Theses and Dissertations at Montana State University (MSU)
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Item Understanding resistance and transcriptional responses to potato virus Y infection in potato plants(Montana State University - Bozeman, College of Agriculture, 2021) Ross, Brian Thomas; Chairperson, Graduate Committee: Michelle Flenniken; Nina Zidack and Michelle L. Flenniken were co-authors of the article, 'Extreme resistance to viruses in potato and soybean' in the journal 'Frontiers in plant science' which is contained within this dissertation.; Nina Zidack and Michelle L. Flenniken were co-authors of the article, 'Transcriptional responses to potato virus Y infection in resistant and susceptible potato cultivars' submitted to the journal 'Cultivars' which is contained within this dissertation.The potato is one of the world's most important crops. Cultivation of potatoes occurs on every continent except Antarctica and in a wide variety of climates. Potatoes are susceptible to a multitude of pathogens that can decrease yield and market quality. Viruses are particularly problematic for potato growers, as most potato production involves the replanting of tubers grown the previous year. Because virus-infected potato plants can harbor virus in their tubers, these tubers can in turn be the source of infection in the next generation of plants. Strains of Potato virus Y are the most economically burdensome viruses for potato growers worldwide. In field settings, Potato virus Y is primarily transmitted to plant by aphids feeding on leaves, but PVY can also be transmitted mechanically through infected plant sap. The use of insecticides and the application of mineral oil to leaves can help limit aphid populations and prevent infection to an extent but are generally both less effective and more environmentally impactful than genetic antiviral resistance mechanisms. The incorporation of genes that provide durable resistance to Potato virus Y into commercial potatoes is a major focus of potato breeders. One form of resistance, called extreme resistance, is characterized by a lack of symptoms and little to no virus replication occurring at the site of infection, but the molecular mechanisms of this response are not well understood. A comprehensive analysis of the extreme resistance literature indicates that movement of the resistance protein from the cytoplasm to the nucleus of the cell directly after virus infection may be a key aspect of this immune response. The downstream, transcriptional aspects of the extreme resistance response are also not well understood. We analyzed the gene expression from a Potato virus Y-resistant potato variety, Payette Russet, and a commonly grown susceptible variety, Russet Burbank, at a series of time points after virus infection using RNA sequencing. Results of these analyses indicate that an immune response likely occurs in Payette Russet quickly after virus inoculation. These analyses also indicate that the virus-susceptible variety, Russet Burbank, exhibits changes in gene expression that are similar to other susceptible potato varieties during asymptomatic or tolerant infection. Furthering our understanding of the molecular mechanisms controlling resistance and severity of virus infections will help inform future breeding and genetic engineering efforts, which require detailed knowledge of the mechanisms of virus resistance.Item Allosteric activation of the CRISPR-associated transcription factor Csa 3 by cyclic tetra-adenylate (cA 4)(Montana State University - Bozeman, College of Letters & Science, 2020) Charbonneau, Alexander Anthony; Chairperson, Graduate Committee: C. Martin LawrenceThe CRISPR-Cas immune system provides adaptive and heritable immunity to archaea and bacteria to combat viral infection, and is a source of biochemical tools to researchers. This work combines structural biology and biochemical approaches to provide insight into mechanisms prokaryotes use to control the CRISPR-Cas immune system, linking subsystems into a coordinated response. The first structure of S. solfataricus Csa3 determined by Lintner et al. revealed a dimer with a C-terminal wHTH DNA-binding domain and an N-terminal CARF domain with a putative ligand binding site predicted to bind a two-fold symmetric molecule with both negatively charged and hydrophobic/aromatic moieties, such as dinucleoside polyphosphates or nucleic acid molecules. 1 Later, analysis by Topuzlu et al. of the A. fulgidis Csx3 structure containing a 4 base RNA molecule in a binding pocket revealed similarities between Csx3 and the Csa3 CARF domain, and suggested CARF proteins could bind cyclic or pseudosymmetric linear RNA tetranucleotides represented by the ring-shaped RNA density in the Csx3 binding pocket. 2 Functional studies with S. islandicus Csa3 identified that SiCsa3 regulates transcription of acquisition genes (cas1, cas2, and cas4) and several CRISPR loci. 3,4 Additionally, two groups simultaneously showed that the Type III surveillance complexes produce cyclic oligoadenylate messengers, including cyclic tetra-adenylate (cA 4), which allosterically regulate the RNase activity of Csm6 and Csx1, other CARF proteins. 5,6 These advances support the original predictions by Lintner et al. and suggest that Csa3 binds a cyclic RNA as proposed by Topuzlu et al. Binding of cA 4 likely allosterically causes conformation changes in the wHTH, and regulates the protein's transcriptional regulation. We present the crystal structure of S. solfataricus Csa3 complexed with cyclic tetraadenylate (cA 4). cA 4, as predicted, 1 is bound in the CARF domain 2-fold symmetric pocket, which stimulates conformational changes in the C-terminal domain. Additionally, we identify the presence of a palindromic predicted binding motif upstream of the Type I-A(2) acquisition cassette and CRISPR loci C and D, and reveal through EMSA analysis that Csa3 binds dsDNA nonspecifically with high affinity. Finally, ring nuclease activity is not detected in Csa3, suggesting longer term potentiation of the cA 4 in Csa3 than observed for Csx1/Csm6. 5,6Item Effect of the WRKY76 transcription factor on starch biosynthesis and plant growth(Montana State University - Bozeman, College of Agriculture, 2016) Estabrooks, Hannah Margaret; Chairperson, Graduate Committee: Jack MartinStarch is an important contributor to plant growth as excess photosynthate is stored in leaves as starch during the day to be mobilized at night and re-synthesized in sink tissues. Starch is also the principal constituent of cereal seeds and its variation greatly influence crop yields. The starch pathway is complex and its regulation is not fully understood. Transcription Factors (TFs) are known to act as master regulators of whole biosynthetic pathways and the work presented here was aimed at gaining a better understanding of starch production in leaves by identifying a TF which specifically regulates the leaf starch biosynthetic pathway. Leaf starch levels are regulated in part by ADP-glucose pyrophosphorylase (AGPase), the rate limiting step of starch biosynthesis. Transgenic rice event (NR16+) with increased leaf AGPase activity (due to overexpression of the AGPase large and small subunit transgenes Sh2r6hs and Bt2) was subjected to RNA-sequencing. The results indicated that the leaf specific AGP transgene, which increased leaf starch, also had upregulation of the WRKY76 TF. Another regulatory protein, F-Box, was chosen as a candidate due to the F-box family's involvement in plant development. The current study examines the potential of these gene products for increasing starch biosynthesis in leaves via leaf specific overexpression. Results indicate that overexpression of WRKY76 increases leaf starch an average of 39% at both the one month and anthesis growth stages in comparison to the Varietal Control Nipponbare. WRKY76 transgenic lines have enhanced phenotype with an improved harvest index due to biomass and immature panicles trending down by 4% and 21% respectively, while seed weight trended 12% higher. Events overexpressing WRKY76 were also found to upregulate important starch biosynthetic and carbon metabolism genes including AGPL1, AGPS2, SSIIIb, GBSII, Rbcs, PRK, and GS2 as well as leading to a general upregulation of leaf tissue carbohydrates. Events 1, 2, and 12 additionally had on average 13% increased photosynthetic rate at the one month growth stage. The findings of this study support WRKY76 as a dynamic regulator of the starch biosynthetic pathway conferring more efficient carbon assimilation leading to an increased harvest index.Item Mathematical modeling for transcription of DNA with pausing : stochastic model with torque, and diffusive transport model(Montana State University - Bozeman, College of Letters & Science, 2016) Heberling, Tamra Lindsey; Chairperson, Graduate Committee: Lisa DavisIn fast-transcribing prokaryotic genes, like an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases. In an effort to further understand transcription, we investigate the Brownian ratchet model for nucleotide translocation. We model elongation as diffusive particle transport in a tilted periodic potential. To incorporate the RNAP pauses, a second periodic potential is added to the first. We present a formula for the mean escape time from a tilted, periodic potential composed of multiple periodic functions as the product of the mean escape time from each individual periodic function. This formula is extended to an arbitrary finite number of periodic functions. Two examples using truncated Fourier series are presented and analyzed.Item Discontinuous Galerkin finite element method for simulation of a transcription process model(Montana State University - Bozeman, College of Letters & Science, 2013) Thorenson, Jennifer Rae; Chairperson, Graduate Committee: Lisa DavisThe classical traffic flow PDE from the 1950s is used to model the biological process of transcription; the process of transferring genetic information from DNA to mRNA, in an E. coli gene. Polymerase elongating along the DNA strand encounter frequent but short pauses which are incorporated into the transcription model as several traffic lights. These pauses result in a delay in the transcription time and a delay function is defined to quantify this effect. Numerical simulations of the PDE model are conducted using a discontinuous Galerkin finite element method (DG) formulation. The entropy satisfying weak solution of the PDE model with a single pause is derived using the method of characteristics. This weak solution is used to show convergence of the DG formulation even though the flux function is not smooth. Once convergence of the DG solution is established for one pause, the numerical simulation for multiple pauses is used to calculate the delay due to the pauses and determine their effect on the overall transcription time. Preliminary parameter studies show a complex relationship between pause location and delay values. To determine the effect of pause clustering on protein production, an ongoing research goal is optimization of the delay function with respect to pause location. For preliminary work on this optimization problem, a DG formulation used to solve a sensitivity equation for a linear hyperbolic PDE with a spatial interface parameter is derived to gain insight for the more complicated nonlinear traffic flow PDE.Item Identification and characterization of novel protein-protein interactions with the basal transcription factor, TATA-binding protein(Montana State University - Bozeman, College of Agriculture, 2006) Prigge, Justin Robert; Chairperson, Graduate Committee: Ed Schmidt.Recruitment of the TATA-Binding Protein, TBP, to the promoter is a critical, rate-limiting step that drives the initial phase of nearly all gene transcription events. Because of this, many transcriptional regulators target TBP, either to localize TBP at the promoter, or to relay signals between other promoter-bound protein complexes and the basal transcription machinery. Studies described herein were designed to identify novel protein-protein interactions with TBP. To do this, we screened mid-gestational pregnancy-associated cDNA prey libraries using two different yeast two-hybrid systems. Screens in both systems revealed both known and novel TBP interactors. B'-Related Factor 1 and Transcription Factor II A were identified in screens that used full-length TBP as bait. These proteins are known to interact with TBP and thus validated our system. In addition to known interactors, novel interactions with both the N-terminal (TBP-N) and C-terminal (TBP-C) domains of TBP were identified. Coactivator- Associated Arginine Methyltransferase 1 (CARM1), Pax Transactivation Domain- Interacting Protein (PTIP), and Lipopolysaccharide-Induced Tumor Necrosis Factor Alpha Factor (LITAF) all interacted with TBP-N. Proteins that interacted with TBP-C were Huntingtin-Associated Protein 1 (HAP1), four members of the Protein Inhibitor of Activated STAT (PIAS) family of transcriptional regulatory proteins, and Zinc Finger Protein 523 (ZFP523). The TBP interaction domains on PIAS1 and HAP1 were mapped to further define each interaction. Mapping studies revealed that TBP interacts with a single region on PIAS1, and with two separate regions on HAP1. We also show that TBP co-precipitates with PIAS1, PIAS3, HAP1, and PTIP. In conclusion, our studies, in agreement with previous published data suggest that TBP interacts with many classes of regulatory proteins, including transcriptional activators, repressors, and individual components of the transcriptional co-regulatory complexes. They also support the hypothesis that the TBP N-terminus is a protein interaction module and may provide clues to the function of the vertebrate-specific N terminus of TBP.Item Loss of the murine TATA-binding protein N terminus leads to placental labyrinth defects but not maternal adaptive immune responses(Montana State University - Bozeman, College of Agriculture, 2007) Sealey, Amy Lynn; Chairperson, Graduate Committee: Edward E. Schmidt.The TATA-binding protein (TBP) is a component of the basal transcription machinery. The TBP C-terminal core is conserved in all eukaryotes, but the N terminal region is shared between vertebrates. To study this, we generated a mouse line lacking 111 of the 135 amino acids of the vertebrate-specific sequence. The mutant tbp allele was designated tbp?N, and the majority of homozygous mutants, tbp?N/?N, died at midgestation due to defects in the placenta. Previous studies in our laboratory showed that tbp?N/?N fetuses survived the midgestational crisis if the mother was severely immunocompromised or if mutant fetuses were supplied tbp+/+ placentas. From these data, we hypothesized that the TBP N terminus regulates placental activity that is required for tolerizing the maternal immune system to the conceptus. Recent histological analysis of embryonic day 8.5 (E8.5) to E12.5 placentas in immune wildtype mothers revealed that the tbp?N/?N placental vascular region, or labyrinth, does not develop.Item Molecular and systemic functions of the vertebrate-specific TATA-binding protein N terminus(Montana State University - Bozeman, College of Agriculture, 2009) Lucas, Olivier; Chairperson, Graduate Committee: Edward E. Schmidt; Michael W. White (co-chair)The invertebrate/vertebrate transition and associated innovations can be regarded as a major event in evolution. Recent molecular progresses invite to an analysis of the events leading to the apparition of vertebrates and the underlying embellishment in gene regulation. In eukaryotes, the TATA-Binding Protein (TBP) has a central role in transcription initiation of most genes. TBP is comprised of a highly conserved DNA binding domain and, in vertebrates, it also contains a novel region: the N-terminal TBP protein coding sequence. The role of the TBP-N is largely unknown, but previous studies suggest that it is important for fetal survival. Most animals lacking the TBP-N (tbp Delta N/Delta N) die before weaning. The goal of the present work was to establish a deeper knowledge of the vertebrate-specific TBP-N. It was hypothesized that TBP-N could be involved in protein-protein interactions and that the high degree of similarity of TBP-N protein sequences in different species could correlate with similar functions. To test those hypotheses, two independent approaches were taken: (1) Protein-protein interactions involving the TBP-N via unbiased screens were characterized. (2) The mouse TBP-N was replaced by a similar and homologous TBP-N, in vivo, through homologous recombination. The TBP-N-replacement mutation was characterized through pathway analyses, bioinformatics, and whole-animal physiology. Screens for proteins interacting with the TBP-N of hagfish (hf), a basal vertebrate, uncovered hfPitxA. The Pitx family of transcription factors are proteins important in vertebrate development. The mouse paralogs of hfPitxA, Pitx1 and Pitx2, were found to interact with the mouse TBP-N. Moreover, the interaction appeared functional as it regulated the expression of nppa, a known target gene of Pitx2. In vivo replacement of the mouse TBP-N with the similar hfTBP-N did not affect the survival. Gene expression analysis indicated that lipid metabolism pathways were affected in animals lacking the TBP-N or when the hfTBP-N was present. Further analyses pointed toward a potential defect in insulin response and an abnormal hepatic fat storage. The data presented here argues in favor of an important role for TBP-N in vertebrate-specific gene regulation. More specifically, it is likely involved in heart development and in regulation of lipid metabolism.Item Mid-and late-gestation lethality in mice lacking the N terminus of TATA-binding protein(Montana State University - Bozeman, College of Agriculture, 2004) Hobbs, Nicole Kay; Chairperson, Graduate Committee: Edward E. Schmidt.TATA-binding protein (TBP) is a transcription factor comprised of a 180 amino acid core that is shared by all eukaryotes. TBP also has an N-terminal region that, in vertebrates, is highly conserved. We have generated mice bearing a mutant tbp allele, tbp deltaN, that lacks 111 of the 135 amino acids of the vertebrate-specific N terminus. Most homozygous mutants, tbp deltaN/deltaN, die at midgestation from an apparent defect in their placentas. tbp deltaN/deltaN fetuses were rescued at this midgestational crisis if supplied with a wild-type tetraploid placenta. tbp deltaN/deltaN fetuses also survived in immune-normal mothers when fetal/placental beta 2m expression was genetically disrupted. When reared in immunocompromised mothers, tbp deltaN/deltaN fetuses also survived midgestation. These results suggest the N terminus of TBP functions in beta 2M-dependent processes and within the placenta to favor immunotolerance during pregnancy at midgestion. Beyond midgestation, tbp deltaN/deltaN fetuses that survive in immunocompromised mothers were found to be runted at the perinatal period and died shortly after birth. These latter results suggest that the N terminus of TBP also functions in non-immune processes required for normal birth weight and successful pregnancy.