A maioria das proteínas organelares são codificadas pelo núcleo, sintetizadas no citosol e direcionadas especificamente ao seu destino final. O direcionamento aos diferentes subcompartimentos subcelulares é feito por uma complexa e ampla maquinaria que envolve sequências de direcionamento, proteínas citossólicas e receptores organelares específicos. Entretanto, relativamente pouco se conhece sobre o processo na qual uma proteína recém sintetizada é transportada ao seu destino final. Parte significativa das proteínas destinadas às organelas possui a informação necessária ao seu transporte localizada na extremidade N-terminal. Vários estudos têm buscado caracterizar as etapas que envolvem a localização de uma proteína, desde os estágios iniciais após a sua síntese até os fatores que regulam o seu correto endereçamento. Modificações pós-traducionais, regiões 5-UTR, região C-terminal, transporte por vias alternativas e interações proteína-proteína podem agir na localização subcelular de proteínas. O estudo de redes biomoleculares se tornou um dos focos de estudo da biologia de sistemas e demonstra um enorme potencial na descoberta de diversos processos biológicos, como as interações proteína-proteína. As proteínas que possuem duplo direcionamento (DD) em Arabidopsis thaliana foram analisadas em redes de interação proteína-proteína (PPI) e proteínas que interagem com proteínas de DD foram escolhidas quanto a função e localização para a verificação de um eventual papel dessas proteínas na localização subcelular de outras proteínas. Para tanto, foram realizadas varreduras em ensaios de duplo-híbrido em levedura para os genes de GRF9 (14-3-3) e ATH7 (tiorredoxina tipo h). Os resultados para GRF9 incluem as proteínas peroxidase PRXR1 e dihidrolipoamida acetiltransferase. Já os resultados para ATH7 mostram a interação com glutamina sintetase (AT5G35630.3). A combinação dos estudos in silico com a varredura via duplo-híbrido de levedura abrem novas perspectivas no entendimento do controle da localização subcelular de proteínas. / Most organellar proteins are nuclear encoded, synthesized in the cytosol and then targeted to their destination. Specific subcellular targeting is conducted by a complex machinery for the specific localization of the proteins, which includes targeting sequences, cytosolic proteins and specific organelar receptors. However, little is known about the process that happens from the synthesis of a protein and the transport to its final destination. Most organellar proteins contain the information for their localization in the N-terminal sequence. Many studies have searched to characterize the steps involved in protein targeting, from the early stages after its synthesis to the cytosolic factors regulating its correct localization. Post-translational modifications, 5-UTR regions, the C-terminal extension on the protein, alternative transport pathways and proteinprotein interactions may influence the subcellular location of some proteins. The use of biomolecular netwoks has become one of the main focus of systems biology studies and possess a major potential in the discovery of several biological processes, such as protein-protein interactions (PPI). Dual-targeted (DT) proteins in Arabidopsis thaliana were analyzed through a PPI network, and the proteins displaying interactions with DT proteins were selected by their funtion and location. The selected proteins were analyzed for their eventual role in the subcellular targeting of other proteins. Screenings in yeast two-hibrid assays were performed for the genes GRF9 (14-3-3) and ATH7 (h-type thioredoxin). The results for GRF9 include a peroxidase (PRXR1) and dihydrolipamide acetyltransferase. The results for ATH7 include glutamine synthetase (AT5G35630.3). Combination of in silico analysis with yeast two-hibrid screenings provide new perspectives for understanding the control of subcellular localization.

O complexo FtsH em Arabidopsis, presente nos tilacóides, é formado pelas subunidades FtsH1/FtsH5 (tipo A) e FtsH2/FtsH8 (tipo B). Os tipos A e B apresentam grande identidade em seus domínios maduros, porém nenhuma similaridade é observada na região amino-terminal do peptídeo de trânsito. Em um experimento de importação em cloroplastos isolados, FtsH2 e FtsH5 foram importadas e subsequentemente integradas aos tilacóides através de um mecanismo de processamento em duas etapas que resultou em um domínio lumenal amino-proximal, uma única âncora transmembrânica e um domínio carboxi-proximal estromal. A integração da FtsH2 em tilacóides isolados foi totalmente dependente do gradiente de prótons, enquanto que a integração da FtsH5 foi dependente de NTPs, sugerindo que a inserção na membrana ocorre pelas vias TAT e Sec, respectivamente. Tal observação foi corroborada por experimentos de competição in-organello e inibição por anticorpos específicos. Os domínios amino-proximais até as âncoras transmembrânicas foram suficientes para a correta integração aos tilacóides. A região madura da FtsH2 apresentou incompatibilidade com a maquinaria Sec, como demonstrado pela troca de peptídeos de trânsito. A incompatibilidade não parece ser determinada por qualquer elemento específico da FtsH2, uma vez que nenhum domínio isolado apresentou incompatibilidade com a via Sec de transporte. Tal fato sugere uma incompatibilidade estrutural que requer a FtsH2 intacta. A descoberta que as subunidades FtsH do tipo A e B, que apresentam grande identidade e usam diferentes vias de integração para formar o mesmo complexo multimérico é uma observação nova e interessante para o estudo da biogênese de proteínas de membranas. O mecanismo de regulação que governa a atividade do complexo FtsH em Arabidopsis é ainda desconhecido, entretanto é proposta a existência de fatores adicionais. Dessa forma, a proteína plastidial FtsH de Arabidopsis foi usada como isca em um rastreamento por duplohíbrido de levedura. O rastreamento resultou em 48 colônias que ativaram os genes repórteres histidina e adenina. Entre todos os cDNAs sequenciados, foi encontrado um candidato em potencial denominado FIP (FtsH5 Interacting Protein). Experimentos GST Pull-Down também indicam uma interação entre FtsH5 e FIP. O precursor FIP radioativo foi incubado com cloroplastos de ervilha. Após a incubação, os cloroplastos foram lisados e separados em estroma e tilacóides. FIP permaneceu associada exclusivamente à fração membranosa dos tilacóides. A inserção na membrana foi verificada através da resistência ao tratamento com álcali e o tratamento dos tilacóides com protease resultou em um fragmento protegido, característico de proteínas inseridas na membrana. A construção FtsH5::GFP transformada em Nicotiana tabacum resultou no direcionamento do gene quimérico aos cloroplastos. Dessa forma, assim como FtsH5, FIP é uma proteína plastidial que está localizada na membrana dos tilacóides. Géis nativos utilizando FIP radioativa mostram que ela está associada a um complexo de aproximadamente 450 kDa, que é o tamanho esperado para o complexo tilacoidal FtsH em Arabidopsis. Como as proteínas FtsH apresentam tanto o domínio ATPase quanto protease, acreditamos que FIP pode de alguma forma modular a atividade do complexo FtsH nos tilacóides. / The Arabidopsis thylakoid FtsH protease complex is composed of FtsH1/FtsH5 (type A) and FtsH2/FtsH8 (type B) subunits. Type A and type B subunits display a high degree of sequence identity throughout their mature domains, but no similarity in their amino-terminal targeting peptide regions. In chloroplast import assays, FtsH2 and FtsH5 were imported and subsequently integrated into thylakoids by a two-step processing mechanism that resulted in an amino-proximal lumenal domain, a single transmembrane anchor, and a carboxyl proximal stromal domain. FtsH2 integration into washed thylakoids was entirely dependent on the proton gradient, whereas FtsH5 integration was dependent on NTPs, suggesting their integration by Tat and Sec pathways, respectively. This finding was corroborated by in organello competition and by antibody inhibition experiments. The amino proximal domains through the transmembrane anchors were sufficient for proper integration. The mature FtsH2 protein was found to be incompatible with the Sec machinery as determined with targeting peptide-swapping experiments. Incompatibility does not appear to be determined by any specific element in the FtsH2 domain as no single domain was incompatible with Sec transport. This suggests an incompatible structure that requires the intact FtsH2. That the highly homologous type A and type B subunits of the same multimeric complex use different integration pathways is a striking example of the notion that membrane insertion pathways have evolved to accommodate structural features of their respective substrates. The regulation mechanism which governs the Arabidopsis FtsH complexs activity is still unknown, but it is proposed the presence of additional factors. For this reason, the plastidial Arabidopsis FtsH5 was used as bait in a yeast two hybrid screening. The screening resulted in 48 colonies that activated the histidine and adenine reporter genes. Among all the sequenced cDNAs we have found a potential candidate named FIP (FtsH5 Interacting Protein). GST Pull-Down experiments also indicate an interaction between FtsH5 and FIP. Radiolabeled FIP was incubated with intact isolated chloroplasts. After incubation, intact chloroplasts were lysated and separated into stroma and thylakoids. FIP remained associated exclusively with the thylakoid membrane fraction. The insertion into membrane was verified throughout resistance to alkali treatment and the thylakoid protease treated fraction resulted in a protected fragment, characteristic of membrane-inserted proteins. Agroinfiltrated Nicotiana tabacum leaves with a FtsH5::GFP construct resulted that the chimeric gene was targeted to chloroplasts. Thus, as FtsH5, FIP is a plastidial protein which is located into thylakoid membrane. Blue native gels using radiolabeled FIP protein show that it runs associated with a complex around 450 kDa, which is the expected size for the Arabidopsis FtsH thylakoidal complex. As FtsH proteins present both ATPase and protease domains, we believe that FIP can somehow modulates the activity of the thylakoidal FtsH complex.

O presente trabalho foi subdividido em quatro capítulos com os seguintes objetivos: (i) elaborar uma minuciosa revisão de literatura abordando os principais aspectos da interação viróide-hospedeiro e as relações evolutivas dos viróides e virusóides; (ii) identificar e caracterizar viróides associados a videiras, no Brasil; (iii) purificar, clonar e caracterizar, um RNA circular de seqüência totalmente desconhecida; (iv) estudar alguns aspectos relacionados à interação viróidehospedeiro. Inicialmente, foram identificadas e caracterizadas duas espécies de viróides (o Citrus exocortis viroid CEVd e o Hop stunt viroid, HSVd) isolados de videiras no Brasil. Para tal, promoveu-se extração de RNAs totais de folhas de Vitis vinifera ‘Cabernet Sauvignon’ e V. labrusca ‘Niagara Rosada’, seguida de RT-PCR com oligonucleotídeos específicos. Os fragmentos de DNA amplificados foram clonados e seqüenciados. Os resultados revelaram que as videiras estavam duplamente infectadas com o CEVd e HSVd. As análises filogenéticas mostraram que os clones de HSVd de videira agruparam-se com outros variantes de videira, formando um grupo separado de um segundo formado por variantes de citros. Já os clones de CEVd de videira agruparam-se com isolados de citros e videira. No capítulo 3, empregou-se um método para a clonagem e caracterização de um pequeno RNA circular (com aproximadamente 300 nucleotídeos) de seqüência totalmente desconhecida. Este RNA, quando submetido à eletroforese dupla em géis de poliacrilamida desnaturantes, apresentou um retardamento na migração, similar aos viróides. Após a clonagem de fragmentos do RNA, amplificados via RTPCR com oligonucleotídeos aleatórios (apresentando seis nucleotídeos degenerados no terminal 3&#145),os clones obtidos foram seqüenciados. A partir desses dados, dois oligonucleotídeos adjacentes de polaridades opostas foram desenhados e empregados para amplificar via RT-PCR a seqüência completa do RNA circular. A análise das seqüências revelou a presença da CCR (central conserved region) do Apple scar skin viroid (ASSVd), espécie tipo do gênero Apscaviroid, e compartilha similaridade com outros membros deste gênero, o que sugere fortemente que o RNA circular é um viróide recombinante. Finalmente, no capítulo 4, foram realizados experimentos que comprovaram a existência do motivo loop E (presente na CCR de algumas espécies dos Pospiviroidae) in vivo no PSTVd. Demonstrou-se também, utilizando ensaios de união in vitro (análise de retardo em gel, EMSA e entrecruzamento com luz ultravioleta), que as proteínas L5 e TFIIIA de Arabidopsis thaliana se unem especificamente ao PSTVd com a mesma afinidade que elas se unem ao seu substrato natural, o rRNA 5S, enquanto que a afinidade por um viróide cloroplástico (Avocado sunblotch viroid, ASBVd) foi significativamente menor. Estas duas proteínas devem participar na síntese e movimento intracelular do PSTVd in vivo. / The present work has been divided into four chapters to: (i) review the main points in viroid-host interactions and present different aspects in the evolutionary relationship of the viroids and virusoids; (ii) identify and characterize viroids infecting grapevine in Brazil; (iii) purify, clone and sequence what appears to be a novel citrus viroid; (iv) study some aspects related to the viroid-host protein interactions. Firstly, two viroid species (Citrus exocortis viroid, CEVd and Hop stunt viroid, HSVd) were identified and characterized from grapevine in Brazil. Total RNAs, extracted from leaves of Vitis vinifera ‘Cabernet Sauvignon’ and V. labrusca ‘Niagara Rosada’, were RT-PCR amplified with specific primers for the five viroids described infecting grapevines. The resulting products were separated by agarose gel electrophoresis and the DNA fragments of the expected full-size were eluted, cloned and sequenced. The grapevines analyzed were doublyinfected by CEVd and HSVd. A phylogenetic analysis showed that the Brazilian grapevine HSVd variants clustered with other grapevine HSVd variants forming a specific group separated from citrus variants, whereas the Brazilian CEVd variants clustered with other citrus and grapevine variants. On the other hand, a method for cloning small circular RNAs of unknown sequence has been applied to an RNA of this kind from citrus (with ca. 300 nucleotides). This RNA, when analyzed by PAGE in denaturing conditions, showed the slow mobility typical of viroid RNAs. After denaturation, the purified RNA was RT-PCR amplified using a primer with six randomized positions at its 3? terminus, with the resulting products being then cloned and sequenced. From these data, two adjacent primers of opposite polarities were designed and used to RT-PCR amplify the complete sequence. Analysis of the sequences revealed the presence of the CCR (central conserved region) of the Apple scar skin viroid (ASSVd), the type member of the genus Apscaviroid, and scattered similarities with other members of this genus, suggesting that the circular RNA is a viroid recombinant. Finally, UV irradiation of infected tissue has revealed the existence in vivo of an RNA motif (loop E) in Potato spindle tuber viroid (PSTVd), the type member of the family Pospiviroidae (nuclear viroids), and RNA-protein binding followed by eletrophoretic mobility shift (EMSA) and UV cross-linking label transfer assays have shown that transcription factor IIIA (TFIIIA) and L5 ribosomal protein from Arabidopsis thaliana bind this RNA in vitro with the same affinity as they bind 5S rRNA, whereas the affinity for a chloroplastic viroid (Avocado sunblotch viroid, ASBVd) is significantly lower. These two proteins may participate in synthesis and delivery of PSTVd in vivo.

Proteínas que se ligam a RNAs geralmente regulam estabilidade, localização e tradução de mensageiros por interação com seqüências específicas na região 3 não traduzida. A proteína PUMILIO foi descrita pela primeira vez em Drosophila, apresentando a função de controlar a tradução de mensageiros alvo durante o desenvolvimento. Homólogos podem ser encontrados em outras espécies filogeneticamente distantes com funções similares. O seqüenciamento do genoma de Arabidopsis thaliana indicou a presença de quatro genes que codificam homólogos ao PUMILIO de Drosophila. Três deles estão no cromossomo II (APUM-1, 2 e 3), com alto grau de identidade e situados muito próximos uns dos outros. A terceira cópia está no cromossomo IV (APUM-4) e sua seqüência tem menor similaridade em relação aos três anteriores. Neste trabalho, foi clonado e caracterizado APUM-2. Ensaios de northern blot e RT-PCR indicaram que o mensageiro de Apum-2 pode ser encontrado em amostras de raiz, caule, folha, flores e frutos. Entretanto, sistemas repórteres, APUM-2::GUS e APUM-2::GFP, foram introduzidos no vegetal e a expressão foi observada nos ápices do caule e raízes, especificamente nas regiões meristemáticas. Também foram feitas construção para ensaios de genética reversa e as plantas contendo construções constitutivas (35S::APUM-2) se desenvolveram sem dominância apical e com grande quantidade de ramos, folhas e raízes secundárias, mostrando perturbações nos meristemas. Os resultados obtidos sugerem que APUM-2 possui papel relevante durante o desenvolvimento meristemático, possivelmente através de interações com mRNAs. / RNA-binding proteins often regulate the stability, localization, and translation of mRNAs by interaction with specific motifs in the 3-UTR. The PUMILIO protein from Drosophila was shown to control translation of specific mRNAs during development. PUMILIO homologs were found in several species and constitute the PUF family. The Arabidopsis thaliana sequencing project revealed four genes homolougs to PUMILIO. Three are situated in chromosome II (APUM-1, 2, and 3) that are nearly identical among themselves, and that contain a region that is 52% homologous to the PUMILIO. RNA-binding domain. The fourth is in chromosome IV (APUM-4), and shows low similarity to the other three. In this work, we characterized APUM-2 in further detail. Northern blots indicated that Apum-2 is expressed in shoot and root apices. Reporter transgenic plants were made that contained either APUM-2::GUS or Apum2::GFP constructs. Reporter gene expression confirmed that APUM-2 is active in shoot and root apices, specifically in the meristematic regions. Finally transgenic plants containing the 35S::APUM-2 construct were created. Constitutive APUM-2 expression resulted in plants with no apical dominance and a high number of leaves, stems and lateral roots. These results suggest that APUM-2 plays an important role during meristem development, possibly through a mRNA interaction.

O presente trabalho foi subdividido em quatro capítulos com os seguintes objetivos: (i) elaborar uma minuciosa revisão de literatura abordando os principais aspectos da interação viróide-hospedeiro e as relações evolutivas dos viróides e virusóides; (ii) identificar e caracterizar viróides associados a videiras, no Brasil; (iii) purificar, clonar e caracterizar, um RNA circular de seqüência totalmente desconhecida; (iv) estudar alguns aspectos relacionados à interação viróidehospedeiro. Inicialmente, foram identificadas e caracterizadas duas espécies de viróides (o Citrus exocortis viroid CEVd e o Hop stunt viroid, HSVd) isolados de videiras no Brasil. Para tal, promoveu-se extração de RNAs totais de folhas de Vitis vinifera ‘Cabernet Sauvignon’ e V. labrusca ‘Niagara Rosada’, seguida de RT-PCR com oligonucleotídeos específicos. Os fragmentos de DNA amplificados foram clonados e seqüenciados. Os resultados revelaram que as videiras estavam duplamente infectadas com o CEVd e HSVd. As análises filogenéticas mostraram que os clones de HSVd de videira agruparam-se com outros variantes de videira, formando um grupo separado de um segundo formado por variantes de citros. Já os clones de CEVd de videira agruparam-se com isolados de citros e videira. No capítulo 3, empregou-se um método para a clonagem e caracterização de um pequeno RNA circular (com aproximadamente 300 nucleotídeos) de seqüência totalmente desconhecida. Este RNA, quando submetido à eletroforese dupla em géis de poliacrilamida desnaturantes, apresentou um retardamento na migração, similar aos viróides. Após a clonagem de fragmentos do RNA, amplificados via RTPCR com oligonucleotídeos aleatórios (apresentando seis nucleotídeos degenerados no terminal 3&#145),os clones obtidos foram seqüenciados. A partir desses dados, dois oligonucleotídeos adjacentes de polaridades opostas foram desenhados e empregados para amplificar via RT-PCR a seqüência completa do RNA circular. A análise das seqüências revelou a presença da CCR (central conserved region) do Apple scar skin viroid (ASSVd), espécie tipo do gênero Apscaviroid, e compartilha similaridade com outros membros deste gênero, o que sugere fortemente que o RNA circular é um viróide recombinante. Finalmente, no capítulo 4, foram realizados experimentos que comprovaram a existência do motivo loop E (presente na CCR de algumas espécies dos Pospiviroidae) in vivo no PSTVd. Demonstrou-se também, utilizando ensaios de união in vitro (análise de retardo em gel, EMSA e entrecruzamento com luz ultravioleta), que as proteínas L5 e TFIIIA de Arabidopsis thaliana se unem especificamente ao PSTVd com a mesma afinidade que elas se unem ao seu substrato natural, o rRNA 5S, enquanto que a afinidade por um viróide cloroplástico (Avocado sunblotch viroid, ASBVd) foi significativamente menor. Estas duas proteínas devem participar na síntese e movimento intracelular do PSTVd in vivo. / The present work has been divided into four chapters to: (i) review the main points in viroid-host interactions and present different aspects in the evolutionary relationship of the viroids and virusoids; (ii) identify and characterize viroids infecting grapevine in Brazil; (iii) purify, clone and sequence what appears to be a novel citrus viroid; (iv) study some aspects related to the viroid-host protein interactions. Firstly, two viroid species (Citrus exocortis viroid, CEVd and Hop stunt viroid, HSVd) were identified and characterized from grapevine in Brazil. Total RNAs, extracted from leaves of Vitis vinifera ‘Cabernet Sauvignon’ and V. labrusca ‘Niagara Rosada’, were RT-PCR amplified with specific primers for the five viroids described infecting grapevines. The resulting products were separated by agarose gel electrophoresis and the DNA fragments of the expected full-size were eluted, cloned and sequenced. The grapevines analyzed were doublyinfected by CEVd and HSVd. A phylogenetic analysis showed that the Brazilian grapevine HSVd variants clustered with other grapevine HSVd variants forming a specific group separated from citrus variants, whereas the Brazilian CEVd variants clustered with other citrus and grapevine variants. On the other hand, a method for cloning small circular RNAs of unknown sequence has been applied to an RNA of this kind from citrus (with ca. 300 nucleotides). This RNA, when analyzed by PAGE in denaturing conditions, showed the slow mobility typical of viroid RNAs. After denaturation, the purified RNA was RT-PCR amplified using a primer with six randomized positions at its 3? terminus, with the resulting products being then cloned and sequenced. From these data, two adjacent primers of opposite polarities were designed and used to RT-PCR amplify the complete sequence. Analysis of the sequences revealed the presence of the CCR (central conserved region) of the Apple scar skin viroid (ASSVd), the type member of the genus Apscaviroid, and scattered similarities with other members of this genus, suggesting that the circular RNA is a viroid recombinant. Finally, UV irradiation of infected tissue has revealed the existence in vivo of an RNA motif (loop E) in Potato spindle tuber viroid (PSTVd), the type member of the family Pospiviroidae (nuclear viroids), and RNA-protein binding followed by eletrophoretic mobility shift (EMSA) and UV cross-linking label transfer assays have shown that transcription factor IIIA (TFIIIA) and L5 ribosomal protein from Arabidopsis thaliana bind this RNA in vitro with the same affinity as they bind 5S rRNA, whereas the affinity for a chloroplastic viroid (Avocado sunblotch viroid, ASBVd) is significantly lower. These two proteins may participate in synthesis and delivery of PSTVd in vivo.

Indiana University-Purdue University Indianapolis (IUPUI) / The root system architecture of higher plants plays an essential role in the uptake of water and nutrients as well as the production of hormones. These root systems are highly branched with the formation of post-embryonic organs such as lateral roots. The initiation and development of lateral roots has been well defined. WAG1 and WAG2 are protein-serine/threonine kinases from Arabidopsis that are closely related to PINOID and suppress root waving. The wag1;wag2 double mutants exhibit a strong root waving phenotype on vertical hard agar plates only seen in wild-type roots when the seedlings are grown on inclined plates. Here an additional root phenotype in the wag1;wag2 mutant is reported. The wag1;wag2 double mutant displays both an increased total number and density of emerged lateral roots (approximately 1.5-fold). An increased LRP density of 1.5-fold over wild-type is observed. To ascertain the role of WAG1 and WAG2 in lateral root development we examined promoter activity in the WAG1::GUS and WAG2::GUS lines. The WAG1 promoter showed no detectable activity at any stage of development. The WAG2 promoter was active in stage IV onward, however there was no detectable activity in the cell types associated with initiation events. The lateral root density and spatial patterning in wild-type, when grown on inclined hard agar plates, was similar to wag1;wag2 on vertical plates. Seedlings of both genotypes were treated with hormones such as auxin and MeJA, and inhibitors. Auxin response in wag1;wag2 was normal with a similar number of LR as the wild-type after treatment. Treatment with MeJA resulted in a similar induction of LRP in both genotypes, however the percent lateral root emergence in wag1;wag2 was reduced while Col-0 was increased compared to controls. Treatment with the calcium blocker tetracaine resulted in wag1;wag2 displaying a wild-type level of LR but had no significant effect on wild-type. Genetic analysis of the wag1;wag2 LR pathway revealed that WAG1 and WAG2 are acting in the same pathway as AUX1, AXR1and PGM1. pgm1-1 was not previously reported to have a LR defect but showed decreased LR formation here, while pgm1;wag1;wag2 had a similar LR density to wag1;wag2. TIR7 and ARG1 were both deduced to operate in separate pathways from WAG1 and WAG2. The data presented here shows that the wag1;wag2 double mutant has an increased number of LR compared to Col-0. This defect appears to be caused by increased pre-initiation events and seems to be tied to the root waving phenotype. However, the treatment with MeJA revealed a possible role for WAG1 or WAG2 in LRP development, potentially under stress conditions. Calcium also seems to play a significant role in the wag1;wag2 LR phenotype, possibly independent of the root waving phenotype.

Os isolados protéicos de soja são utilizados como ingredientes em diversos alimentos e sua utilização vêm aumentando juntamente com o aumento das pesquisas sobre os metabólitos secundários da soja, as isoflavonas. Alguns efeitos benéficos vem sendo associados às isoflavonas, entre estes a sua ação antioxidante, a redução ao risco de câncer, doenças cardiovasculares e osteoporose. O objetivo deste estudo foi o de otimizar as condições de extração das isoflavonas e de suas formas conjugadas a partir da farinha desengordurada de soja, visando o preparo de isolado protéico de soja. Os resultados mostraram que a obtenção de isolados protéicos de soja com teor aumentado de isoflavonas depende da utilização de condições brandas de centrifugação para a separação do precipitado isoelétrico, assim como da utilização de água acidificada na sua lavagem. A presença de isoflavonas no isolado resulta de três fatores, o primeiro referindo-se à associação entre isoflavonas e proteínas através de interações hidrofóbicas, eletrostáticas, e pontes de hidrogênio; o segundo à menor solubilidade das isoflavonas presentes na farinha desengordurada de soja no pH isoelétrico; e o último ao processo de carreamento (físico) das isoflavonas pelas proteínas insolubilizadas. / Soy protein isolates are used as ingredients in several food products and their use is increasing together with the increase of the researches on the secondary metabolites of soy, the isoflavones. Some beneficial effects have been associated to the isoflavones, among these their antioxidant action, prevention of cancer, cardiovascular diseases and osteoporosis. The objective of this study was to optimize the extraction conditions of the isoflavones from the defatted soy flour, seeking the preparation of soy protein isolates. The results showed that the obtention of soy protein isolates with increased content of isoflavones depends on the use of mild conditions of centrifugation for the separation of the isoelectric precipitate, as well as on the use of water acidified in the washing step. The presence of isoflavones in the isolates resulted from three factors, the first refers to the association between isoflavones and proteins through hydrophobic; and electrostatic interactions, and hydrogen bonding; the second to the decreased solubility of the isoflavones extracted from the defatted soy flour in the isoelectric pH; and the last to the carrying process (physical) of isoflavones by the precipitating proteins.

THI1 é provavelmente uma proteína bifuncional, uma vez que está envolvida na biossíntese de tiamina e na estabilidade do DNA organelar, notadamente o mitocondrial. Interessantemente, a biossíntese de tiamina ocorre em compartimentos distintos em plantas (cloroplastos) e em leveduras (mitocôndrias). Ensaios de complementação funcional mostraram que o gene thi1 de Arabidopsis thaliana é capaz de complementar uma cepa mutante de levedura para o gene ortólogo. A proteína THI1 de Arabidopsis thaliana é codificada por um único gene. Uma análise detalhada da região N-terminal da proteína, responsável pela sua localização na células, revelou a presença de duas sequências de direcionamento adjacentes. Na extremidade N-terminal encontra-se um peptídeo de trânsito cloroplástico seguida por uma região capaz de formar uma α-hélice anfifílica, tipicamente encontrada em pré-sequências de direcionamento mitocondriais. Com o objetivo de avaliar se a localização final de THI1 pode apresentar um tipo de regulação temporal ou espacial, foram obtidas plantas transgênicas expressando a proteína THI1 fundida a GFP ("green fluorescent protein"). Análises dessas plantas por meio de microscopia confocal revelaram que THI1 está presente majoritariamente em cloroplastos e raramente em mitocôndrias. Ao contrário do que acontece em Arabidopsis thaliana, em cana de açúcar foram encontrados pelo menos três isoformas/parálogos de thi1. O alinhamento da seqüência de aminoácidos dessas isoformas com a THI1 de Arabidopsis thaliana revelou alta similaridade, inclusive na seqüência de direcionamento. Com o intuito de avaliar o padrão de direcionamento dessas isoformas de cana de açúcar foram obtidas construções gênicas contendo ou a seqüência de direcionamento completa ou o peptídeo de trânsito cloroplástico ou a pré-seqüência mitocondrial, fundidas a GFP sob o comando do promotor 35S. A expressão transiente dessas construções em epiderme de cebola, revelou que no caso das construções contendo a seqüência de direcionamento completa ou o peptídeo de trânsito, o direcionamento ocorreu apenas para os cloroplastos. No caso das construções contendo somente a seqüência de direcionamento mitocondrial a GFP permaneceu difundida no citoplasma. Além do aspecto do direcionamento, THI1 foi avaliada sob o ponto de vista filogenético. As análises filogenéticas mostram que thi1 é raramente encontrado em bactérias mas é amplamente distribuído em Archaea. As distâncias genéticas indicam que provavelmente os eucariontes herdaram thi1 de Archaea. As poucas bactérias que possuem esse gene provavelmente obtiveram-no por meio de herança horizontal. / THI1 is probably a bifunctional protein, since it is involved in thiamin biosynthesis and organelar genome stability mainly the mitochondrial. Interestingly, the thiamin biosynthesis occurs at different compartments in plants (chloroplasts) and yeasts (mitochondria). Functional complementation assays showed that Arabidopsis thaliana thi1 gene is able to complement a yeast mutant strain for the hortolog gene. The Arabidopsis thaliana THI1 is encoded by a single copy gene. A detailed analysis of the THI1 N-terminal region, that is responsible for its targeting in cells, reveled the presence of two in tanden directing sequences. At N-terminal region there is a chloroplastic transit peptide followed by a region able to form an anfifilic α-helix frequently present in mitochondrial presequences. Aiming to evaluate if the THI1 final localization could present a temporal or spacial regulation, transgenic plants expressing THI1 fused to GFP ("green fluorescent protein") where obtained. Confocal microscopy analysis of these transgenic plants showed that THI1 is mainly found in chloroplasts and barely found in mitochondrias. Different from what happens in Arabidopsis thaliana, in sugar cane where founded at least three thi1 isoforms/paralogs. The amino acids sequence alignment of these isoforms with the thi1 one, reveled high similarity including the targeting sequence. To evaluate the directing standard of these sugarcane isoforms, gene constructions made by the complete targeting sequence or the chloroplastic transit peptide or the mitochondrial presequence, fused to GFP under the guidance of 35S promotor, where obtained. A transient expression of these gene constructios in epidermal onion cells prove that in the case of the constructions containing either the complete targeting sequence or the chloroplastic transit peptide the directing occurred only to chloroplasts. On the other hand, the constructions containing the mitochondrial pre sequence, GFP were kept defused in the citoplasm. Besides the directing aspect, THI1 were evaluated under the filogenetic point of view. Filogenetic analysis showed that thi1 is rarely found in bacteria but is widely distributed in Archaea. The genetic distances pointed out that probably eucaryotes THI1 came from Archaea. This gene in a few bacterias probably were inherited by lateral transference.

病原體感染是包括植物的高等生物的主要健康危害之一。為抵禦入侵者，大多數植物會製造防禦蛋白，包括凝集素、蛋白酶抑製劑、抗真菌蛋白、核糖核酸酶和核糖體失活蛋白，並分佈在不同的器官，如葉、根、種子和塊莖。一些植物防禦蛋白被發現能表現出多種生物活性，如抗腫瘤活性、抗細菌活性和抗病毒活性，能抵抗多種植物病原菌和人類病原體。因此，一些植物防禦蛋白可能有潛力用於治療人類疾病，或保護農作物免受感染。 / 我們在研究中從不同的植物來源成功純化出各種防禦蛋白，包括：小芋頭塊莖中的血凝素、日本長芋中的凝集素、東北紅豆中的血凝素和抗真菌多肽、棕色芸豆中的凝集素、抗真菌多肽和胰蛋白酶抑製劑，玉豆一號中的凝集素以及小斑豆中的胰蛋白酶抑製劑。小芋頭血凝素被發現能誘導脾細胞的有絲分裂反應。日本長芋凝集素和東北紅豆血凝素被發現能對一些腫瘤細胞株（如乳腺癌MCF7細胞及鼻咽癌CNE2細胞）發揮抗增殖的作用。棕色芸豆凝集素能誘導脾臟細胞的有絲分裂反應以及抑制腫瘤細胞株（如乳腺癌MCF7細胞、肝癌HepG2及鼻咽癌CNE1和 CNE2細胞）的生長，而棕色芸豆抗真菌蛋白能抑制數種病原真菌物種的生長。研究這些防禦蛋白的生物活性有助找出其潛在應用價值，如藥用前景。 / Infection from pathogens is one of the major health hazards in higher organisms including plants. To defend against harmful invaders, most plants produce a variety of defense proteins including lectins, protease inhibitors, antifungal proteins, ribonucleases and ribosome-inactivating proteins. They may be present in different organs of the plants, such as leaves, roots, seeds and tubers. Some of the plant defense proteins were found to exhibit a variety of biological activities such as anti-tumor activity, anti-bacterial activity and anti-viral activity that act against various plant pathogens and also some human pathogens. Therefore, some plant defense proteins may have potential for therapeutic applications in human diseases, or protecting the crops from infections. / This study involved purification of defense proteins from different plant sources. The proteins that were successfully isolated included a hemagglutinin from small taro tubers, a lectin from Japanese yam tubers, a lectin and an antifungal peptide from northeast red beans, a lectin, an antifungal peptide and a trypsin inhibitor from brown kidney beans, a lectin from French bean cultivar no. 1 and a trypsin inhibitor from mini pinto beans. The small taro hemagglutinin was found to induce mitogenic response in splenocytes. The Japanese yam lectin and northeast red bean hemagglutinin were found to exert anti-proliferative activity toward some tumor cell lines including MCF7 and CNE2 cells. The brown kidney bean lectin induced a mitogenic response from murine splenocytes as well as inhibited the growth of tumor cell lines including MCF7, HepG2, CNE1 and CNE2 cells, while the brown kidney bean antifungal protein inhibited the growth of several pathogenic fungal species including M. arachidicola, S. turcica and B. maydis. Studying the biological activities of these defense proteins helps to find out their potential applications like therapeutic uses. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Chan, Yau Sang. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves i-xvii). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Abstract --- p.i-ii / 論文摘要 --- p.iii / Acknowledgements --- p.iv / List of Publications --- p.v / Table of Contents --- p.vi-vii / List of Figures --- p.viii-ix / List of Tables --- p.x / List of Abbreviations --- p.xi / Chapter Chapter 1 --- Introduction on plant defense proteins / Chapter 1.1 --- General introduction to plant defense proteins --- p.1-2 / Chapter 1.2 --- An overview on lectins --- p.3-18 / Chapter 1.2.1 --- History of lectins --- p.3-6 / Chapter 1.2.2 --- Classification of lectins --- p.7-11 / Chapter 1.2.3 --- Biological activities of lectins --- p.12-16 / Chapter 1.2.4 --- Applications of plant lectins --- p.16-18 / Chapter 1.3 --- An overview on defensins --- p.18-25 / Chapter 1.3.1 --- Types of defensins --- p.18-21 / Chapter 1.3.2 --- Mechanism of anti-microbial activity of defensins --- p.22-23 / Chapter 1.3.3 --- Application of defensins --- p.23-25 / Chapter 1.4 --- An overview on trypsin inhibitors --- p.25-38 / Chapter 1.4.1 --- Serpins --- p.26-28 / Chapter 1.4.2 --- Kunitz-type protease inhibitors --- p.29-31 / Chapter 1.4.3 --- Bowman-Birk protease inhibitors --- p.32-34 / Chapter 1.4.4 --- Physiological functions of protease inhibitors --- p.35-38 / Chapter 1.5 --- Aim of study --- p.38-41 / Chapter Chapter 2 --- Isolation and characterization of a hemagglutinin from small taros and a lectin from yam tubers / Chapter 2.1 --- Introduction --- p.42-45 / Chapter 2.2 --- Materials and Methods --- p.46-55 / Chapter 2.3 --- Results --- p.56-78 / Chapter 2.4 --- Discussion --- p.79-84 / Chapter Chapter 3 --- Isolation and characterization of two defense proteins from seeds of Phaseolus vulgaris cv. “northeast red bean“ / Chapter 3.1 --- Introduction --- p.85-86 / Chapter 3.2 --- Materials and Methods --- p.87-93 / Chapter 3.3 --- Results --- p.93-119 / Chapter 3.4 --- Discussion --- p.120-129 / Chapter Chapter 4 --- Isolation and characterization of three defense proteins from seeds of Phaseolus vulgaris cv. “brown kidney bean“ / Chapter 4.1 --- Introduction --- p.130-131 / Chapter 4.2 --- Materials and Methods --- p.131-136 / Chapter 4.3 --- Results --- p.136-175 / Chapter 4.4 --- Discussion --- p.176-189 / Chapter Chapter 5 --- Isolation and characterization of a lectin from French bean cultivar no. 1 beans and a trypsin inhibitor from mini pinto beans / Chapter 5.1 --- Introduction --- p.190-191 / Chapter 5.2 --- Materials and Methods --- p.191-194 / Chapter 5.3 --- Results --- p.195-212 / Chapter 5.4 --- Discussion --- p.213-221 / Chapter Chapter 6 --- General discussion / Chapter 6.1 --- Summary on purification protocols of the defense proteins in the study --- p.222-228 / Chapter 6.2 --- Chemical properties of the defense proteins in the study --- p.228-232 / Chapter 6.3 --- Biological activities of the defense proteins in the study --- p.232-238 / Chapter 6.4 --- Potential application of these defense proteins and future perspectives --- p.238-242 / References --- p.i-xvi

A existência de uma proteína mitocondrial desacopladora em plantas, PUMP, foi demonstrada em 1995. A PUMP, como a proteína desacopladora de mitocôndrias de tecido adiposo marrom, UCP1, e outras proteínas homólogas descobertas posteriormente, aumenta a condutividade de membrana a H+. Nucleotídeos de purina, PN, inibem a atividade das proteínas desacopladoras e o mecanismo de condução de H+ depende da presença de ácidos graxos livres, FFA. A atividade e a expressão da PUMP são estimuladas pela exposição ao frio e mudam durante o amadurecimento de frutos. A expressão do gene da PUMP de Arabidopsis thaliana em E. coli permite a obtenção de AtPUMP. Neste trabalho, analisando a funcionalidade da AtPUMP incorporada em proteolipossomos, demonstramos que esta proteína é funcional. A incorporação de proteínas desacopladoras em proteolipossomos fornece um sistema modelo que permite analisar as suas propriedades funcionais e mecanísticas. A condutância a H+ em proteolipossomos contendo PUMP isolada de batata foi claramente ativada por FFA. Contudo, a inibição por PN não se mostrou reprodutível. A AtPUMP, reconstituída em proteolipossomos, foi ativada por FFA com Km\'s aparentes de: 42 µM (ácido linoleico, LA), 55 µM (ácido láurico) e 70 µM (ácido palmítico), e inibida por PN com Ki\'s aparentes de: 0.8 mM (GDP), 0.85 mM (ATP), 0.98 mM (GTP) e 1.4 mM (ADP). O efluxo de H+ ativado por LA mediado por AtPUMP aumentou exponencialmente em função do potencial transmembrânico (Δψ). O coeficiente de partição (KP) entre a fase aquosa e proteolipossomos contendo AtPUMP para o LA de 64170, foi ~1,6 vezes superior que ao KP obtido para o LA em lipossomos. Em ensaios de ligação obtidos usando microcalorimetria de titulação isotérmica (ITC), determinou-se que a AtPUMP tem, provavelmente, dois sítios de ligação para o LA e que essa interação é exotérmica. Em ensaios de microcalorimetria com suspensão de mitocôndrias de batatas, determinou-se que há uma correlação linear entre o calor produzido e o oxigênio consumido (65,6 kcal/mol O2) quando a PUMP foi ativada por LA. Através dos resultados obtidos até então, concluo que a PUMP (AtPUMP) é um desacoplador mitocondrial presente em plantas. Os estudos apresentados aqui, de reconstituição em lipossomos, foram essenciais para a compreensão da regulação da atividade dessa proteína. Além disso, foram obtidas as primeiras medidas diretas de liberação de calor pela PUMP por microcalorimetria. / In 1995, a plant mitochondrial uncoupling protein, PUMP, was first described. PUMP, like the known uncoupling protein from brown adipose tissue, UCP1, increases the inner mitochondrial membrane permeability to H+. H+ transport is dependent on the presence of free fatty acids, FFA, and it is inhibited by purine nucleotides, PN. PUMP expression and activity are stimulated by cold exposure, which may vary during fruit ripening. By expressing a full length cDNA encoding the Arabidopsis UCP in E. coli, the recombinant AtPUMP was obtained. In this study, AtPUMP was incorporated in proteoliposomes and the functionality of the protein was demonstrated. The incorporation of uncoupling proteins in proteoliposomes constitutes a model that allows the functional and the mechanistic analysis of these proteins. The H+ conductance mediated by reconstituted potato PUMP was, undoubtedly, activated by FFA. However, the inhibition by PN was not reproducible. Reconstituted AtPUMP was activated by FFA and the apparent Km\'s were determined: 42 µM (linoleic acid, LA), 55 µM (lauric acid) and 70 µM (palmitic acid). Reconstituted AtPUMP was inhibited by PN, and the apparent Kis were determined: 0.8 mM (GDP), 0.85 mM (ATP), 0.98 mM (GTP) and 1.4 mM (ADP). AtPUMP mediated H+ efflux rate, activated by LA, was exponentially dependent on membrane potential (Δψ). The partition coefficient (KP) between the aqueous phase and the membrane phase was determined for LA. The KP was 1.6 times higher for AtPUMP proteoliposomes than for liposomes. Using Isothermal Titration Microcalorimetry (ITC), we verified that there is a linear correlation between the heat produced and oxygen depletion (65,2 kcal/mol O2) in a suspension of potato mitochondria, when PUMP was activated by LA. Using ITC we also determined that LA might bind to two different sites in AtPUMP. Based on the results obtained, we concluded that PUMP (or AtPUMP) is a plant mitochondrial uncoupler. The reconstitution assays permitted the study of FFA and PN regulation. In addition, our results represent the first direct confirmation that fatty acids regulate heat release in plant mitochondria, a process that may play a role in cold adaptation, fruit ripening and flower blossoming.