Download or read book Expression of Genes in Neurospora Crassa Outside of the Quinic Acid Gene Cluster During Quinic Acid Metabolism written by John William Savopoulos and published by . This book was released on 2018 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: The quinic acid (qa) gene cluster in Neurospora crassa (N. crassa) consists of two regulatory genes (qa-1F and qa-1S) as well as five structural genes (qa-2, qa-3, qa-4, qa-y, and qa-x) that are transcribed in the presence of quinic acid with suppressed levels of glucose (Greever R.F., et al. 1988). The corresponding activation and repression of this cluster enables the survival of the organism in less than hospitable environments. A research study hypothesized that some 50 genes were under the control of the qa-1F gene and another qa transcription factor. Furthermore, it was shown at the proteomic level in the work of Kayla Brown, Katie Allen, and Dana Tirabassi that glycogen phosphorylase (NCU07027), peptidyl-prolyl cis-trans isomerase (NCU04140), and NCU08332 Hex-1: Woronin Body Coding Protein all had heightened expression at the proteomic level in the presence of quinic acid. Therefore, the scope of this work aimed to analyze these three genes to determine their levels of transcription in the presence of quinic acid (utilizing qRT-PCR), and to determine if they are related to the quinic acid gene cluster. The results indicate that heightened glycogen phosphorylase expression seen in prior works is not related to quinic acid metabolism and is not a result of starvation. However, it is predicted that the cell may be holding on to this protein for other purposes not related to the scope of this work. Peptidyl prolyl cis-trans isomerase appeared to not be related to the quinic acid gene cluster, but rather showed heightened expression as a result of starvation. Last, the NCU08332 Hex-1 Woronin body major protein gene appeared to have a direct relation to quinic acid metabolism and the quinic acid gene cluster. Furthermore, bioinformatics analyses presented also supported this assumptions.

Download or read book Changes in Gene Expression of Neurospora Crassa in Response to Quinic Acid written by Kayla A. Brown and published by . This book was released on 2016 with total page 82 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a filamentous fungus, Neurospora crassa serves as an ideal model for eukaryotic organisms. Like many fungi, Neurospora is able to utilize many different carbon sources for energy. This however, requires the presence of genes that code for a variety of metabolic pathways that are not always needed. An example of such a group of genes would be the genes involved in utilizing quinic acid. When Neurospora grows in the presence of a less preferred carbon source, such as quinic acid, gene expression of the quinic acid (qa) gene cluster is up-regulated. This allows the organism to metabolize quinic acid and survive in the less favorable conditions. In contrast, when in the presence of a preferred carbon source, such as dextrose or sucrose, the qa genes are repressed. This study examines how changing the carbon source effects gene expression in wild-type N.crassa. N.crassa was first grown in presence of either quinic acid or sucrose and harvested for tissue. Then, protein was extracted from this tissue and analyzed by 1- Dimensional Gel Electrophoresis (1-DGE). Differences in protein expression was compared using the Quantity One® 1-D analysis software. Proteins unique to growth on quinic acid were identified after being submitted for mass spectrometry. Finally, gene transcription was quantitated in order to determine which genes coded for proteins expressed only in the presence of quinic acid by reverse transcriptase polymerase chain reaction (RT-PCR) and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR).

Download or read book Expression Kinetics of the Quinic Acid qa Gene Cluster in Neurospora Crassa written by Melissa Fleeger and published by . This book was released on 2010 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Eukaryotic genes are tightly regulated through a highly complex system with a number of checks and balances. When environmental conditions change, organisms need to adapt. Part of this reaction may be a shift in gene expression based on the regulation of that particular gene or gene cluster. The quinic acid (qa) gene cluster of Neurospora crassa is such a system. The up-regulation in gene expression for the qa cluster is triggered by the carbon source quinic acid. When the fungus is grown on quinic acid as a sole carbon source, the qa genes are expressed at high levels. However, when a preferred carbon source, such as dextrose, is used, the qa genes are repressed. This study will quantify the effects of changing carbon source over a three hour time period in the wild type strain of N. crassa, 74A. The focus of this study is the kinetics of induction of the various quinic acid genes as the environment changes. RNA was isolated from N. crassa grown under various conditions. Transcript levels of the various genes are detected by SYBR Green using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Results are normalized to the internal control gene, 18s rRNA, and analyzed with Bio-Rad iQ5 software. These results reveal that the up-regulation in expression of the qa genes is detectable within 15 minutes of incubation with quinic acid and reaches peak levels, higher than previously thought, within 3 hours.

Download or read book Studies on Quinic Acid QA Gene Cluster in Various Strains of Neurospora Crassa written by Rathna J. Veeramachaneni and published by . This book was released on 2010 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Quinic Acid Gene Cluster in Neurospora written by Diana R. Arnett and published by . This book was released on 2005 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: The quinic acid (qa) cluster of Neurospora crassa is subject to two levels of control. The primary mechanism is dependent on the presence of the inducer, quinic acid: in the absence of inducer, the genes are expressed at low basal levels. The cluster is also subject to catabolite repression--the genes are repressed in the presence of a preferred carbon source, such as dextrose, even in the presence of inducer. To focus on this second level of control, I utilized a constitutive mutant of the qa gene cluster which contains a deletion of the qa-1S repressor gene. This deletion removes the primary control mechanism, ensuring that any observed effect is due to catabolite repression. Northern blot analysis indicates that transcription of the qa-y gene, which encodes a quinate permease, is repressed by the presence of dextrose even in the absence of the qa 1S repressor, demonstrating that catabolite repression of the qa cluster may be occurring by inducer exclusion. Transcription of the remainder of the qa genes does not appear to be repressed to a significant degree in the constitutive mutant by the presence of dextrose. Additionally, I used 2-dimensional protein gel electrophoresis to examine the expression of the qa proteins in samples grown under different growth conditions. Preliminary results show changes in protein expression in repressor mutants when compared to wild-type. Gene regulation mechanisms can be revealed by comparing homologous sequences in related species. I sequenced the permease and repressor genes, along with the associated regulatory regions in the homothallic Neurospora species N. africana and N. terricola. The coding regions of both species share a high degree of homology to N. crassa: the permease genes are 93% identical and the repressor 91-92% identical. The noncoding region upstream of the repressor is less conserved, with N. africana showing 41% identity and N. terricola 59% identity to N. crassa. In contrast, the region upstream of the permease gene is highly conserved, with both species 83% identical to N. crassa. This highly conserved region could contain binding sites needed to affect catabolite repression of the permease gene.

Download or read book Effects of the Qa 1F Activator Protein on the Expression of Quinic Acid Induced Genes in Neurospora Crassa written by Dana Marie Tirabassi and published by . This book was released on 2013 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neurospora crassa, like most fungi, is very flexible metabolically. When a preferred carbon source, such as dextrose, is unavailable, N. crassa has the ability to metabolize quinic acid. To do this, the quinic acid gene cluster is up-regulated by the qa-1F activator. This study uses a mutant form of N. crassa in which the qa-1F gene is knocked out. The protein profiles of N. crassa wild-type and qa-1F knockout when grown on both dextrose and quinic acid were analyzed and compared. The wild-type and knockout strains were first grown on 2% dextrose and then shifted either to fresh dextrose or 0.3% quinic acid. The proteins from these tissues were then extracted, quantitated, and separated using two-dimensional gel electrophoresis (2DGE). The 2DGE gels were then analyzed using PDQUESTTM. Cross-conditional comparisons were made and protein spots unique to each condition were identified. These gel comparisons show that, when grown on a preferred carbon source, nearly twice as many proteins are up-regulated than when grown on quinic acid. Also, the qa-1F knockout protein profiles had far fewer protein spots than their wild-type counterparts for both carbon sources. Protein spots were then selected, excised, and sent to the Ohio State University for mass spectrometry and bioinformatic analysis. Two proteins affected by the presence of qa-1F when grown on quinic acid were identified as hypothetical proteins NCU 04072 and NCU 08332 likely be a catechol dioxygenase and a translational protein SH3-like protein, respectively.

Download or read book Induction of the Qa y and Qa 1F Genes in Neurospora Crassa at Differing Times of Quinic Acid Exposure written by Kory George and published by . This book was released on 2016 with total page 70 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neurospora crassa, a model filamentous fungus, contains the quinic acid (qa) gene cluster, allowing the organism to effectively metabolize quinic acid as an alternative carbon source. In the presence of quinic acid, the qa gene cluster is significantly unregulated, showing an increased expression of both regulatory proteins as well as the structural proteins required for the utilization of quinic acid as an energy source. Of these structural genes, qa-2, qa-3, and qa-4 encode for the enzymes required for the conversion of quinic acid to protocathechuic acid while qa-y encodes for a quinate permease and the function of qa-x remains unknown. The present study aims to elucidate the expression pattern of qa-y, the quinate permease-producing gene required for efficient uptake and utilization of quinic acid in N. crassa, as well as qa-1F, the activator protein of the qa gene cluster, at differing times of quinic acid exposure. Quantitative real-time PCR (RT-qPCR) using reverse transcriptase was first used to determine Histone-3 as the optimal housekeeping reference gene. This gene was then used to accurately quantify the expression of both qa-y and qa-1F at differing times of exposure to quinic acid (0min, 15min, 30min, 1hr, 2hr, and 3hr). The expression of qa-y was observed to steadily increase for the first 30 minutes, showing up to a 17-fold change in expression after only 30 minutes following introduction of quinic acid. A prompt response of the qa-1F gene was also observed. At the 15-minute time point, a 3-fold increase in expression of the qa-1F occurred, presumably to initiate activation of transcription of the genes of the qa gene cluster, including itself. When combined, these data allow for a comprehensive representation of the timing and method of regulation of the qa gene cluster in N. crassa.

Download or read book Studies on the Quinic Acid qa Gene Cluster of Neurospora Africana written by Kimberly Anne Rutledge and published by . This book was released on 1996 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: The qa-IS-qa-IF intergenic sequence of N. afrieana was chosen for study because this region may playa role in the carbon catabolite repression of the genes within the quinic acid (qa) gene cluster. Evidence has indicated that expression of the GAL genes, within the galactose pathway of S. eerevisiae , is reduced in the presence of a preferred carbon source such as glucose. This process results from the inability of the GAL4 activator protein to bind to its GAL4 binding sites within the GAL promoters. However, the exact mechanism of GAL4 inhibition is unknown. A similar mechanism may occur within the qa gene cluster of N. erassa. In the presence of a preferred carbon source, qa gene expression is repressed. Asch and Case (1992) provided evidence that some qa genes were slightly repressed in the presence of glucose, while other qa genes were higWy repressed. The qaIF activator gene was amongst the highly repressed genes. The exact mechanism of catabolite repression is unclear. We attempted to study the qa-IS-qa-IF intergenic sequence of N. afrieana because this region may influence the qa gene repression in the presence of glucose. Two plasmid clones, pR1 and pRX2, were established. Plasmid pR1 contains a 3.8-kb insert spanning the entire qa-IS-qa-IF region of N. afrieana. Whereas, plasmid pRX2 contains a 2.7-kb fragment spanning a portion of the qa-IS-qa-IF intergenic region. Southern blot analysis of both plasmids pR1 and pRX2 confirmed that these clones contain the qa-IS-qa-IF intergenic sequence. Sequence analysis of the plasmid pR1, using the M13/pUC reverse primer, determined the qa-IF end of the 3.8-kb insert. Although sequencing of both plasmids was limited, the established clones were characterized and can be used in future experiments.

Download or read book Genetical and Biochemical Studies on the Inducible Quinic Acid Catalbolic Pathway in Neurospora Crassa written by Howard Wayne Rines and published by . This book was released on 1969 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Genetic and Biochemical Studies on the Inducible Quinic Acid Catabolic Pathway in Neurospora Crassa written by Howard W. Rines and published by . This book was released on 1969 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Investigations Into the Gene Expression of Neurospora Crassa During Mycelial Contact with Fungi of Increasing Phylogenetic Distance written by Christopher Francisco Villalta and published by . This book was released on 2011 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the first chapter, using phylogenetic information about Neurospora, I designed a successful two restriction enzyme digest assay that separated PS 1-3 from the other known Neurospora species and found one new PS1, nine new PS2, and one new PS3. The topography of the phylogenetic tree did not change with the addition of the new PS isolate data and neither did the interspecific mating patterns between Neurospora. As a result of finding new PS isolates and successfully retesting the PSR concept, the PS 1-3 were properly named and described as N. hispaniola, N. metzenbergii, and N. perkinsii. In the second chapter I observed changes in N. crassa gene expression during contact with the mycelia of other Neurospora. I framed the question from a phylogenetic perspective and collected mycelia from N. crassa during a self-self interaction, a intrapopulation interaction, a interpopulation interaction, and a intragenus interaction. After comparing RNAseq profiles of N. crassa interacting with the different fungi I found that the smallest change in gene expression occurred between the self-self interaction and the largest difference occurred in the interpopulation interaction. The intrapopulation and intragenus interactions shared the most in common. There was a large downregulation of metabolism in N. crassa when comparing N. crassa growing alone to N. crassa growing on a plate with another Neurospora, but before contact between mycelia. During contact with the mycelia of the other nonself Neurospora there was an upregulation of genes related to reactive oxygen species metabolism and melanin synthesis in N. crassa. In the interpopulation interaction there was visible production of melanin after mycelial contact between both N. crassa specimens. In interactions between nonself Neurospora there was a downregulation of genes involved in cell signaling and polar cell growth. Two genes, NCU01219 and NCU01074, were significantly upregulated in wild type N. crassa after contact between mycelia. Deletion mutants of both genes displayed reduced aerial mycelia in comparison to wild type N. crassa after contact. NCU01074 is an undescribed bzip transcription factor we found is closely related YAP bzip transcription factor family in S. cerevisiae and NCU01219 is a glutaredoxin. In the third chapter I characterized N. crassa gene expression during growth with a young 24 hour P. chrysogenum colony that did not inhibit mycelial growth and an old 72 hour P. chrysogenum colony that inhibited mycelia growth with the anti fungal protein, PAF. I wanted to find the genes, functional categories, and pathways that were affected by PAF induced growth inhibition in N. crassa and gain better insight into how fungi behave in the wild. I compared expression data of N. crassa interacting with P. chrysogenum to the Neurospora interaction data from Chapter 2. N. crassa interacting with P. chrysogenum had very different expression profiles from the other interactions, but genes related to melanin synthesis were upregulated similar to interactions between nonself Neurospora. A large amount of gene upregulation occurred in N. crassa when grown with the 72 hour old P. chrysogenum colony while the smallest change in gene expression occurred in N. crassa when interacting with the 24 hour old P. chrysogenum colony in comparison to all interactions from Chapter 2 and 3. I found 19 genes that were significantly differentially expressed in N. crassa during PAF induced growth inhibition caused by the 72 hour old P. chrysogenum colony that would be interesting candidates for further study with gene deletion and over expression mutants. The genes were related to the cell wall, cell membrane, cross membrane transporters, Ca2+ dependent signaling, virulence, and transcriptional regulation.

Download or read book Cumulated Index Medicus written by and published by . This book was released on 1991 with total page 1320 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Journal of Cellular Biochemistry written by and published by . This book was released on 1985 with total page 834 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Abstracts 14th Annual Meetings April 6 April 25 1985 written by and published by . This book was released on 1985 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Fungal Genetics Newsletter written by and published by . This book was released on 1989 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Bibliography of Agriculture written by and published by . This book was released on 1988-05 with total page 1450 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Genetics of Circadian Rhythms written by and published by Academic Press. This book was released on 2011-09-16 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: This latest volume in Advances in Genetics covers the genetics of Circadian rhythms. With an international group of authors this volume is the latest offering in this widely praised series.