Orthologous and heterologous expression of a protein from Saccharomyces cerevisiae: Optimization for a biotechnological application

In this thesis (TFG) the results of the comparison between different methods to obtain a recombinant protein, by orthologous and heterologous expression, are exposed. This study will help us to identify the best way to express and purify a recombinant protein that will be used for biotechnology applications. In the first part of the project the goal was to find the best expression and purification system to obtain the recombinant protein of interest. To achieve this objective, a system expression in bacteria and in yeast was designed. The DNA was cloned into two different expression vectors to create a fusion protein with two different tags, and the expression of the protein was induced by IPTG or glucose. Additionally, in yeast, two promoters where used to express the protein, the one corresponding to the same protein (orthologous expression), and the ENO2 promoter (heterologous expression). The protein of interest is a NAD-dependent enzyme so, in a second time, its specific activity was evaluated by coenzyme conversion. The results of the TFG suggest that, comparing the model organisms, bacteria are more efficient than yeast because the quantity of protein obtained is higher and better purified. Regarding yeast, comparing the two expression mechanisms that were designed, heterologous expression works much better than the orthologous expression, so in case that we want to use yeast as expression model for the protein of interest, ENO2 will be the best option. Finally, the enzymatic assays, done to compare the effectiveness of the different expression mechanisms respect to the protein activity, revealed that the protein purified in yeast had more activity in converting the NAD coenzyme.

Evolutionary analysis of mitogenomes from parasitic and free-living flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

Muscarinic toxins : characterization of adrenoceptor binding and applicability of membrane anchoring via glycosylphosphatidylinositol tail

Adrenoceptors (ARs), G-protein coupled receptors (GPCRs) at the plasma membrane, respond to endogenous catecholamines noradrenaline and adrenaline. These receptors mediate several important physiological functions being especially important in the cardiovascular system and in the regulation of smooth muscle contraction. Impairments in the function of these receptors can thus lead to severe diseases and disorders such as to cardiovascular diseases and benign prostatic hyperplasia. The Eastern green mamba (Dendroaspis angusticeps) venom has been shown to contain toxins that can antagonize the functions of GPCRs. The most well-known are muscarinic toxins (MTs) targeting muscarinic acetylcholine receptors (mAChRs) with high affinity and selectivity. However, some reports have indicated that these toxins might also act on the α1- and α2-ARs which can be divided into various subtypes; the α1-ARs to α1A-, α1B- and α1D-ARs and α2-ARs to α2A-, α2B- and α2C-ARs. In this thesis, the interaction of four common MTs (MT1, MT3, MT7 and MTα) with the adrenoceptors was characterized. It was also evaluated whether these toxins could be anchored to the plasma membrane via glycosylphosphatidylinositol (GPI) tail. Results of this thesis reveal that muscarinic toxins are targeting several α-adrenoceptor subtypes in addition to their previously identified target receptors, mAChRs. MTα was found to interact with high affinity and selectivity with the α2B-AR whereas MT7 confirmed its selectivity for the M1 mAChR. Unlike MTα and MT7, MT1 and MT3 have a broad range of target receptors among the α-ARs. All the MTs characterized were found to behave as non-competitive antagonists of receptor action. The interaction between MTα and the α2B-AR was studied more closely and it was observed that the second extracellular loop of the receptor functions as a structural entity enabling toxin binding. The binding of MTα to the α2B-AR appears to be rather complex and probably involves dimerized receptor. Anchoring MTs to the plasma membrane did not interfere with their pharmacological profile; all the GPI-anchored toxins created retained their ability to block their target receptors. This thesis shows that muscarinic toxins are able to target several subtypes of α-ARs and mAChRs. These toxins offer thus a possibility to create new subtype specific ligands for the α-AR subtypes. Membrane anchored MTs on the other hand could be used to block α-AR and mAChR actions in disease conditions such as in hypertension and in gastrointestinal and urinary bladder disorders in a cell-specific manner and to study the physiological functions of ARs and mAChRs in vivo in model organisms.

Inducing mutations in the mouse genome with the chemical mutagen ethylnitrosourea

When compared to other model organisms whose genome is sequenced, the number of mutations identified in the mouse appears extremely reduced and this situation seriously hampers our understanding of mammalian gene function(s). Another important consequence of this shortage is that a majority of human genetic diseases still await an animal model. To improve the situation, two strategies are currently used: the first makes use of embryonic stem cells, in which one can induce knockout mutations almost at will; the second consists of a genome-wide random chemical mutagenesis, followed by screening for mutant phenotypes and subsequent identification of the genetic alteration(s). Several projects are now in progress making use of one or the other of these strategies. Here, we report an original effort where we mutagenized BALB/c males, with the mutagen ethylnitrosourea. Offspring of these males were screened for dominant mutations and a three-generation breeding protocol was set to recover recessive mutations. Eleven mutations were identified (one dominant and ten recessives). Three of these mutations are new alleles (Otop1mlh, Foxn1sepe and probably rodador) at loci where mutations have already been reported, while 4 are new and original alleles (carc, eqlb, frqz, and Sacc). This result indicates that the mouse genome, as expected, is far from being saturated with mutations. More mutations would certainly be discovered using more sophisticated phenotyping protocols. Seven of the 11 new mutant alleles induced in our experiment have been localized on the genetic map as a first step towards positional cloning.

Pharmacology and toxicology of diphenyl diselenide in several biological models

The pharmacology of synthetic organoselenium compounds indicates that they can be used as antioxidants, enzyme inhibitors, neuroprotectors, anti-tumor and anti-infectious agents, and immunomodulators. In this review, we focus on the effects of diphenyl diselenide (DPDS) in various biological model organisms. DPDS possesses antioxidant activity, confirmed in several in vitro and in vivo systems, and thus has a protective effect against hepatic, renal and gastric injuries, in addition to its neuroprotective activity. The activity of the compound on the central nervous system has been studied since DPDS has lipophilic characteristics, increasing adenylyl cyclase activity and inhibiting glutamate and MK-801 binding to rat synaptic membranes. Systemic administration facilitates the formation of long-term object recognition memory in mice and has a protective effect against brain ischemia and on reserpine-induced orofacial dyskinesia in rats. On the other hand, DPDS may be toxic, mainly because of its interaction with thiol groups. In the yeast Saccharomyces cerevisiae, the molecule acts as a pro-oxidant by depleting free glutathione. Administration to mice during cadmium intoxication has the opposite effect, reducing oxidative stress in various tissues. DPDS is a potent inhibitor of d-aminolevulinate dehydratase and chronic exposure to high doses of this compound has central effects on mouse brain, as well as liver and renal toxicity. Genotoxicity of this compound has been assessed in bacteria, haploid and diploid yeast and in a tumor cell line.

Le vieillissement chronologique de Schizosaccharomyces pombe : Implication des voies de détection du glucose

La première augmentation de la longévité en laboratoire fût observée à la suite d’une intervention nutritionnelle consistant en une réduction de l’apport alimentaire chez le rat. Plus tard, ce phénomène a été reproduit dans de très nombreuses espèces et référé en tant que restriction calorique. Le développement des techniques de biologie moléculaire moderne a permis de montrer dans des organismes modèles simples que cette flexibilité du processus de vieillissement était régulée par des facteurs génétiques. De fait, plusieurs mécanismes cellulaires ont alors pu être identifiés comme responsables de ce contrôle du vieillissement. Ces voies de régulation ont révélées être conservées entre les espèces, depuis les levures jusqu’aux organismes multicellulaires tels que le nématode, la mouche ou la souris, suggérant l’existence d’un programme universel de vieillissement dans le vivant. La levure s’est avéré à plusieurs reprises être un modèle puissant et fiable pour la découverte de gènes impliqués dans ce phénomène. Mon étude a consisté au développement d’un nouveau modèle unicellulaire d’étude du vieillissement à travers l’espèce Schizosaccharomyces pombe appelée aussi levure à fission. La première étape de mon travail a montré que les voies de détection des nutriments gouvernées par la sérine/thréonine protéine kinase A (Pka1) et la sérine/thréonine kinase Sck2 contrôlent le vieillissement chronologique de ces cellules comme il était connu dans la levure Saccharomyces cerevisiae. Ceci permit de valider l’utilisation de la levure à fission pour l’étude du vieillissement. Ensuite, nous avons analysé plus en détail l’effet pro-vieillissement du glucose en étudiant le rôle de sa détection par le récepteur membranaire Git3 couplé à la protéine G (Gpa2) en amont de la kinase Pka1. La perte du signal du glucose par la délétion de Git3 imite partiellement l’effet d’augmentation de longévité obtenu par baisse de la concentration en glucose dans le milieu. De plus, l’effet néfaste du signal du glucose est maintenu en absence de tout métabolisme du glucose suite à la mutation des hexokinases, premières enzymes de la glycolyse. L’ensemble de ces résultats suggèrent que la signalisation du glucose est prédominante sur son métabolisme pour son effet pro-vieillissement. D’autre part, à la fois la suppression de cette signalisation et la baisse de niveau de glucose disponible allongent la durée de vie en corrélation avec une augmentation de la résistance au stress, une hausse d’activité mitochondriale et une baisse de production de radicaux libres. Finalement, le criblage d’une banque de surexpression d’ADNc a permis d’identifier plusieurs gènes candidats responsables de ces effets en aval de la voie de signalisation Git3/PKA. La recherche sur les mécanismes moléculaires du vieillissement propose une nouvelle approche, un nouvel angle de vue, pour la compréhension des fonctions cellulaires et promet d’apporter de précieuses clefs pour mieux comprendre certaines maladies. En effet, le vieillissement est la première cause d’apparition de nombreuses affections comme les cancers, les maladies cardiovasculaires et métaboliques ou les maladies neurodégénératives tels que les syndromes d’Alzheimer et de Parkinson.

Developmental, morphological, and behavioural plasticity in the reproductive strategies of stink bugs and their egg parasitoids

L’environnement façonne la physiologie, la morphologie et le comportement des organismes par l’entremise de processus écologiques et évolutifs complexes et multidimensionnels. Le succès reproducteur des animaux est déterminé par la valeur adaptative d’un phénotype dans un environnement en modification constante selon une échelle temporelle d’une à plusieurs générations. De plus, les phénotypes sont façonnés par l’environnement, ce qui entraine des modifications adaptatives des stratégies de reproduction tout en imposant des contraintes. Dans cette thèse, considérant des punaises et leurs parasitoïdes comme organismes modèles, j’ai investigué comment plusieurs types de plasticité peuvent interagir pour influencer la valeur adaptative, et comment la plasticité des stratégies de reproduction répond à plusieurs composantes des changements environnementaux (qualité de l’hôte, radiation ultraviolette, température, invasion biologique). Premièrement, j’ai comparé la réponse comportementale et de traits d’histoire de vie à la variation de taille corporelle chez le parasitoïde Telenomus podisi Ashmead (Hymenoptera : Platygastridae), démontrant que les normes de réaction des comportements étaient plus souvent positives que celles des traits d’histoires de vie. Ensuite, j’ai démontré que la punaise prédatrice Podisus maculiventris Say (Hemiptera : Pentatomidae) peut contrôler la couleur de ses œufs, et que la pigmentation des œufs protège les embryons du rayonnement ultraviolet; une composante d’une stratégie complexe de ponte qui a évoluée en réponse à une multitude de facteurs environnementaux. Puis, j’ai testé comment le stress thermique affectait la dynamique de la mémoire du parasitoïde Trissolcus basalis (Wollaston) (Hymenoptera : Platygastridae) lors de l’apprentissage de la fiabilité des traces chimiques laissées par son hôte. Ces expériences ont révélé que des températures hautes et basses prévenaient l’oubli, affectant ainsi l’allocation du temps passé par les parasitoïdes dans des agrégats d’hôtes contenant des traces chimiques. J’ai aussi développé un cadre théorique général pour classifier les effets de la température sur l’ensemble des aspects comportementaux des ectothermes, distinguant les contraintes des adaptations. Finalement, j’ai testé l’habileté d’un parasitoïde indigène (T. podisi) à exploiter les œufs d’un nouveau ravageur invasif en agriculture, Halyomorpha halys Stål (Hemiptera : Pentatomidae). Les résultats ont montré que T. podisi attaque les œufs de H. halys, mais qu’il ne peut s’y développer, indiquant que le ravageur invasif s’avère un « piège évolutif » pour ce parasitoïde. Cela pourrait indirectement bénéficier aux espèces indigènes de punaises en agissant comme un puits écologique de ressources (œufs) et de temps pour le parasitoïde. Ces résultats ont des implications importantes sur la réponse des insectes, incluant ceux impliqués dans les programmes de lutte biologique, face aux changements environnementaux.

Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination

Progressive telomere shortening from cell division (replicative aging) provides a barrier for human tumor progression. This program is not conserved in laboratory mice, which have longer telomeres and constitutive telomerase. Wild species that do ⁄ do not use replicative aging have been reported, but the evolution of different phenotypes and a conceptual framework for understanding their uses of telomeres is lacking. We examined telomeres ⁄ telomerase in cultured cells from > 60 mammalian species to place different uses of telomeres in a broad mammalian context. Phylogeny-based statistical analysis reconstructed ancestral states. Our analysis suggested that the ancestral mammalian phenotype included short telomeres (< 20 kb, as we now see in humans) and repressed telomerase. We argue that the repressed telomerase was a response to a higher mutation load brought on by the evolution of homeothermy. With telomerase repressed, we then see the evolution of replicative aging. Telomere length inversely correlated with lifespan, while telomerase expression co-evolved with body size. Multiple independent times smaller, shorter-lived species changed to having longer telomeres and expressing telomerase. Trade-offs involving reducing the energetic ⁄ cellular costs of specific oxidative protection mechanisms (needed to protect < 20 kb telomeres in the absence oftelomerase) could explain this abandonment of replicative aging. These observations provide a conceptual framework for understanding different uses of telomeres in mammals, support a role for human-like telomeres in allowing longer lifespans to evolve, demonstrate the need to include telomere length in the analysis of comparative studies of oxidative protection in the biology of aging, and identify which mammals can be used as appropriate model organisms for the study of the role of telomeres in human cancer and aging. Key words: evolution of telomeres; immortalization; telomerase; replicative aging; senescence.

Chicken skeletal muscle-associated macroarray for gene discovery

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Uso de recursos e padrão de co-ocorrência com insetos predadores em comunidades sub-tropicais de girinos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelagem de nicho ecológico de anuros da Mata Atlântica

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structure and post-translational modifications of the web silk protein spidroin-1 from Nephila spiders

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Organização genômima e análise da expressão do gene hnRNP Q-like (Heterogeneous nuclear ribonucleoprotein A-like) retroinserido no cromossomo B de Astatotilapia latifasciata

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.