The mechanism by which plants synthesize and store high amounts of triacylglycerols (TAG) in tissues other than seeds is not well understood. The comprehension of controls for carbon partitioning and oil accumulation in nonseed tissues is essential to generate oil-rich biomass in perennial bioenergy crops. Persea americana (avocado), a basal angiosperm with unique features that are ancestral to most flowering plants, stores ~ 70 % TAG per dry weight in its mesocarp, a nonseed tissue. Transcriptome analyses of select pathways, from generation of pyruvate and leading up to TAG accumulation, in mesocarp tissues of avocado was conducted and compared with that of oil-rich monocot (oil palm) and dicot (rapeseed and castor) tissues to identify tissue- and species-specific regulation and biosynthesis of TAG in plants.

<p>Iron is an essential micronutrient for plant growth, development and productivity. Although it is abundant in soil, the bio-availability of iron is often low for plants in many areas of the world. The insufficient quantity of usable iron in plants causes reduction in chlorophyll synthesis, reduced photosynthesis rate and decreased growth and yield. Two major strategies, Strategy I and II, have been discovered to be involved in response to low iron and a complex network of biochemical and molecular pathways participate in the processes. </p> <p> </p> <p>Cellular transcriptional regulation is associated with iron deficiency responses. Multiple genes and pathways involved in iron-deficiency responses have been identified in plants in the past decade. Here, we measured different physiological parameters and used RNA-Seq to elucidate the physiological and molecular responses in early stage of iron deficiency in the whole leaf of model plant species Arabidopsis thaliana. In this study, Arabidopsis showed reduced chlorophyll content, increased ferric reductase activity and reduced antioxidant enzyme activities when stressed by iron deficiency. In addition, we have identified multiple pathways that may play promising roles in the response to iron deficiency, e.g., 1) we found that the auxin biosynthesis under iron deficiency is preferentially depended on the TAA-YUC pathway rather than the CYP79 pathways; 2) TCA cycle is involved in mediating the acclimation process to the stress condition; 3) glucosinolate synthesis could be a limiting factor for iron deficiency response due to its negative relationship with hormone and energy metabolism.</p> <p> </p> Systemic signals generated from leaves are critical for triggering iron deficiency responses in roots. Due to the physiological characteristic and cellular ultrastructure of companion cells (CCs), we hypothesize that the CCs located in phloem play essential roles in regulating systemic nutrient signaling. In this study, by using a cell-specific TRAP-Seq, we discovered that not only CCs respond more drastically than the other cells in leaf, the altered molecular pathways in the CCs are also more diverse during early iron deficiency response. In particular, we found that auxin and sucrose transport and metabolism in the CCs may be two of the key regulatory processes that plants use to exert the shoot-to-root signaling process. Our discoveries have collectively suggested that CCs may function as the central machinery in the systemic signaling in response to iron deficiency. A comparison between whole leaf transcriptome and translatome also suggested that translatomic analysis is a more sensitive method for gene profiling than conventional transcriptomic analysis.

No description available.

No description available.

No description available.

Small RNAs (sRNAs), circa 21-26nt RNA molecules, are a novel class of regulatory molecules that influence many aspects of plant biology. The first objective of this thesis was to utilize computational approaches both to investigate how microRNAs (miRNAs), a type of sRNA, as a class affect their target transcripts’ accumulation and to identify novel miRNAs in Arabidopsis thaliana. The second objective of this thesis was to examine the regulation of protein coding (PC) cis natural antisense transcripts (cis-NATs), which have the potential to make double stranded RNA. Computational analysis of the expression of miRNA-regulated genes demonstrated that the transcriptomes of the inflorescences of plants defective in miRNA biogenesis were similar to normal leaf tissues and dissimilar to normal pollen and seed. Thus, miRNAs cause the plant transcriptome to shift from a vegetative to reproductive state. Known miRNA targets fail to explain miRNA-defective mutant transcriptome patterns. Novel computational approaches were used to discover five new mature miRNAs. Interestingly, two miRNAs have different functions but are encoded by perfect complements of the same precursor molecule. Genome-wide analysis of cis-NAT abundances revealed that protein coding (PC) cis-NATs tend to be co-expressed, broadly expressed, and highly expressed across diverse abiotic stress conditions. These expression patterns were negatively associated with sRNAs because sRNAs were under-represented within PC cis-NATs compared to PC non-cis-NATs. sRNAs also mapped to cis-NATs and non-cis-NATs at similar frequencies in mutants defective in nat-siRNA biogenesis relative to other genotypes. We suggest a common euchromatin environment and possibly antisense RNA stabilization of mRNA transcripts may contribute to the high level, breadth, and co-expression of cis-NATs. However, cis-NATs are correlated less frequently than expected, and cis-NAT transcript abundances often differ more than expected. In addition, sRNAs matched PC cis-NATs relative to PC non-cis-NATs more frequently in abiotic stress conditions than in control conditions. Thus, although sRNAs do not have a widespread role in regulating cis-NATs, sRNAs may have a focused role in regulating cis-NAT transcript abundances. / PhD thesis / NSERC

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第21875号 / 人博第904号 / 新制||人||215(附属図書館) / 2018||人博||904(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 加藤 眞, 教授 市岡 孝朗, 准教授 西川 完途 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22281号 / 理博第4595号 / 新制||理||1659(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 沼田 英治, 准教授 森 哲, 教授 曽田 貞滋 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Polyamines play an important role in DNA, RNA and protein synthesis as well as a variety of other biological processes (cell division, differentiation and death) as outlined in Chapter 1. Assaraf and co-workers (1984) demonstrated that treatment with DFMO resulted in the inhibition of polyamine biosynthesis as well as schizogony arrest in P. falciparum. However, they did not elaborate on any other consequences that polyamine depletion could exert on the parasite. This dissertation aims to elucidate the significance of the inhibition of polyamine biosynthesis within P. falciparum by using differential transcriptome profiling. Suppression subtractive hybridisation generated transcripts which were potentially up-and down-regulated due to endogenous polyamine depletion within the human malaria parasite P. falciparum. The resulting transcripts were subjected to a restriction enzyme analysis and those with unique digestion profiles were selected and sequenced. The sequences were analysed using PlasmoDB to identify the genomic sequences to which they were best matched. To confirm that the selected transcripts were indeed differentially expressed a reverse virtual Northern dot blot was performed. Transcripts for proteins involved in protein processing, methionine and polyamine metabolism, various transporters, proteins involved in cellular differentiation and signal transduction were found to be upregulated in the absences of polyamines. This could be suggestive of a metabolic response induced by the parasite in order to overcome this deficiency. Polyamines seem to influence protein synthesis and haemoglobin degradation as well since depletion of endogenous polyamines within the parasite seems to result in increased food vacuole acidification, haemoglobin degradation, transport of proteins to the cytoplasm and protein synthesis and stabilisation. The majority of downregulated transcripts were found to be involved in cell-cell adhesion and erythrocyte invasion, protein processing and transport indicating that these processes are dependent on polyamines. Further validation of these findings by microarray as well as proteomic analysis will need to be undertaken. These results validate that polyamines do play an essential role in the cellular biology of the parasite. They also confirm that the inhibition of polyamine biosynthesis is a viable route to undertake in the search for new and improved antimalarial targets. This would be especially useful if it was combined with other antimalarials and their synergistic effects were investigated by transcriptomic, proteomic and bioinformatic analysis / Dissertation (MSc (Biochemistry))--University of Pretoria, 2007. / Biochemistry / MSc / unrestricted

No description available.