This study provides information to support the use of plant cell wall, from sugarcane bagasse, to produce cellulosic ethanol. Therewith, cell wall proteins from sugarcane cells cultures, leaves and culms were identified. To do so, different protocols were used. Using two-month-old leaves and culms, the extractions were performed using a destructive method, based on griding the tissues, submitting them to a growing gradient of succrose and centrifugation, being the cell wall extract later isolated by washing on a nylon net. After that, the cell wall proteins were extracted using two salts, 0,2 M CaCl2 and 2 M LiCl. Using cultured cells, a similar protocol was used, but it had a previous step of separation of the cell wall through grinding and precipitation in glycerol 15%. Using culms of the same age, a nondestructive protocol was tested based on vacuum infiltration of the tissues in the same salts already described, 0,2 M CaCl2 and 2 M LiCl, and posterior centrifugation. Two replicates were used from two-month-old plants and three in the case of suspension cells. The complex samples were digested, fractionated and sequenced through mass spectrometry, using SYNAPT G2HDMS coupled to nanoACQUITY, both from Waters. Peptides were processed using ProteinLynx 2.5 Global Server against sugarcane translated-EST database. Using bioinformatic programs, such as Blast2GO, it was possible to find the annotation and classification of similar proteins. Only proteins equally found in all repetitions were considered in the main analysis. SignalP, WolfPSORT, TargetP, TMHMM and Predotar were used to predict the subcellular location, both from ESTs and blasted proteins, and only the proteins predicted to be secreted in two or more programs were considered as cell wall proteins. Altogether, 157 different SAS related to sugarcane cell wall were found. Among these, 101 different cell wall proteins were characterized from eight functional classes. The method based on vacuum infiltration seems to be the most efficient one, since it had almost half, 48,84% of the proteins predicted to be secreted, which is a good percentage when comparing to other studies. From secreted proteins most of them were related to lipid metabolism, as lipid-transfer proteins, oxido-reductases, such as peroxidases, cell wall modifying enzymes, like glycoside-hydrolases, proteases, proteins with interacting domains, signaling proteins and several others. Results are in agreement with the expected role of the extracellular matrix in polysaccharide metabolism and signaling phenomena. Therefore, this work provided valuable information about sugarcane cell wall that can lead to future studies to enhance cellulosic ethanol production. / Este estudo fornece informação para auxiliar o uso da parede celular vegetal, a partir do bagaço de cana, para a produção de etanol celulósico. Com isso, as proteínas da parede celular de folhas, colmos e células em suspensão foram identificadas. Para isso, foram utilizados diferentes protocolos. Utilizando folhas e colmos de cana-de-açúcar de dois meses de idade, as extracções foram realizadas por meio de método destrutivo, com base na trituração dos tecidos, submetendo-os a gradiente crescente de sacarose e centrifugação, sendo a parede da célula extraída e depois isolada por lavagem sobre uma rede de nylon. Depois disso, as proteínas de parede celular foram extraídas utilizando dois sais, 0,2 M de CaCl2 e 2 M de LiCl. Para células em suspensão, um protocolo semelhante foi utilizado, contendo, no entanto, um passo anterior de separação da parede celular por meio de maceração e precipitação em glicerol 15%. Usando colmos da mesma idade, dois meses, um protocolo não destrutivo foi testado com base na infiltração a vácuo dos tecidos nos mesmos sais já descritos, 0,2 M de CaCl2 e 2 M de LiCl, e posterior centrifugação. Duas repetições foram usadas nos experimentos com plantas de dois meses de idade, e três, no caso de células em suspensão. As amostras complexas foram digeridas, fracionadas e seqüenciadas por espectrometria de massas, utilizando o equipamento SYNAPT G2HDMS acoplado ao cromatógrafo nanoACQUITY, ambos da Waters. Os peptídeos foram processadas utilizando ProteinLynx 2,5 comparando com a base de dados de ESTs traduzidos da cana. Utilizando programas de bioinformática, como Blast2GO, foi possível encontrar a anotação e classificação de proteínas semelhantes. Apenas proteínas igualmente encontradas em todas as repetições foram consideradas na análise principal. SignalP, WolfPSORT, TargetP, TMHMM e Predotar foram softwares utilizados para prever a localização subcelular, tanto para ESTs como proteínas, e apenas as proteínas preditas para serem secretadas por dois ou mais programas foram consideradas como proteínas de parede celular. Ao todo, 157 SAS diferentes relacionados à parede celular da cana foram encontrados. Dentre eles, 101 diferentes proteínas de parede foram caracterizadas em oito classes funcionais. O método baseado na infiltração a vácuo mostrou-se o mais eficiente, uma vez que apresentou quase metade, 48,84%, das proteínas preditas para serem secretadas, o que é um bom valor quando comparado com outros estudos. A maioria das proteínas secretadas estava relacionada com o metabolismo lipídico, como proteínas de transporte de lípidos, oxido-redutases, tais como peroxidases, enzimas modificadoras da parede, como as glicosil-hidrolases, proteases, proteínas com domínios de interação, proteínas sinalizadoras, entre outras. Os resultados estão de acordo com o papel que se espera da matriz extracelular no metabolismo de polissacarídeos e fenômenos de sinalização. Portanto, este trabalho forneceu informações valiosas sobre a parede celular da cana, tornando possível a utilização desses dados em futuros estudos para otimizar a produção de etanol celulósico.

La paroi végétale assure des fonctions biologiques majeures définissant la singularité des plantes ; elle est également à l'origine de multiples applications en tant que ressource agro-alimentaire, source de biomatériaux ou encore pour la production de biocarburants. Malgré cette importance fondamentale et pratique de la paroi végétale, la connaissance de sa biosynthèse apparaît à ce jour toujours très limitée. En effet, la faible abondance des glycosyltransférases (GTs) responsables de sa biosynthèse, l'absence de substrat spécifique et les difficultés à obtenir certains nucléotides-sucres nécessaires aux tests enzymatiques, a souvent rendu difficile les approches de biochimie classiques. Cependant, le séquençage de génomes (Arabidopsis thaliana, Oryza sativa, Poplar populus), la création de banques de mutants d'insertion et la classification des activités glycosyltransférases dans la base de données CAZy (www.cazy.org) sont autant d'outils récents ayant permis des avancées significatives vers la compréhension de la biosynthèse de la paroi des végétaux. Le CERMAV a participé à ce type d'avancée en 2009, en publiant une liste de 24 gènes candidats, nommés « NGT » pour « Nouvelles GlycosylTransférases », présentant des signatures caractéristiques des glycosyltransférases. Afin de démontrer l'implication des gènes NGT dans les processus d'édification de la paroi végétale, nous avons développé une approche de génomique fonctionnelle, analysant en parallèle des lignées mutantes d'Arabidopsis altérées pour les gènes NGT et testant l'activité GT de ces protéines exprimées en systèmes hétérologues. Durant mes travaux de thèse j'ai pu caractériser 15 lignées mutantes à l'état homozygote pour 7 des 24 gènes NGT. Ces lignées homozygotes ont été criblées afin de rechercher un phénotype d'altération du développement ou de la composition en sucres de leur paroi qui soit corrélé à l'altération des gènes NGT. Ce travail de criblage a conduit à s'intéresser plus particulièrement aux mutants ngt1-1 et ngt1-2 altérés pour le gène NGT1 (At5g28910). La caractérisation des lignées mutantes ngt1-1 et ngt1-2 a permis de quantifier un phénotype de croissance foliaire réduit de 38%, par comparaison au développement des feuilles de la plante sauvage. Par ailleurs, la caractérisation biochimique de la paroi des mutants a révélé des réductions significatives et quantitatives de l'arabinose, du galactose et du rhamnose dans la paroi des mutants, ainsi que des modifications qualitatives marquées principalement des arabinanes. L'altération des arabinanes a d'ailleurs pu être confirmée par microscopie après immuno-marquage de sections d'hypocotyle de mutants à l'aide des anticorps monoclonaux LM6 et LM13 dirigés contre des épitopes α-1,5-arabinanes. Il a pu être montré également que la complémentation des mutants par une construction 35S::NGT1 permet de restaurer un phénotype sauvage à ces mutants. Par ailleurs, de façon à tester l'activité glycosyltransférase de la protéine NGT1, nous avons réalisé son expression en système hétérologue. A ce jour, malgré des résultats préliminaires encourageants, il n'a pas été possible de déterminer des conditions de tests permettant d'observer une activité glycosyltransférase suffisante et reproductible pour la protéine NGT1, que ce soit une activité fucosyltransférase (correspondant à la signature de la séquence du gène) ou bien une activité arabinosyltransférase (correspondant au phénotype biochimique des mutants ngt1). / The plant cell wall not only defines the unique biology of the plants but also have practical applications as feedstock for biomaterials and for the production of biofuels. Plant primary cell wall is mainly composed of cellulose, hemicelluloses and pectins. Significant progress has been made recently in identifying the enzymes involved in plant cell wall biosynthesis, but only a handful of those have been involved in pectin biosynthesis. With the aim of identifying new putative glycosyltransferases (GTs), in lab Hansen et al 2009 designed a bioinformatic strategy and identified a new group of 24 genes called “NGT” for (Novel Glycosyltransferase) which were considered “strong” candidates for putative glycosyltransferase activities. In order to determine the putative role of these NGT genes in plant cell wall biosynthesis, we designed a functional genomics strategy, analysing in parallel Arabidopsis T-DNA mutant lines and performing heterologous expression of candidate genes. I have characterized 15 homozygous mutant lines among the group of 24 putative NGT genes through PCR. We analysed the homozygous mutants for phenotypic alteration such as dwarfing or organ malformation and found that some of mutant lines have narrow leaves as compared to Wild type plants. In parallel I have carried out the cell wall chemical analysis of 12 homozygous mutant lines and did not get any strong difference in neutral monosaccharide composition. The detailed and complete analysis (chemical, expression and microscopic analysis) of all the above mentioned genes could have been time consuming and an overwhelming work, so I focused on At5g28910 (named NGT1) which harbours a fucosyltransferase peptide signature and on At5g14550 (named P), a gene belonging to the DUF266 gene family. Homozygous T-DNA mutant lines ngt1-1 and ngt1-2 lines were analyzed and showed a reduced growth phenotype (leaf area). Leaf area was quantified at various development stages using ImageJ, and showed a 38% reduction in mutants. Additionally, biochemical characterization of the cell wall was performed showing a reduction in neutral monosaccharide contents, like arabinose, rhamnose and galactose in mutant cell wall. Furthermore glycosyl linkage analysis of mutant lines ngt1-1 and ngt1-2 has shown that 5-Arabinofuranose (5-Araf) and 3,5-Arabinofuranose (3,5-Araf ) contents were decreased as compared to Wild type Col0 cell wall. These results were also confirmed by immunolabeling of stem cross section of mutant and wild type plants. The complementation of the mutant plants through Agrobacterium transformation resulted in the complete restoration of plant phenotype. Taken together, these data suggest that NGT1 could be an arabinosyltransferase. In order to characterize its biochemical activity, the NGT1 protein was heterologously expressed in Pichia pastoris. The recombinant protein was used to perform in vitro activity tests, but we were unable to demonstrate any neither fucosyltransferase (on the basis of peptide signature) nor arabinosyltransferase activity. In parallel to this study, I contributed to the heterologous expression and characterization of two biochemically characterized Arabidopsis GTs involved in xyloglucan synthesis: the fucosyltransferase (AtFUT1) and xylosyltransferase (AtXT1). I have successfully expressed a truncated and active form of AtFUT1, which represents an essential step for further structural studies that will be undertaken in the lab.

No description available.

The same fundamental questions that have driven enquiry into cytoskeletal mechanics can be asked of the considerably less-studied, yet arguably just as important, biopolymer matrix in the plant cell wall. In this case, it is well-known that polysaccharides, rather than filamentous and tubular protein assemblies, play a major role in satisfying the mechanical requirements of a successful cell wall, but developing a clear structure–function understanding has been exacerbated by the familiar issue of biological complexity. Herein, in the spirit of the mesoscopic approaches that have proved so illuminating in the study of cytoskeletal networks, the linear microrheological and strain-stiffening responses of biopolymeric networks reconstituted from pectin, a crucial cell wall polysaccharide, are examined. These are found to be well-captured by the glassy worm-like chain (GWLC) model of self-assembled semi-flexible filaments. Strikingly, the nonlinear mechanical response of these pectin networks is found

A thesis submitted to the School of Graduate Studies in partial fulfilment of the requirements of the Master of Applied Science degree / This thesis investigated structure-function relationships of materials designed to mimic the plant cell wall by comparing their mechanical properties measured using strain-induced buckling methods. The plant cell wall mimics are submicrometer-thick films composed of cellulose nanocrystals (CNCs) and various types of xyloglucan (XG), a common plant hemicellulose. Our goal was to establish links between film composition/architecture and elastic modulus, to better understand the interactions between plant cell wall components and their influence on mechanical properties. Three buckling methods for measuring mechanical properties of supported films were compared. All methods involved compressing a thin film deposited onto a shape memory polymer or an elastomeric substrate, through thermal shrinking or mechanical compression, respectively. Two thermal shrinking methods (constrained in one axis or unconstrained) and one compression method (using a mechanical strain stage) were used. Based on the mismatch of mechanical properties between the film and the substrate, the rigid thin film “buckles” upon compression to dissipate strain. The resulting surface wrinkle sizes are characteristic of the mechanical properties of the thin film. A Fourier analysis algorithm with Gaussian curve fitting was optimized to extract wrinkle sizes accurately and reproducibly from microscopy images to reliably quantify the elastic moduli of thin films. To select the most precise strain-induced buckling method, model layer-by-layer (LbL) thin films composed of CNCs and polyethylene imine were tested. All three buckling methods precisely quantified the elastic moduli of the films and helped us build connections between the mechanical properties and the film composition. Elastic moduli determined were 15-44 GPa (depending on composition) and films up to 350 nm-thick were tested. Based on sensitivity analyses, however, unconstrained thermal shrinking proved to be the most robust method for calculating the elastic modulus. We believe these buckling methods may find widespread use in the characterization and surface structuring of thin films for applications in biosensors, flexible electronics, point-of-care diagnostics, and for studying plant cell wall mimics. Using the unconstrained thermal shrinking method, plant cell wall mimics were constructed using LbL thin film assembly with various concentrations of CNCs and XG. Three types of XG were compared: (1) unmodified XG, (2) XG with a fraction of the galactosyl residues removed (degalactosylated), and (3) a fragmented lower molecular weight XG. It was inferred that molecular weight impacts the stiffness of XG-CNC based on adsorption conformation of XG onto CNCs, where lower molecular weight XG results in a higher modulus film (27 ± 1 vs. 19 ± 2 GPa). As well, saccharide residues of XG, specifically galactosyl, impact XG’s capacity for self-association and interaction with CNCs, because saccharide residues hinder association through their glucan backbone. This is evidenced by the higher elastic moduli calculated for degalactosylated XG-CNC films (75 ± 6, GPa), compared to native XG-CNC films (19 ± 2 GPa). This work highlights the importance of material structure as it relates to overall performance and therefore function in natural systems, such as the plant cell wall. These studies contribute to a greater understanding of the mechanical properties of the plant cell wall and serve as a basis to extend bio-based and biomimetic materials to applications such as drug delivery, packaging, and coatings. / Thesis / Master of Applied Science (MASc) / The plant cell wall boasts impressive mechanical properties, balancing seemingly opposing properties of structural strength with flexibility. These natural materials have been a source of inspiration for new material design, but the phenomena that govern interactions between components and how their structures translate into function, have yet to be fully understood. In this work, we have constructed thin multilayered films to mimic the plant cell wall, composed of cellulose nanocrystals (rod-shaped nanoparticles derived from plant cellulose) and xyloglucan (a common hemicellulose “glue”). When the films on flexible supports are compressed, they buckle into wrinkled surface patterns that can be used to calculate their mechanical properties. This investigation compares three buckling methods and supports the notion that the mechanical performance of the plant cell wall is strongly dependent on the structure of the different components and the way they interact.

This study presents the first attempt to combine the fields of ultraviolet (UV) photobiology, plant cell wall biochemistry, aerobic methane production and reactive oxygen species (ROS) mechanisms to investigate the effect of UV radiation on vegetation foliage. Following reports of a 17% increase in decomposition rates in oak (Quercus robur) due to increased UV, which were later ascribed to changes in cell wall carbohydrate extractability, this study investigated the effects of decreased UV levels on ash (Fraxinus excelsior), a fast-growing deciduous tree species. A field experiment was set up in Surrey, UK, with ash seedlings growing under polytunnels made of plastics chosen for the selective transmission of either all UV wavelengths, UV-A only, or no UV. In a subsequent field decomposition experiment on end-of-season leaves, a significant increase of 10% in decomposition rate was found after one year due to removal of UV-B. However, no significant changes in cell wall composition were found, and a sequential extraction of carbohydrate with different extractants suggested no effects of the UV treatments on cell wall structure. Meanwhile, the first observations of aerobic production of methane from vegetation were reported. Pectin, a key cell wall polysaccharide, was identified as a putative source of methane, but no mechanism was suggested for this production. This study therefore tested the effect of UV irradiation on methane emissions from pectin. A linear response of methane emissions against UV irradiation was found. UV-irradiation of de-esterified pectin produced no methane, demonstrating esters (probably methyl esters) to be the source of the observed methane. Addition of ROS-scavengers significantly decreased emissions from pectin, while addition of ROS without UV produced large quantities of methane. Therefore, this study proposes that UV light is generating ROS which are then attacking methyl esters to create methane. The study also demonstrates that this mechanism has the potential to generate several types of methyl halides. These findings may have implications for the global methane budget. In an attempt to demonstrate ROS generation in vivo by UV irradiation, radio-labelling techniques were developed to detect the presence of oxo groups, a product of carbohydrate attack by ROS. Using NaB3H4, the polysaccharides of ash leaflets from the field experiment were radio-labelled, but did not show any significant decrease in oxo groups due to UV treatments. However, UV-irradiation of lettuce leaves showed a significant increase in radio-labelling, suggesting increased UV irradiation caused an increase in the production of ROS. The study shows that the use of this radio-labelling technique has the potential to detect changes in ROS production due to changes in UV levels and could be used to demonstrate a link between ROS levels and methane emissions.

A ocorrência de mamões Golden com casca verde e polpa mole, em determinadas épocas do ano, tem sido relatada por produtores da região Norte do Espírito Santo. Não sendo possível distinguir frutos com o distúrbio do amolecimento precoce (DAP) apenas pela análise da cor da casca e da firmeza da polpa no momento da colheita, o objetivo deste trabalho foi estudar aspectos da fisiologia e bioquímica do amadurecimento que pudessem auxiliar no entendimento da perda precoce da firmeza. As coletas ocorreram no período de maior frequência de frutos com o distúrbio (meados de verão a final de outono). Os frutos foram coletados no estádio 1 de maturação, armazenados a 10º±1oC e 85±10% UR, durante 10 dias e submetidos à metodologia do Índice de Amolecimento (IA). O sintoma do amolecimento precoce foi observado claramente no 4°dia após o armazenamento sendo verificada a perda de firmeza nos frutos com DAP entre o 2° e o 8°dia a 10°C, sendo o decréscimo na firmeza equivalente a 71% da firmeza inicial, comportamento atípico para frutos armazenados sob refrigeração. Frutos com e sem DAP não apresentaram diferença significativa no teor de sólidos solúveis, acidez titulável e ácido ascórbico. A atividade respiratória e a produção de etileno foram reduzidas com o armazenamento refrigerado, sem diferença entre os frutos com e sem DAP, o que sugere que o aparecimento do distúrbio não se deve ao aumento na produção de etileno no período póscolheita. Os resultados indicam forte associação entre o amolecimento precoce e mudanças na parede celular. O rendimento das frações solúvel em água (FSA) e em NaOH (FSH) nos frutos com DAP, foi superior ao observado nos frutos sem DAP, durante todo o período de armazenamento. O menor nível da fração solúvel em imidazol (FSI) no tempo 0 pode estar associado à maior atividade da pectinametilesterase nos frutos com DAP. O decréscimo na fração celulose (CEL) em frutos com DAP pode indicar modificação na parede celular, ao nível celulose-hemicelulose. A produção de etileno não acompanhou as modificações na parede celular, sugerindo que alterações na estrutura da parede podem ter ocorrido durante o crescimento do fruto. Frutos com DAP apresentaram níveis de auxina (AIA) 6 vezes menor do que frutos sem DAP, no dia 0, sem diferença durante o armazenamento. Possivelmente os níveis de AIA nos frutos com DAP estavam reduzidos quando o fruto ainda estava ligado à planta. O distúrbio possivelmente está relacionado à alteração na parede celular e níveis de AIA. Desta forma, uma alteração hormonal durante o desenvolvimento do fruto anterior à colheita -, associada à sensibilidade do fruto à essa sinalização hormonal, levaria à mudanças na parede celular, o que determinaria a ocorrência do distúrbio do amolecimento precoce. / The occurrence of green skin and soft pulp in Golden papaya fruit during certain seasons has been reported by orchards in northern Espírito Santo State, Brazil. It is not possible solely by skin color and pulp firmness analysis to distinguish early softening disorder fruits (DAP), at the time of harvest, from those without the disorder. The aim of this work was to study the physiological and biochemical ripening aspects that might help to understand the early softening disorder. Fruits were harvested on the most common seasons (mid-summer to mid-autumn) in maturity stage 1 and evaluated for 10 days. Fruits were stored at 10°C, and submitted to softening index (IA). The symptoms of early softening disorder were clearly observed on the 4th day after storage. However, the firmness decrease in DAP fruits happened between the 2nd and 8th day at 10°C, with a decrease of 71% of initial firmness, presenting an atypical behavior for fruits stored under refrigeration. There was no difference between fruits with DAP and without DAP for soluble solids, titratable acidity and ascorbic acid content. Besides that, there was no difference between fruits with DAP and without DAP for respiration rate and ethylene production under refrigerated storage, which suggests that the disorder occurrence is not related to an increase in ethylene in the postharvest period. The results indicate a strong association between early softening disorder and changes in the cell wall composition. The cell wall polymers fractionation show that the yield of water soluble polymers (FSA) and NaOH soluble polymers (FSH) was higher in fruits with DAP than on fruits without DAP during the entire storage period. The smallest level of the imidazole soluble fraction (FSI) in DAP fruit, on day 0, may be related to a higher activity of pectinmethylesterase. The decrease in cellulose-rich polysaccharides (CEL) in the DAP fruit suggest modifications in the cellulose-hemicellulose domain. Ethylene production did not follow cell wall modification, suggesting that changes in the cell wall structure could be happening during fruit growth. DAP fruit presented an AIA level 6 times smaller than fruit without DAP, in day 0, without storage differences. Possibly, AIA levels in DAP fruit were reduced while fruits were still connected to the plant. The disorder may be related to cell wall changes and to AIA level. Should a hormonal change occur during fruit development i. e. prior to harvesting -- and still depending on fruit sensibility to hormonal signaling, cell wall changes could have different intensities, which determine if the fruit will or not have the flesh early softening observed after harvest.

Even though the structure of the plant cell wall is by and large quite well characterized, its synthesis and regulation remains largely obscure. However, it is accepted that the building blocks of the polysaccharidic part of the plant cell wall are nucleotide sugars. Thus to gain more insight into the cell wall biosynthesis, in the first part of this thesis, plant genes possibly involved in the nucleotide sugar interconversion pathway were identified using a bioinformatics approach and characterized in plants, mainly in Arabidopsis. For the computational identification profile hidden markov models were extracted from the Pfam and TIGR databases. Mainly with these, plant genes were identified facilitating the “hmmer” program. Several gene families were identified and three were further characterized, the UDP-rhamnose synthase (RHM), UDP-glucuronic acid epimerase (GAE) and the myo-inositol oxygenase (MIOX) families. For the three-membered RHM family relative ubiquitous expression was shown using variuos methods. For one of these genes, RHM2, T-DNA lines could be obtained. Moreover, the transcription of the whole family was downregulated facilitating an RNAi approach. In both cases a alteration of cell wall typic polysaccharides and developmental changes could be shown. In the case of the rhm2 mutant these were restricted to the seed or the seed mucilage, whereas the RNAi plants showed profound changes in the whole plant. In the case of the six-membered GAE family, the gene expressed to the highest level (GAE6) was cloned, expressed heterologously and its function was characterized. Thus, it could be shown that GAE6 encodes for an enzyme responsible for the conversion of UDP-glucuronic acid to UDP-galacturonic acid. However, a change in transcript level of variuos GAE family members achieved by T-DNA insertions (gae2, gae5, gae6), overexpression (GAE6) or an RNAi approach, targeting the whole family, did not reveal any robust changes in the cell wall. Contrary to the other two families the MIOX gene family had to be identified using a BLAST based approach due to the lack of enough suitable candidate genes for building a hidden markov model. An initial bioinformatic characterization was performed which will lead to further insights into this pathway. In total it was possible to identify the two gene families which are involved in the synthesis of the two pectin backbone sugars galacturonic acid and rhamnose. Moreover with the identification of the MIOX genes a genefamily, important for the supply of nucleotide sugar precursors was identified. In a second part of this thesis publicly available microarray datasets were analyzed with respect to co-responsive behavior of transcripts on a global basis using nearly 10,000 genes. The data has been made available to the community in form of a database providing additional statistical and visualization tools (http://csbdb.mpimp-golm.mpg.de). Using the framework of the database to identify nucleotide sugar converting genes indicated that co-response might be used for identification of novel genes involved in cell wall synthesis based on already known genes. / Obwohl der Aufbau der pflanzlichen Zellwand im Großen und Ganzen relativ gut charakterisiert ist, ist relativ wenig über ihre Synthese bekannt. Allgemein akzeptiert ist jedoch, dass die Nukleotidzucker die Vorstufe für den polysaccharidären Teil der Zellwand stellen. Im Rahmen der vorliegenden Arbeit wurden neue Kandidatengene für die Zellwandbiosynthese mittels bioinformatorischer Analysen ermittelt und deren Rolle in Pflanzen, hauptsächlich Arabidopsis thaliana untersucht. Zur Identifizierung von Arabidopsis thaliana Kandidatengenen des Nukleotidzucker-Stoffwechselweges wurden „hidden Markov Modelle“ für Gene desselben aus den Datenbanken Pfam und TIGR extrahiert. Unter anderem wurden diese dann unter Zuhilfenahme des Programms hmmer zur Identifikation von pflanzlichen Genen benutzt. Es wurden einige Genfamilien identifiziert und drei von diesen wurden weiter charakterisiert. Hierbei handelte sich um eine UDP-Rhamnose Synthase Familie (RHM), eine UDP-Glucuronsäurepimerase Familie (GAE) und eine myo-Inositol Oxygenase Familie (MIOX). Für die RHM Kandidatengenfamilie, mit drei Mitgliedern, wurde die relativ ubiquitäre Expression aller Gene mittels verschiedener Methoden gezeigt und für eines der Gene, RHM2, konnten T-DNA Linien bezogen werden. Außerdem wurde die Transkription der gesamten Familie mittels eines RNAi Konstruktes herunter geregelt. In beiden Fällen konnte eine Veränderung von zellwandtypischen Polysacchariden sowie schwere Entwicklungsstörungen gezeigt werden. Diese waren bei der rhm2 Funktionsverlustpflanze auf den Samenschleim bzw. den Samen reduziert, bei den RNAi Pflanzen hingegen war die gesamte Pflanze betroffen. Im Falle der zweiten Kandidatengenfamilie, GAE, wurde das höchst-exprimierte Gen (GAE6) kloniert, heterolog exprimiert und die Funktion charakterisiert. So konnte gezeigt werden, dass GAE6 für ein Enzym kodiert, welches UDP-Glukuronsäure in UDP-Galakturonsäure wandelt. Allerdings zeigten Pflanzen mit veränderter Transkriptmenge, erreicht durch T-DNA Insertionen (gae2, gae5, gae6), Überexpression (GAE6) oder RNAi / keine robuste Veränderung der Zellwand. Die letzte betrachtete Kandiatengenfamilie myo-Inositol Oxygenase wurde im Gegensatz zu den beiden anderen Familien, durch eine BLAST Suche gefunden, da zur Zeit der Durchführung noch zu wenig myo-inositol Oxygenasen bekannt waren, um daraus „hidden Markov Modelle“ abzuleiten. Dennoch konnten erste bioinformatorische Analysen zu dieser Genfamilie gemacht werden. Insgesamt gesehen wurden in diesem Teil der Arbeit die beiden Genfamilien identifiziert und charkterisiert, die bei der Synthese der beiden Pektinrückgradzucker Rhamnose und Galakturonsäure die tragende Rolle spielen. Weiterhin wurde mit der Identifizierung der MIOX Genfamilie, eine Genfamilie identifiziert, die wichtige Vorstufen in der Synthese der Nukleotidzucker liefert. In einem zweiten Teil der Arbeit wurden öffentlich zugängliche Mikroarray-Daten durch ihr Gleich -oder Ungleichverhalten charakterisiert. Dieses erfolgte auf globaler Ebene für zunächst fast 10.000 Gene. Die Daten wurden in Form einer allgemein zugänglichen Datenbank der Allgemeinheit zur Verfügung gestellt (http://csbdb.mpimp-golm.mpg.de). Eine Anwendung der Methode auf Gene des Nukleotidzuckerstoffwechsels, deutet darauf hin, dass so neue Kandiatengene, die bei der Zellwandsynthese eine Rolle spielen, von bereits bekannten Genen abgeleitet werden können.

Orientadores: Márcia Regina Braga, Simone de Pádua Teixeira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-16T00:05:19Z (GMT). No. of bitstreams: 1 Caccere_Rodrigo_M.pdf: 5287310 bytes, checksum: 7433584cc6dacc1485f7ed86dd51116e (MD5) Previous issue date: 2010 / Resumo: Inga vera Pennington produz sementes com alta sensibilidade à dessecação, o que dificulta seu armazenamento. Diversos mecanismos estão relacionados tolerância à dessecação, dentre eles o acúmulo de reservas insolúveis e de moléculas protetoras, redução do metabolismo e dobramento da parede celular. Desse modo, o objetivo deste trabalho foi analisar o comportamento de eixos embrionários e cotilédones de I. vera com respeito a seus teores e composição de açúcares solúveis, de reserva e de parede celular e quanto à ultra-estrutura durante a maturação e após a secagem. Eixos embrionários e cotilédones de I. vera durante a maturação, acumulam altos níveis de amido e armazenam também outras substâncias como compostos fenólicos. O acúmulo de massa seca e o processo de vacuolização durante todo o desenvolvimentos dos embriões desta espécie indicam alta atividade metabólica até o momento da dispersão. Além disso, as paredes celulares de eixos embrionários e cotilédones acumulam galactanos que podem lhe conferir maior rigidez. Embriões de I. vera secos até 35% de teor de água apresentaram redução da capacidade germinativa. Esta desidratação parcial provocou um estímulo metabólico, evidenciado pela mobilização de reservas e deposição de material nas paredes celulares, além de intensa atividade do retículo endoplasmático rigoso, observada nos eixos embrionários. A secagem severa (17% de teor de água) provocou rompimento das membranas resultando no aparecimento de células completamente colapsadas. Dessa forma, pode-se concluir que embriões I. vera mantém o metabolismo ativo durante a desidratação até que os processos de injúria comecem a ocorrer. / Abstract: Inga vera Pennington produces recalcitrant seeds, characterized by desiccation sensibility and short post-harvest life span, no longer than one mouth. Mechanisms proposed to explain the ability of organisms to survive desiccation include accumulation of insoluble reserves and protective molecules, metabolic "switch off" and cell wall folding, among others. The aim of the present study was to analyze the behavior of I.vera embryos (axes and cotyledons) with respect to sugar content, cell wall composition and ultrastructure during different stages of development and after desiccation. Axes and cotyledons accumulate starch and phenolic compounds and also showed vacuolization all over development, suggesting high metabolic activity up to the end of the maturation period. Moreover, cell walls of axes and cotyledons cantain polysaccharides, like galactans, that can provide more rigidity to the cell wall. Mature I.vera seeds were dried 35% or 17% and seed variability was skilghtly reduced due to drying to 35% of water content, but no seeds survived to severe desiccation (17% water content). Starch mobilization, increase in the cell wall thickness in axes and cotyledons, and high degree of development of the rough endoplasmic reticulum in axes suggest that drying to 35% of water content enhanced metabolic activity. Severe desiccation resulted in membrane breaking leading to collapsed protoplasm. Therefore we can conclude that I.vera embryos keep high metabolic activity during desiccation until damage processes start. / Mestrado / Biologia Celular / Mestre em Biologia Celular e Estrutural

A ocorrência de mamões Golden com casca verde e polpa mole, em determinadas épocas do ano, tem sido relatada por produtores da região Norte do Espírito Santo. Não sendo possível distinguir frutos com o distúrbio do amolecimento precoce (DAP) apenas pela análise da cor da casca e da firmeza da polpa no momento da colheita, o objetivo deste trabalho foi estudar aspectos da fisiologia e bioquímica do amadurecimento que pudessem auxiliar no entendimento da perda precoce da firmeza. As coletas ocorreram no período de maior frequência de frutos com o distúrbio (meados de verão a final de outono). Os frutos foram coletados no estádio 1 de maturação, armazenados a 10º±1oC e 85±10% UR, durante 10 dias e submetidos à metodologia do Índice de Amolecimento (IA). O sintoma do amolecimento precoce foi observado claramente no 4°dia após o armazenamento sendo verificada a perda de firmeza nos frutos com DAP entre o 2° e o 8°dia a 10°C, sendo o decréscimo na firmeza equivalente a 71% da firmeza inicial, comportamento atípico para frutos armazenados sob refrigeração. Frutos com e sem DAP não apresentaram diferença significativa no teor de sólidos solúveis, acidez titulável e ácido ascórbico. A atividade respiratória e a produção de etileno foram reduzidas com o armazenamento refrigerado, sem diferença entre os frutos com e sem DAP, o que sugere que o aparecimento do distúrbio não se deve ao aumento na produção de etileno no período póscolheita. Os resultados indicam forte associação entre o amolecimento precoce e mudanças na parede celular. O rendimento das frações solúvel em água (FSA) e em NaOH (FSH) nos frutos com DAP, foi superior ao observado nos frutos sem DAP, durante todo o período de armazenamento. O menor nível da fração solúvel em imidazol (FSI) no tempo 0 pode estar associado à maior atividade da pectinametilesterase nos frutos com DAP. O decréscimo na fração celulose (CEL) em frutos com DAP pode indicar modificação na parede celular, ao nível celulose-hemicelulose. A produção de etileno não acompanhou as modificações na parede celular, sugerindo que alterações na estrutura da parede podem ter ocorrido durante o crescimento do fruto. Frutos com DAP apresentaram níveis de auxina (AIA) 6 vezes menor do que frutos sem DAP, no dia 0, sem diferença durante o armazenamento. Possivelmente os níveis de AIA nos frutos com DAP estavam reduzidos quando o fruto ainda estava ligado à planta. O distúrbio possivelmente está relacionado à alteração na parede celular e níveis de AIA. Desta forma, uma alteração hormonal durante o desenvolvimento do fruto anterior à colheita -, associada à sensibilidade do fruto à essa sinalização hormonal, levaria à mudanças na parede celular, o que determinaria a ocorrência do distúrbio do amolecimento precoce. / The occurrence of green skin and soft pulp in Golden papaya fruit during certain seasons has been reported by orchards in northern Espírito Santo State, Brazil. It is not possible solely by skin color and pulp firmness analysis to distinguish early softening disorder fruits (DAP), at the time of harvest, from those without the disorder. The aim of this work was to study the physiological and biochemical ripening aspects that might help to understand the early softening disorder. Fruits were harvested on the most common seasons (mid-summer to mid-autumn) in maturity stage 1 and evaluated for 10 days. Fruits were stored at 10°C, and submitted to softening index (IA). The symptoms of early softening disorder were clearly observed on the 4th day after storage. However, the firmness decrease in DAP fruits happened between the 2nd and 8th day at 10°C, with a decrease of 71% of initial firmness, presenting an atypical behavior for fruits stored under refrigeration. There was no difference between fruits with DAP and without DAP for soluble solids, titratable acidity and ascorbic acid content. Besides that, there was no difference between fruits with DAP and without DAP for respiration rate and ethylene production under refrigerated storage, which suggests that the disorder occurrence is not related to an increase in ethylene in the postharvest period. The results indicate a strong association between early softening disorder and changes in the cell wall composition. The cell wall polymers fractionation show that the yield of water soluble polymers (FSA) and NaOH soluble polymers (FSH) was higher in fruits with DAP than on fruits without DAP during the entire storage period. The smallest level of the imidazole soluble fraction (FSI) in DAP fruit, on day 0, may be related to a higher activity of pectinmethylesterase. The decrease in cellulose-rich polysaccharides (CEL) in the DAP fruit suggest modifications in the cellulose-hemicellulose domain. Ethylene production did not follow cell wall modification, suggesting that changes in the cell wall structure could be happening during fruit growth. DAP fruit presented an AIA level 6 times smaller than fruit without DAP, in day 0, without storage differences. Possibly, AIA levels in DAP fruit were reduced while fruits were still connected to the plant. The disorder may be related to cell wall changes and to AIA level. Should a hormonal change occur during fruit development i. e. prior to harvesting -- and still depending on fruit sensibility to hormonal signaling, cell wall changes could have different intensities, which determine if the fruit will or not have the flesh early softening observed after harvest.