute-space geometries.Comment: 40 pages, 7 figure

Exploring the bZIP transcription factor regulatory network in Neurospora crassa

Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Exploring the bZIP transcription factor regulatory network in Neurospora crassa.

Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution

A Credit-Based Congestion-Aware Incentive Scheme for DTNs

In Delay-Tolerant Networks (DTNs), nodes may be selfish and reluctant to expend their precious resources on forwarding messages for others. Therefore, an incentive scheme is necessary to motivate selfish nodes to cooperatively forward messages. However, the current incentive schemes mainly focus on encouraging nodes to participate in message forwarding, without considering the node congestion problem. When many messages are forwarded to the nodes with high connection degree, these nodes will become congested and deliberately discard messages, which will seriously degrade the routing performance and reduce the benefits of other nodes. To address this problem, we propose a credit-based congestion-aware incentive scheme (CBCAIS) for DTNs. In CBCAIS, a check and punishment mechanism is proposed to prevent forwarding nodes from deliberately discarding message. In addition, a message acceptance selection mechanism is proposed to allow the nodes to decide whether to accept other messages, according to self congestion degree. The experimental results show that CBCAIS can effectively stimulate selfish nodes to cooperatively forward messages, and achieve a higher message delivery ratio with lower overhead ratio, compared with other schemes