Die Verknüpfung einer exergonischen mit einer endergonischen Reaktion zur Ermöglichung der letzteren ist eine in biologischen Systemen weit verbreitete Strategie. Energetisch benachteiligte Elektronenübertragungsreaktionen im Rahmen der reduktiven Aktivierung von Nitrogenasen, Radikal-abhängigen β,α-Dehydratasen, der zu diesen verwandten Benzoyl-CoA-Reduktasen und diversen Cobalamin-abhängigen Methyltransferasen sind gekoppelt an die Hydrolyse von ATP. Der Methylgruppentransfer des reduktiven Acetyl-CoA-Weges von Carboxydothermus hydrogenoformans erfordert den Co(I)-Zustand des Corrinoid/Eisen-Schwefel Proteins (CoFeSP). Um diese superreduzierte Form nach einer oxidativen Inaktivierung zu regenerieren ist ein „Reparaturmechanismus“ erforderlich. Ein offenes Leseraster (orf7), welches möglicherweise für eine reduktive Aktivase von Corrinoid Enzymen (RACE) kodiert, wurde in dem Gencluster der am reduktiven Acetyl-CoA-Weg beteiligten Proteine entdeckt. Im Rahmen dieser Arbeit wurde dieses potenzielle RACE Protein biochemisch und strukturell charakterisiert und die ATP-abhängige reduktive Aktivierung von CoFeSP untersucht. Auf Grundlage der in dieser Arbeit gewonnenen Ergebnisse wurde ein Mechanismus für die ATP-abhängige Aktivierung entworfen. Dieser gibt Einblicke wie die durch ATP-Hydrolyse bereitgestellte Energie einen energetisch ungünstigen Elektronentransfer ermöglichen kann. Hierzu kombiniert RACo das Ausgleichen von Bindungsenergien mit Modulationen am Elektronenakzeptor. Eine vergleichbare Strategie wurde bisher in keinem anderen ATP-abhängigen Elektronenübertragungssystem wie dem von Nitrogenasen, Radikal-abhängigen β,α-Dehydratasen oder Benzoyl-CoA-Reduktasen beobachtet und könnte ein für RACE Proteine allgemein gültige Eigenschaft darstellen. / The principle of coupling an exergonic to an endergonic reaction to enable the latter is a widespread strategy in biological systems. Unfavoured electron transfer reactions in the reductive activation of nitrogenases, radical-dependent β,α-dehydratases and the related benzoyl- CoA reductases, as well as different cobalamin-dependent methyltransferases are coupled to the hydrolysis of ATP. The reductive acetyl-CoA pathway of Carboxydothermus hydrogenoformans relies on the superreduced Co(I)-state of the corrinoid/iron-sulfur protein (CoFeSP) that requires a “repair mechanism” in case of incidental oxidation. An open reading frame (orf7) coding for a putative reductive activase of corrinoid enzymes (RACE) was discovered in the gene cluster of proteins involved in the reductive acetyl-CoA pathway. In this work, this putative RACE protein was biochemically and structurally characterised and the ATP-dependent reductive activation of CoFeSP was investigated. Based on the results of this study, a mechanism for the ATP-dependent reactivation of CoFeSP was deduced providing insights into how the energy provided by ATP could trigger this unfavourable electron transfer. The reductive activator of CoFeSP combines balance of binding energies and modulations of the electron acceptor to promote the uphill electron transfer to CoFeSP. A comparable strategy has not been observed in other ATP-dependent electron transfer systems like nitrogenases, radical-dependent β,α-dehydratases and benzoyl- CoA reductases and could be a universal feature of RACE proteins.

Le domaine de la bioénergie moléculaire concerne le transfert et le stockage d’énergie dans les cellules biologiques. Ce projet s’articule autour de la respiration et plus précisément le mécanisme de pompage de sodium et de protons, et son couplage au transfert d’électrons. Premièrement, nous nous sommes intéressés au pompage d’ions sodium par la NADH : quinone oxidoreductase de la bactérie Vibrio cholerae. L’importance de flavines spécifiques et des résidus acides dans le transfert de sodium ont été démontrée. Par la suite, l’interaction entre protéines, notamment le cytochrome c552 et le fragment CuA de l’oxidase de type ba3 de l’organisme Thermus thermophilus a été étudié. Une réorganisation structurelle induit par le transfert d’électron a été démontrée par la spectroscopie IRTF différentielle. Enfin, dans la dernière partie de ce travail, l’interaction au sein du supercomplex bc1-aa3 de la chaîne respiratoire du Corynebacterium glutamicum a été analysée. / The field of molecular bioenergetics deals with the energy transduction in biological cells. In this project, respiration and more specifically proton and sodium pumping enzymes and their coupling to electron transfer have been in focus. First we have been interested in the Na+-pumping NADH:quinone reductase from Vibrio cholerae which is the entry site of electrons in the respiratory chain of several pathogens. The role of specific flavin cofactors and amino acids involved in Na+ transfer has been shown in a combined IR spectroscopic and electrochemical approach. The interaction between proteins, namely the cytochrome c552 and the CuA fragment from the terminal ba3 oxidase from the organism Thermus thermophilus was then investigated. Structural reorganization during electron transfer was revealed by IR spectroscopy. Finally, in the third part of the project the interaction within the bc1-aa3 supercomplex from the respiratory chain from Corynebacterium glutamicum was analyzed.

Le domaine de la bioénergétique concerne l’étude des échanges et des transformations de l’énergie au sein des organismes vivants. Cette thèse propose une étude électrochimique et spectroscopique de protéines issues de la chaine respiratoire, les oxydases terminales, afin de comprendre l’influence de différentes propriétés de ces enzymes (potentiels des cofacteurs, dépendance pH…) sur leur mécanisme réactionnel. La première partie de ce travail décrit le développement d’une méthode d’immobilisation permettant de conserver l’intégrité et l’activité de ces enzymes. Cette technique a d’abord été utilisée pour étudier l’inhibition de la cytochrome aa3 oxydase de P. denitrificans et a permis de mettre en avant l’importance du transfert de protons sur la réaction de réduction de l’oxygène. Une deuxième étude propose de comparer deux isoformes de la cytochrome cbb3 oxydase dont aucune différence n’a été observée à ce jour. La spectroscopie IRTF couplée à l’électrochimie montre l’implication de résidus acides différents au cours de la réaction d’oxydoréduction suggérant des différences mécanistiques. La dernière partie propose une étude comparative d’oxydases terminales de différents types et met en perspective l’influence des potentiels relatifs des hèmes sur la réaction de réduction de l’oxygène. / The field of bioenergetics concerns the study of exchange and transformation of energy in living organisms. This manuscript proposes an electrochemical and spectroscopic study of the fourth complex of the respiratory chain, the terminal oxidases. The aim of this study was to understand the influence of some properties of these enzymes (potential of the cofactors, pH dependency…) on the catalytic mechanism. The first part describes an immobilization procedure which retains the protein activity and structure. This procedure has been applied for the study the inhibition of the proton pathways of cytochrome aa3 oxidase from P. denitrificans and shows the importance of proton transfer on the oxygen reduction. In a second study, two isoforms of cytochrome cbb3 oxidase were compared. No differences were observed between them until now. Our electrochemically induced FTIR spectroscopy study suggests the implication of different acidic residues during the redox reaction implying differences in the mechanism of these enzymes. The last part deals with the comparison of terminal oxidases of different types and shows the influence of the relative order of the midpoint potentials of the hemes on the oxygen reduction.

Many communities are currently seeking to balance urban water needs with preservation of sensitive fish habitat. As part of that effort, CE-QUAL-W2, a hydrodynamic and temperature model, was developed for Chester Morse Lake and the lower Cedar River, WA. Chester Morse Lake is approximately 10 km long with a maximum depth at full pool of 40 m. The Cedar River model started immediately downstream of the Chester Morse dam and ended 21 km downstream at Landsburg, where drinking water is diverted for the City of Seattle. This water quality model was coupled with a fish habitat and bioenergetics model for bull trout and was calibrated to temperature data between 2005 and 2008. Bull trout fish bioenergetics parameters were provided by the USGS. The CE-QUAL-W2 model was found to be highly accurate in modeling temperature variation in the lake - at most locations having an average absolute mean error of between 0.5 and 0.8 oC. The Cedar River model had an average absolute mean error of 0.7oC. This tool is designed to allow managers and operators to estimate the impact to fish habitat and growth potential from various management decisions including extent of drawdown, timing/volume of flows, and various pumping operations. Future studies could include incorporating further water quality parameters such as nutrients, algae, and zooplankton as they relate to fish productivity.

Indiana University-Purdue University Indianapolis (IUPUI) / The multi-protein complex of F0F1 ATP synthase has been of great interest in the fields of microbiology and biochemistry, due to the ubiquitous use of ATP as a biological energy source. Efforts to better understand this complex have been made through structural determination of segments based on NMR and crystallographic data. Some experiments have provided useful data, while others have brought up more questions, especially when structures and functions are compared between bacteria and species with chloroplasts or mitochondria. The epsilon subunit is thought to play a signi cant role in the regulation of ATP synthesis and hydrolysis, yet the exact pathway is unknown due to the experimental difficulty in obtaining data along the transition pathway. Given starting and end point protein crystal structures, the transition pathway of the epsilon subunit was examined through computer simulation.The purpose of this investigation is to determine the likelihood of one such proposed mechanism for the involvement of the epsilon subunit in ATP regulation in bacterial species such as E. coli.

Body size explains much of the interspecific variation in the physiology, behavior, and morphology of birds, such as metabolic rate, diet selection, intake rate, gut size, and bill size. Based on mass-specific metabolic requirements and relative energetic costs of activities, being a certain body size has both advantages and disadvantages. In particular, avian herbivores such as geese possess a relatively simple digestive system, consume foods with low digestibility and poor nutrient content, and have increased energetic demands compared to other bird taxa; therefore, any effects of body size on foraging strategies should be readily apparent in this foraging guild. The influence of body size on the behavior and management of Canada Geese (Branta canadensis) and Cackling Geese (B. hutchinsii) as avian herbivores has not been well studied. My dissertation explores the role of body size in comparative foraging behavior, habitat selection, and winter conservation planning for two congeneric geese, the Dusky Canada Goose (B. c. occidentalis; hereafter Duskys) and the Cackling Goose (B. h. minima; hereafter Cacklers). These two taxa share the same over-winter foraging environment (grass seed fields) in the same restricted geographic area (the Willamette Valley) during winter. Duskys and Cacklers differ by more than a factor of two in body size and have different relative bill sizes and social organization. Because of smaller body size, Cacklers have greater relative energy demands and less fasting endurance compared to Duskys; however, Cacklers have comparatively low energetic costs for flight and transport. Duskys, however, have higher total energy requirements than Cacklers. Additionally, Cacklers form large, high-density flocks and have a total over-wintering population size in the study area of about 200,000. Duskys occur in relatively small family groups and have a total over-wintering population size of about 13,000. My study demonstrated that interspecific differences in body size between Cacklers and Duskys was associated with differences in foraging behavior, movements, and habitat selection. Cacklers foraged a greater percentage of time (30%) in all habitats and across the entire winter compared to Duskys. Cacklers had higher peck rates (up to 100 pecks min⁻¹ greater) than Duskys in all foraging habitats expect pasture. The pecking rate of Cacklers was greatest in fields of young grass (200 pecks min⁻¹), which may indicate that Cacklers had relatively high intake rates in this foraging habitat. Based on differences in foraging behavior among habitats, Cacklers may have the foraging strategy of energy intake maximizers, whereas the foraging strategy of Duskys is more towards time-energy expenditure minimizers, at least for part of the winter. Cacklers moved across the landscape very differently from Duskys, exhibiting less site fidelity and greater commuting distances to foraging areas. Cacklers showed a preference for young grass during all periods of the winter, reaffirming that Cacklers are specialized grazers on short green forage, whereas Duskys preferred young grass and pasture. Fields of young grass were the preferred foraging habitat of Cacklers, had less standing crop biomass, and may have enabled higher foraging efficiencies, which may have led to higher intake rates. The ability of the landscape to support wintering geese changed across the winter because total available plant biomass fluctuated with the rate of grass regrowth. The estimated carrying capacity of the landscape for geese decline by almost one-half during mid-winter (mid-December to mid-February) compared to early winter or late winter periods. Although Cacklers have lower individual energy requirements compared to Duskys, due to a much larger target population size, Cacklers required 89% more foraging habitat than Duskys. Forage requirements encountered a bottleneck during mid-winter, when grass regrowth rates were low and day length was short. Commensurate with this pattern of forage availability, goose body condition declined during the mid-winter period. To support Pacific Flyway target populations for geese, approximately 18,000 ha of total grazing habitat in young and mature grass is needed in the Willamette Valley to support a total over-wintering population composed of 340,000 geese belonging to four subspecies. The role of body size in influencing the foraging behavior and decisions of over-wintering geese has important implications for conservation planning of goose populations. Small-bodied Cacklers are selective in field choice, yet more likely to redistribute across the landscape. Disturbances (e.g., hunting, hazing, or predation) will have a disproportionate effect on the movements of smaller-bodied geese compared to larger geese. These characteristics of Cacklers will make conservation planning to retain geese on public land more difficult. Coordinated management with private landowners and farming practices that maximize preferred goose foraging habitat on public lands may attract geese to utilize protected areas and minimize conflicts with agriculture in the Willamette Valley. Availability of resources during critical periods in winter is an important factor affecting the distribution of geese, but may affect small and large bodied geese differently. Management could be targeted during these critical time periods. By considering the role of body size in the context of life history characteristics, foraging behavior and habitat selection, appropriate management strategies can be developed and implemented to reduce the effects of agricultural depredation by geese, while promoting the future conservation of wintering geese in the Willamette Valley. / Graduation date: 2013

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