<p>Plants use an array of photoreceptors to measure the quality, quantity, and direction of light in order to respond to ever-changing light environments. Photoreceptors not only determine how and when individual plants complete their life cycles, but they also have a profound and long-term macroevolutionary influence on species diversification. Despite their significances, very little is known about photoreceptors across plants as whole, and we lack a comprehensive view of photoreceptor evolution. </p><p> In my dissertation, I investigate the origin and evolution of three of the most prominent photoreceptor gene families in plants: phytochromes, phototropins and neochromes. Using newly available transcriptomic and genomic data, I completed the first in-depth survey of these photoreceptor families across land plants, green algae, red algae, glaucophytes, cryptophytes, haptophytes, and stramenopiles. </p><p> Phytochromes are red/far-red photoreceptors that play essential roles in seed germination, seedling photomorphogenesis, shade-avoidance, dormancy, circadian rhythm, phototropism, and flowering. Here, I show that the canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte green algae plus land plants), and I identify the most likely sequence whereby the plant phytochrome structure evolved from its ancestral phytochrome. Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts, and Selaginella apparently possess a single phytochrome gene copy, whereas independent gene duplications occurred within mosses, lycopods, ferns, and seed plants, leading to diverse phytochrome families in these clades. My detailed phylogeny encompasses all of green plants and enables me to not only uncover new phytochrome lineages, but also to make links to our current understanding of phytochrome function in Arabidopsis and Physcomitrella (the major model organism outside of flowering plants). Based on this robust evolutionary framework, I propose new hypotheses and discuss future directions to study phytochrome mechanisms.</p><p> Phototropins are blue-light photoreceptors that regulate key adaptive physiological responses, including shoot-positive phototropism, root-negative phototropism, chloroplast accumulation/avoidance, stomatal opening, circadian rhythm, leaf expansion, and seedling elongation I show that phototropins originated in the common ancestor of Viridiplantae (all green algae [charophytes, chlorophytes, prasinophytes] plus land plants). Phototropins repeatedly underwent independent duplications in all major plant lineages (mosses, lycopods, ferns and seed plants), except for liverworts and hornworts, where phototropin is a single-copy gene. Following each major duplication event, phototropins subsequently differentiated in parallel, resulting in two specialized (yet partially overlapping) functional forms that primarily mediate either low- or high-light responses. My gene phylogeny further suggests that phototropins have co-evolved with phytochromes, as is evident from their molecular interactions and strikingly similar gene duplication patterns. I hypothesize that the co-evolution of phototropins with phytochromes, together with their subsequent convergent functional divergences in phototropic responses, contributed to the success of plants in adapting to diverse and heterogeneous habitats.</p><p> Neochromes are chimeric photoreceptors that, by fusing phytochrome and phototropin modules into a single protein, are able to use both red/far-red and blue light to modulate phototropic responses. Neochromes were first discovered in ferns, and the evolution of neochromes was implicated as a key innovation that facilitated fern diversification under the low-light angiosperm canopies. Despite its significance from an evolutionary standpoint, the origin of neochromes has remained a mystery. Here I present the first evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in my large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 MYA, long after the split between the two plant lineages (at least 400 MYA). By analyzing the draft genome of the Anthoceros punctatus hornwort, I also discovered a novel phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was horizontally transferred to ferns, where it may have played a significant role in the diversification of modern ferns. </p><p> In summary, my studies identified the molecular origins of phytochromes, phototropins and neochromes, and reconstructed their respective evolutionary histories. This new framework for photoreceptor evolution will stimulate new research linking ecology, evolution, and photochemistry to understand how plants adapt to variable light environments.</p> / Dissertation

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-05-02T15:05:38Z No. of bitstreams: 2 Dissertação - Emiliana Licio Mereb - 2017.pdf: 2633385 bytes, checksum: 1abd0e2ce7a888be7e5a1703b59f061f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-05-02T15:05:53Z (GMT) No. of bitstreams: 2 Dissertação - Emiliana Licio Mereb - 2017.pdf: 2633385 bytes, checksum: 1abd0e2ce7a888be7e5a1703b59f061f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-05-02T15:05:53Z (GMT). No. of bitstreams: 2 Dissertação - Emiliana Licio Mereb - 2017.pdf: 2633385 bytes, checksum: 1abd0e2ce7a888be7e5a1703b59f061f (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Phytochromes are protein pigments related to the qualitative and quantitative absorption of light by plants, translating it into biochemical signals that influence plant growth and development. In tomato, fri mutant shows deficiency in the phytochrome A, the mutant tri, deficiency phytochrome B1 and phyB2 mutant is deficient in phytochrome B2. In this paper we analyzed the effects of these changes when the cultivation of plants in the sun and shade treatments by analysis the growth and assimilates partition, photosynthetic rates (A), stomatal conductance (gs), transpiration (E), chlorophyll fluorescence and chlorophyll and carotenoid content in tomato mutants photomorphogenic fri, tri, phyB2 and wild genotype Moneymaker. The plants were grown in a greenhouse and featured throughout its development. The fri and tri mutant exhibited lower total leaf area than the other genotypes in both treatments. All genotypes were taller in shade treatment, and in these conditions the mutant tri presented greater height than the other genotypes. The photosynthetic rate was higher in sun condition, and phyB2 mutant subjected to shading exhibited higher A than the other genotypes. Under sunny conditions were observed lower amounts of chlorophyll a and carotenoid in the tri mutant compared to other genotypes. Fri and tri mutants showed lower potential quantum yield (Fv / Fm) and effective (Fq '/ Fm') of photosystem II in shade conditions. Lower values of Fq '/ Fm' were observed in tri mutant under shady when compared to other genotypes. In both treatments mutants showed higher dry biomass values of roots / total dry weight in relation to control genotype, and 130 DAE fri mutant exhibited reduction of this parameter. Assimilates allocation to 130 DAE in leaves was higher in fri mutants, tri, and phyB2 compared to the wild genotype, which showed the highest dry mass ratio of fruit / total dry mass compared to the mutants.. The area of the vessel element was for the fri mutant in comparison to the other genotypes. The stomatal density of the abaxial face was higher for the fri and phyB2 mutants in sun condition. The thickness of the adaxial epidermal cells, the paliquadic and spongy parenchyma, and the xylem thickness were greater in the sun condition in relation to the shade, greater in the sun condition in relation to the shade. It is concluded that the analyzed characteristics are influenced by specific phytochrome in the studied species and the action of phytochrome differs in sun and shade conditions. / Fitocromos são pigmentos proteicos relacionados com a assimilação qualitativa e quantitativa da luz pelas plantas, traduzindo-a em sinais bioquímicos capazes de influenciar o crescimento e desenvolvimento vegetal. Em tomateiros, o mutante fri, apresenta deficiência no fitocromo A, o mutante tri, deficiência de fitocromo B1 e o mutante phyB2 é deficiente no fitocromo B2. Neste trabalho foram analisados os efeitos dessas mutações quando do cultivo das plantas nos tratamentos sol e sombra, analisando aspectos morfométricos e partição de fotoassimilados, aspectos da anatomia foliar e caulinar, taxas de fotossíntese (A), condutância estomática (gs), transpiração (E), fluorescência da clorofila e conteúdo de clorofila e carotenoides de tomateiros mutantes fotomorfogenéticos fri, tri, phyB2 e o genótipo selvagem Moneymaker. As plantas foram cultivadas em casa de vegetação e caracterizadas ao logo do seu desenvolvimento. O mutante fri e tri obtiveram menor área foliar total que os demais genótipos em ambos os tratamentos. Todos os genótipos apresentaram-se maiores no tratamento sombra, e nestas condições o mutante tri apresentou maior altura que os demais genótipos. A taxa fotossintética foi maior na condição de sol, e o mutante phyB2 submetido ao sombreamento exibiu maior A que os demais genótipos. Em condições de sol foram observadas menores quantidades de clorofila a e carotenoides no mutante tri em relação aos demais genótipos. Os mutantes fri e tri exibiram menor rendimento quântico potencial (Fv/Fm) e efetivo (Fq’/Fm’) do fotossistema II em condições de sombra. Menores valores de Fq’/Fm’ foram observados no mutante tri sob sombreamento quando comparados aos demais genótipos. Em ambos os tratamentos os mutantes apresentaram maiores valores de biomassa seca das raízes/massa seca total em relação ao genótipo controle, e aos 130 DAE o mutante fri exibiu redução desse parâmetro. Alocação de fotoassimilados aos 130 DAE em folhas foi maior nos mutantes fri, tri, e phyB2 comparativamente ao genótipo selvagem, que deteve maior razão massa seca dos frutos/massa seca total em comparação aos mutantes. A área do elemento de vaso foi menor para o mutante fri em comparação aos demais genótipos. A densidade estomática da face abaxial foi maior para os mutantes fri e phyB2 na condição de sol. A altura das células epidérmicas da face adaxial, os parênquimas paliçádico e esponjoso e a espessura do xilema foram maiores na condição de sol em relação à sombra. Conclui-se que as características analisadas são influenciadas por fitocromos específicos na espécie estudada e que a ação dos fitocromos difere nas condições de sol e sombra.

Wheat (triticum aestivum, L.) plants were exposed to three different levels of phytochrome photoequilibria (φ), two different photoperiods, end-of-day far-red radiation, two different levels of blue (400-500 nm) light, three levels of photosynthetic photon flux (PPF), and two types of high intensity discharge lamp types. Tillering was reduced by lowered φ, by reduced amounts on blue light and by end-of-day far-red. Main culm development was increased by lowered φ, by increased PPF, and was reduced by shortened photoperiod and by reduced blue light. Leaf length was increased by increased PPF, lowered φ, and reduced blue light but was not affected by photoperiod, end-of-day far-red or lamp type. Dry-mass accumulation increased under increasing PPF but was unaffected by other treatment in these experiments.

No description available.

Many species of bacteria naturally exist in multicellular structures called biofilms, which are formed when microbes excrete an adherent polymeric matrix. The biofilm lifestyle offers protection from environmental attacks. However, the high density of biomass within these structures also promotes the formation of resource gradients and therefore internal microenvironments with distinct conditions. Unlike the well-mixed liquid cultures routinely used for research, biofilms thus contain differentiated subpopulations that perform different metabolic processes. Such metabolic heterogeneity benefits multicellular systems by allowing for division of labor and cross-feeding of metabolites. Importantly, it also contributes to the robustness of the overall population because metabolic subpopulations commonly differ with respect to their abilities to survive environmental changes or drug treatments. Pseudomonas aeruginosa is a chemotrophic opportunistic pathogen that avidly forms biofilms. It is a leading cause of infections in humans and can occupy a variety of sites, including burn and non-healing skin wounds. One factor that allows the bacterium to thrive in a wide range of environments is its metabolic versatility. P. aeruginosa is able to use oxygen and N-oxides as terminal electron acceptors and produces redox active small molecules called phenazines that support metabolic activity in oxygen-limited biofilm subzones. In many of the environments it inhabits P. aeruginosa is exposed to sunlight, which can act as an environmental cue and can damage light-sensitive enzymes. Light sensing proteins are found in diverse chemotrophic bacteria and have been studied structurally and biochemically for decades. In fact, the bacteriophytochrome BphP, purified from P. aeruginosa, was identified and biochemically characterized in the 1990’s. The physiological role of BphP, and light sensing in general, is still an active field of study. Recently light has been shown to play roles in inhibiting biofilm macrostructure formation, inhibiting aerobic respiration, and providing anticipatory protection from osmotic stress in various pseudomonads. My thesis aims to investigate how light affects metabolism in P. aeruginosa biofilms. Chapter 1 provides the necessary background about bacterial multicellularity, light as an environmental factor, and the relevant aspects of P. aeruginosa metabolism. Chapter 2 explores the phenomenon of the inhibitory effect of light on aerobic respiration. Light/dark and temperature cycling elicits transcriptomically entrenched rings of high and low aerobic respiration which is not restricted to a singular color of light within the visible light spectrum. This chapter also highlights the role of the bacteriophytochrome BphP in red light-dependent respiratory switching. Chapter 3 further explores how the light effect is altered in response to changing the redox state of the biofilm. Light has distinct effects on the use of specific respiratory pathways, on oxygen consumption, and on metabolic activity based on the location in the biofilm and the availability of electron acceptors. Chapter 4 identifies the white light and red light-dependent proteome of P. aeruginosa biofilms and additionally determines the red light-dependent BphP regulon. This chapter also highlights how conversion of BphP between photostates is necessary for red light-dependent respiratory switching in P. aeruginosa biofilms. Understanding how P. aeruginosa metabolism is modulated by light provides information as to how this bacterium thrives in diverse environments, and investigating the phenomenon in a biofilm model expands the relevance of this research. Because they define the relationships between light exposure and physiological responses in an important pathogen, the observations presented in this thesis constitute foundational work with the potential to inform treatment conditions for biofilm based infections.

This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

No description available.

Diss. (sammanfattning) Alnarp : Sveriges lantbruksuniv. / Härtill 4 uppsatser.

Thesis (Ph. D.)--State University of New York at Binghamton, Department of Biological Sciences, 2009. / Includes bibliographical references.

Muitas respostas moduladas pela luz durante o desenvolvimento das plantas também são reguladas por hormônios vegetais, levando à hipótese da interação entre ambos os fatores. Uma ferramenta valiosa para testar tal interação seria o uso de mutantes fotomorfogenéticos e hormonais, bem como duplos mutantes combinando ambos. Em tomateiro, embora sejam disponíveis mutantes com alterações na biossíntese de fotorreceptores e/ou na transdução do sinal da luz, bem como mutantes no metabolismo e/ou sensibilidade hormonal, esses estão presentes em cultivares diferentes, o que pode limitar seu uso de modo integrado e a construção de duplos mutantes. No presente trabalho, foram introgredidas em uma única cultivar de tomateiro, Micro-Tom (cv. MT), dezenove mutações afetando a biossíntese ou a resposta a fitocromo, bem como aos hormônios auxina (AUX), citocinina (CK), giberelina (GA), ácido abscísico (ABA), etileno (ET) e brassinoesteróides (BR). Tomando-se vantagem de tal coleção, duas respostas notadamente controladas tanto pela luz quanto por hormônios foram estudadas: alongamento e acúmulo de antocianinas em hipocótilos. Para tal, foram utilizadas as seguintes abordagens: i) tratamentos exógenos de diferentes classes hormonais em mutantes fotomorfogenéticos, ii) observação de hipocótilos de mutantes hormonais crescidos na luz e no escuro, iii) observação de duplos mutantes combinando mutações hormonais e fotomorfogenéticas. Assim, o acúmulo de antocianinas foi promovido pela CK e ABA e inibido pela GA, concordando com a redução no mutante deficiente em ABA (notabilis ou not) e no mutante hipersensível à GA (procera ou pro). Apesar do mutante com baixa sensibilidade à AUX (diageotropica ou dgt) acumular exageradamente antocianinas, a aplicação exógena não evidenciou o papel da AUX, sendo, porém, coerente com a sugestão de que esse mutante possui um balanço AUX/CK voltado para CK. Tanto a aplicação exógena quanto a avaliação nos mutantes epinastic (epi), super produção de ET, e Never ripe (Nr), baixa sensibilidade ao ET, sugerem uma função limitada desse hormônio na biossíntese de antocianinas. Na luz e no escuro, AUX, CK, ABA e ET exógenos resultaram na inibição do alongamento do hipocótilo, sendo coerente com a promoção em dgt (luz), promoção em sit (luz), inibição em epi (luz e escuro). Por outro lado, GA promoveu o alongamento corroborando a promoção em pro. Contrariando o efeito exógeno da CK, brt reduziu o alongamento na luz e no escuro. No escuro, o único mutante que apresentou alongamento do hipocótilo superior a MT foi o mutante deficiente na biossíntese do phy (aurea ou au). A utilização de duplos mutantes combinando phy- e alterações hormonais mostrou uma interação aditiva (au epi, au Nr, au dgt e au sit), sinergística (au pro) e epinástica (au brt) no acúmulo de antocianinas e alongamento do hipocótilo na luz, porém nessa última resposta, au dgt e au sit indicaram uma interação sinergística. Juntos, esses resultados indicam que, embora phy possui vias distintas da AUX, ET, ABA e GA no controle do acúmulo de antocianinas e alongamento do hipocótilo, parece que esse fotorreceptor partilha vias comuns com CK em ambas as respostas. / Many responses regulated by light during plant development are also regulated by plant hormones, suggesting an interaction between these factors. One important approach to test this hypothesis is the use of photomorphogenic and hormonal mutants and double mutant analysis. Mutants with altered photoreceptor biosynthesis, light signal transduction, hormonal metabolism and hormonal sensitivity are available in tomato. However, since they are in different cultivars, this can be a limitation for their use in a comprehensive study, as well as, for the construction of double mutants. In this work we performed the introgression of nineteen mutations in a single cultivar of tomato, Micro- Tom (cv. MT). These mutations affect biosynthesis or response to phytochrome (phy), auxin (AUX), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), ethylene (ET) and brassinosteroid (BR). Using this collection of hormone mutants, we studied two responses which are controlled by light and hormones: elongation and anthocyanin accumulation in hypocotyls. For this purpose, we used three approaches: i) hormonal treatment in the photomorphogenic mutants, ii) measurement of hypocotyl lengths from hormonal mutants grown under light and dark conditions and iii) double mutant (photomorphogenic-hormonal) analysis. Anthocyanin accumulation was promoted by CK and ABA and inhibited by GA. This is in accordance with the reduction of anthocyanin accumulation in the ABA deficient mutant (not) and in the GA hypersensitive mutant (pro). Although the diageotropica (dgt), auxin-insensitive mutant, showed a high anthocyanin accumulation, the addition of auxin did not supported a role for this hormone in anthocyanin accumulation. On the other hand, this could be due to a low auxin-tocytokinin ratio presented by dgt. Data from mutants with altered metabolism and sensitivity of ethylene, epinastic (epi) and Never ripe (Nr) respectively, and from plants treated with this hormone suggest a limited role of ethylene in the anthocyanin biosynthesis. Exogenous AUX, CK, ABA and ET inhibited the hypocotyl elongation. This is coherent with the promotion of hypocotyl elongation in dgt and sit mutants under light conditions and inhibition of hypocotyl elongation in the epi mutant in the light and dark. On the other hand, GA promoted the hypocotyl elongation corroborating the same effect seen in pro. The brt mutant showed a reduced hypocotyl elongation in light and dark conditions, which contradicts the effect of exogenous cytokinin. The phytochromedeficient aurea (au) mutant was the only one to show an enhanced hypocotyl elongation in the dark compared to the wild type (MT). The combination between photomorphogenic and hormonal mutants (double mutants) showed additive (au epi, au Nr, au dgt e au sit), synergistic (au pro) and epistatic (au brt) interactions considering the anthocyanin accumulation and hypocotyl elongation. Synergistic interaction was observed in the elongation hypocotyl of the au dgt and au sit double mutants. These results indicate that phy and CK may share some signaling/metabolic pathways in the control of anthocyanin accumulation and hypocotyl elongation. On the other hand, our data do not support an interaction between phy and the hormones AUX, ET, ABA and GA in the control of hypocotyls elongation or anthocyanin accumulation.