Browsing by Subject "Neurospora"
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Item Control of rhythmic output from the circadian clock in Neurospora crassa(Texas A&M University, 2005-02-17) Lewis, Zachary AustinCircadian rhythms are visible as daily oscillations in biochemical, physiological, or behavioral processes. These rhythms are produced by an endogenous clock that maintains synchrony with the external environment through responses to external stimuli such as light or temperature. The clock, in turn, coordinates internal processes in a time-dependent fashion. Genetic and molecular analysis of the filamentous fungus Neurospora crassa has demonstrated that the products of the frequency (frq) and white-collar (wc-1 and wc-2) genes interact to form an interlocked feedback loop that lies at the heart of the clock in this fungus. This feedback loop, termed the FRQ/WC oscillator, produces a ~24h oscillation in frq mRNA, FRQ protein, and WC-1 protein. In turn, the FRQ/WC oscillator regulates rhythmic behavior and gene expression. The goal of this dissertation is to understand how rhythmic outputs are regulated by the FRQ/WC oscillator in Neurospora. To this end, we have taken a microarray approach to first determine the extent of clock-controlled gene expression in Neurospora. Here, we show that circadian regulation of gene expression is widespread; 145 genes, representing 20% of the genes we analyzed, are clock-controlled. We show that clockregulation is complex; clock-controlled genes peak at all phases of the circadian cycle. Furthermore, we demonstrate the clock regulates diverse biological processes, such as intermediary metabolism, translation, sexual development and asexual development. WC-1 is required for all light- and clock-regulated gene expression in Neurospora. We have shown that overexpression of WC-1 is sufficient to activate clock-controlled gene expression, but is not sufficient to induce all light-regulated genes in Neurospora. This result indicates that cycling of WC-1 is sufficient to regulate rhythmic expression of a subset of clockcontrolled genes. Conversely, a post-translational mechanism underlies WC-1 mediated light signal transduction in Neurospora. Finally, we have demonstrated the Neurospora circadian system is comprised of mutually coupled oscillators that interact to regulate output gene expression in the fungus.Item Functional analysis of fluffy, a transcriptional regulator for conidial development in Neurospora crassa(Texas A&M University, 2005-08-29) Rerngsamran, PananThe fluffy gene of Neurospora crassa is required for asexual sporulation. It encodes an 88 kDa polypeptide containing a typical fungal Zn2Cys6 DNA binding motif. To identify the target genes on which FL may act, I sought to identify target sequences to which the FL protein binds. Several strategies were attempted to obtain purified FL protein. Purification was achieved by expressing the DNA binding domain of FL in Escherichia coli as a fusion with glutathione S-transferase followed by affinity purification using glutathione sepharose chromatography. DNA binding sites were selected by in vitro binding assays. Comparison of the sequences of selected clones suggested that FL binds to the motif 5??-CGG(N)9CCG-3??. A potential binding site was found in the promoter region of the eas (ccg-2) gene, which encodes a fungal hydrophobin. In vitro competitive binding assays revealed a preferred binding site for FL in the eas promoter, 5??-CGGAAGTTTCCTCCG-3??, which is located 1498 bp upstream of the eas translation initiation codon. In vivo experiments using a foreign DNA sequence tag confirmed that this sequence is a target site for FL regulation. Using Saccharomyces cerevisiae as an experimental system, I demonstrated that the C-terminal portion of FL functions in transcriptional activation. Microarray analysis was performed to study the role of fl in gene regulation on a large scale. mRNA levels in a fl mutant were compared to those in a strain overexpressing the fl gene. Experiments with cDNA microarray containing 13% of the total number of predicted N. crassa genes revealed 122 genes differentially expressed in response to overexpression of fl. Among these, eas displayed the greatest level of response. The cDNA microarray approach also revealed a number of genes that may be indirectly regulated by fl but may be involved in development. This information provides a foundation for further analysis of the role of fl in conidial development.Item Organization of the circadian clock and control of rhythmicity in fungi(Texas A&M University, 2006-10-30) Greene, Andrew VanderfordCircadian rhythms in biological processes occur in a wide range of organisms and are generated by endogenous oscillators. In Neurospora crassa, the FRQ-oscillator (comprised of FRQ, WC-1 and WC-2) is essential for rhythms in asexual sporulation and gene expression. How this oscillator signals to the cell to control rhythmicity is unknown. Furthermore, under certain growth conditions, rhythms are observed in FRQ-null strains, indicating the presence of one or more FRQ-less oscillators (FLOs). Interestingly, while circadian rhythms are observed in the related Aspergillus spp., they lack the frq gene, leading to the hypothesis that a FLO is responsible for rhythms in Aspergillus. Thus, Aspergillus provides a useful organism to investigate the components of the FLO. To investigate how an oscillator controls circadian output, we characterized the role of N. crassa NRC-2. The nrc-2 gene is under control of the clock and encodes a putative serine-threonine protein kinase. In a NRC-2-null strain cultured in low glucose conditions, FRQ-oscillator-dependent outputs are arrhythmic, but are rhythmic in high glucose. Our data suggests a model whereby NRC-2 relays metabolic information to the FRQ-oscillator to control rhythmic output. To understand the role of FLO(s) in the N. crassa circadian system, we examined regulation of the ccg-16 gene. We show that ccg-16 transcript rhythmicity is FRQ-independent, but WC-1-dependent. Furthermore, in contrast to current models for the FRQ-oscillator, we observed that rhythms in WC-1 protein accumulation persist in the absence of FRQ. These data support a new model involving two oscillators that are coupled through the WC-1 protein and that regulate different outputs. One approach to identify components of the FLO involved characterizing circadian rhythms in Aspergillus spp, which lacks FRQ. We find that A. flavus and A. nidulans, display circadian rhythms in sporulation and gene expression, respectively. Together, these findings provide a foundation for the identification of FLO components in both Aspergillus and N. crassa, that will ultimately lead to an understanding of how a multi-oscillator system can generate and coordinate circadian rhythmicity.Item Regulation of the p38 MAPK Signaling Pathway by the Circadian Clock(2013-08-12) Goldsmith, Charles SidneyMitogen activated protein kinase (MAPK) pathways are conserved biochemical signal transduction pathways in eukaryotic organisms. These signaling pathways demonstrate great versatility in their ability to detect various environmental stimuli and direct an appropriate cellular response. The circadian clock is a timekeeping mechanism that temporally coordinates diverse biological functions in an organism with the environment. Thus, it is not surprising that MAPK pathways have been utilized by the circadian clock to regulate many essential functions. Due to the conserved nature of circadian clocks and MAPK signaling pathways in eukaryotes, it is possible to develop hypotheses in simple model organisms, such as the fungus Neurospora, that are relevant to more complex organisms. The OS-2 MAPK pathway in the filamentous fungus Neurospora is rhythmically activated by the circadian clock. In order to generate this rhythmic signal, the circadian oscillator directly regulates the rhythmic transcription of the os-4 MAPKKK and histidine phosphotransferase hpt-1, which are upstream regulators of the OS-2 MAPK. Also, the circadian rhythm in MAPK activation produces a more robust stress response during the time of the day that stress is most likely to be encountered. Based on these data, a model for the clock regulation of MAPK activation is presented, and a biological significance is assigned to the rhythms in this pathway. Informed by these findings in Neurospora, the related p38 MAPK pathway was studied in mammalian cell lines that represent functionally distinct tissues in regards to clock function. A rhythm in p38 MAPK activation was observed in cells derived from the suprachiasmatic nucleus and fibroblasts of a mouse, the master pacemaker and a peripheral tissue, respectively. In cells that lacked a functional circadian oscillator, the rhythm in p38 activation was absent, and overall levels of p38 protein were lower. These data demonstrate a circadian clock-dependent oscillation in p38 activity. These studies provide a basis to understand how the circadian clock generates endogenous rhythms in MAPK signal transduction pathways. Also, the characterization of clock-regulated stress response pathways provides an understanding of the adaptive advantage of the circadian clock.Item Uncovering the circadian output pathways of Neurospora crassa(2009-05-15) Vitalini, Michael WilliamThe ubiquity of circadian systems has allowed their characterization in a broad range of model systems, which has greatly improved knowledge of how these systems are organized and the vast range of cellular and organismal processes under circadian control. Most of the advances, however, have come in describing the central oscillators of these systems, and, in some cases, the input pathways used to coordinate these oscillators to external time. Very little progress has been made in understanding the output pathways that allow circadian systems to regulate the breadth of processes shown to be clock-controlled. A genetic selection was designed to obtain mutations in genes involved in circadianregulated expression of the Neurospora crassa ccg-1 and ccg-2 genes. Some, but not all, of the strains obtained display altered regulation of more than one ccg as well as an ?Easlike? appearance on solid media, and altered circadian period on race tubes. The data suggest a model in which output from the clock to these two genes is through a single, bifurcated pathway. The cloning of the gene mutated (rrg-1) in one of the strains from the above selection led to the first molecular description of a circadian output pathway in Neurospora, the HOG MAP kinase pathway. The HOG pathway has been previously described with regard to its role in the osmotic-stress response. The discovery of the involvement of rrg-1 in circadian regulation of ccg-1 and ccg-2 led to the discovery of regulation of the HOG pathway by the circadian clock. The data indicate that osmotic stress information and time-of-day information are transduced through the HOG pathway and implicate a role for the clock in preparing the organism for daily occurrences of hyperosmotic stress associated with sun exposure. The genetic selection, and the description of the HOG pathway with regard to circadian output, provide a basis for further characterization of circadian output in Neurospora. The ubiquity of MAP kinase pathways, such as the HOG pathway, and the observed similarities in the mechanisms of circadian clock function across multiple phyla, indicate that these findings may well be applicable to other model systems.