BACKGROUND:The opaque2 mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary.RESULTS:In this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered by opaque2 in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content of opaque2 endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly by opaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch.CONCLUSIONS:The results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of the opaque2 mutation. Alteration of amylopectin branching patterns in opaque2 starch could contribute to generation of the soft, starchy endosperm.

Starch is an important component of a wheat grain, comprising 50-70% of its dry weight. Its biosynthesis involves a complex pathway mediated by several enzymes, each of which is encoded by genes that have more than one family member. To better understand starch synthesis in wheat grains, this study characterized the sucrose-starch metabolic pathway using physiological, molecular, biochemical and metabolic approaches. These analyses led to the identification of genes that appear to have predominant expression during grain development in wheat including, TaSUT1, TaSuSy2, AGPL1, SSI, SSIIIa and SBEIIa, suggesting that these genes play a regulatory role in starch accumulation. This was further confirmed by comparative analyses of starch synthesis between cultivars with contrasting thousand kernel weights, which revealed a closer association of the expression of the same set of genes with starch accumulation in developing wheat grains. The effect on starch yield of one of the candidate genes identified, AGPase, was examined through a transgenic approach, which involved expression of a gene encoding modified version of maize AGPase large subunit, designated as Sh2r6hs, in wheat under the control of maize’s constitutive Ubiquitin1 promoter. This manipulation of the wheat AGPase activity produced wheat lines with increased AGPase activity, grain weight and grain starch level, suggesting that the wheat grain size can be enhanced through increasing the capacity of starch synthesis both in the source and sink tissues. The study also identified and characterized a partial fragment of wheat rbcS promoter, and indicated that the promoter fragment can potentially be used as a tool for targeting the expression of genes of interest in photosynthetic source tissues. / October 2014

Storage starch is synthesized in sub-cellular organelles called amyloplasts in higher plants. The synthesis of the starch granule is a result of the coordinated activity of several groups of starch biosynthetic enzymes. There are four major groups of these enzymes, ADP-glucose pyrophosphorylase (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDE). Starch phosphorylase (SP) exists as both dimeric and tetrameric forms in plastids in developing cereal endosperm and catalyses the reversible transfer of glucosyl units from glucose-1-phosphate to the non-reducing end of α-1-4 linked glucan chains, although the precise role in the pathway remains unclear. The present study was conducted to investigate the role and regulation of SP and SSIV in starch biosynthesis in developing maize endosperm. The results of this study showed that the tetrameric form of SP accounts for the majority of measurable catalytic activity, with the dimeric form being barely active and the monomer catalytically inactive. A catalytically active recombinant maize SP was heterologously expressed and used as an affinity ligand with amyloplast lysates to test protein-protein interactions in vitro. Results showed that the different multimeric status of SP influenced interactions with other enzymes of starch synthesis. Tetrameric SP interacted with SBEI and SSIIa, whilst the dimeric form of the enzyme interacted with SBEI, SBEIIb. All of these interactions were enhanced when amyloplasts were pre-treated with ATP, and broken following treatment with alkaline phosphatase (APase), indicating these interactions are regulated by protein phosphorylation. In addition, the catalytic activity of SSIV was reduced following treatment with APase, indicating a role for protein phosphorylation in the regulation of SSIV activity. Protein-protein interaction experiments also suggested a weak interaction between SSIV and SP. Multimeric forms of SP regulated by protein-protein interactions and protein phosphorylation suggested a role for SP in starch biosynthesis in maize endosperm.

BACKGROUND:Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy.RESULTS:A de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated.CONCLUSIONS:The construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome sequence for the Showa strain of B. braunii, race B. Further, the transcriptome database empowers future biosynthetic engineering approaches for strain improvement and the transfer of desirable traits to heterologous hosts.

Le grain de maïs est composé de 3 compartiments : l’embryon et l’albumen issus de la double fécondation et l’enveloppe d’origine maternelle. Le développement du grain et l’accumulation de réserves demande l’établissement d’une communication étroite entre l’embryon et l’albumen pour coordonner leur développement respectif. Si, des régulateurs majeurs impliqués dans le développement de la graine d’Arabidopsis ont été décrits, ces connaissances restent parcellaires chez les céréales. Les objectifs de ma thèse consistaient d’une part à étudier le contrôle de la communication entre l’embryon et l’albumen et d’autre part la régulation du remplissage du grain de maïs. Par l’analyse de lignées transgéniques sous exprimant ZmZHOUPI (ZmZOU-RNAi), nous avons établi que ce facteur de transcription à domaine bHLH, bien que s’exprimant exclusivement dans l’albumen, affecte significativement le développement de l’embryon (taille de l’embryon, persistance du suspenseur). L’analyse de données RNAseq (grains sauvages versus grains ZmZOU-RNAi) a permis d’identifier des gènes cibles potentiels de ZmZOU. De plus, nous avons montré que 3 facteurs de transcription de type bHLH homologues d’INDUCER OF CBP EXPRESSION (ICE) forment un partenariat avec ZmZOU.D’autre part, nous avons étudié les homologues d'ABA INSENSITIVE3, FUSCA3 et LEAFY COTYLEDON2 (AFL) qui forment un réseau de facteurs de transcription, à domaine B3, régulant l’accumulation d’huile et de protéines de réserves dans l’embryon d’Arabidopsis. Grâce à des analyses phylogénétiques et d’expression, nous avons établi que chez le maïs le réseau AFL, constitué de 5 membres (ZmAFLs), est partiellement conservé. Par dosages et analyse d’expression, nous avons montré que ZmAFL4, en particulier, est impliqué dans le contrôle de la biosynthèse de l’amidon dans l’albumen. / Maize kernel is composed of three major compartments: an embryo and an endosperm both produced by double fertilization and the maternally derived seed coat. Seed development and reserves accumulation demands coordination and thus communication between embryo and endosperm allowing specific growth of each compartment. While major regulators involved in seed development have been already described in Arabidopsis, knowledge in cereals remains limited. My thesis purposes were to study on one hand the control of communication between embryo and endosperm and on the other hand regulation of maize kernel filling.By analysis of transgenic lines knock down ZmZHOUPI (ZmZou-RNAi), we showed that this bHLH domain transcription factor, exclusively expressed in endosperm, affect significantly embryo development, size of embryo proper and suspensor persistence. RNAseq data analyses let find putative direct targets of ZmZOU. Additionally, we identified ZmZOU partners, 3 bHLH domain transcription factor homologs of INDUCER OF CBP EXPRESSION (ICE).Furthermore, we studied homologs of three B3 domain transcription factors named ABA INSENSITIVE3, FUSCA3 et LEAFY COTYLEDON2 (AFL) which form a regulatory network governing oil and seed storage proteins accumulation in Arabidopsis embryo. By phylogenetic and expression analysis, we established that 5 genes (ZmAFLs) constitute in maize a partially conserved AFL network. Through dosage and expression analysis, we established that particularly ZmAFL4 is involved in starch biosynthesis regulation.