The Hap2/3/4/5 complex is a heme-activated, CCAATT binding, global transcriptional activator of genes involved in respiration and mitochondrial biogenesis in the yeast species Saccharomyces cerevisiae. Hap4 is the regulatory subunit of the complex and its levelsdetermine the activity of the complex. Hap4 is known to play a signaling role in response toenvironmental conditions; however, little is known about the regulation of Hap4 levels or how it responses to a cell’s functional state. The activity of the Hap2-5 complex is known to be reduced in respiratory-deficient cells. In Liu Lab, it has previously been found that a link between Hap4 stability, mediated through 26S proteasome-dependent degradation, and dependence on mitochondrial functional state plays a regulatory role on downstream targets of the Hap complex. However, the mechanism behind this regulation is still largely unknown. In normally functioning yeast cells, Hap4 is a highly unstable protein with a half-life of ~10 min. We have observed that loss of mitochondrial DNA in respiratory deficient rho 0 cells has a role in the further destabilization of Hap4 to a half-life of ~4 min through the ubiquitin-proteasome pathway. Through the screening of a collection of mutants defective in E2 ubiquitin-conjugating enzymes, we show that Hap4 is greatly stabilized in ubc1Δubc4Δ double mutant cells. We also show that Hap4 stabilization in the ubc1Δubc4Δ mutant leads to increased activity of the Hap2-5 complex, indicating that mitochondrial biogenesis in yeast is regulated by the functional state of mitochondria through ubiquitin/proteasome-dependent degradation of Hap4. Furthermore, studies on Hap4 mutants involving two highly conserved cysteine residues led to a proposed mechanism behind the regulation of Ubc4 activity towards Hap4 in response to changes in the cellular redox state.

Human DDI2 protein is a dimeric aspartic protease that has been recently found to play an important role in DNA damage repair and transcriptional regulation of the proteasome expression. Current insights into the mechanistic details of both functions are still quite limited. We have previously identified the human RAD23B protein to interact with the DDI2 protein. RAD23B also functions in DNA damage repair as part of the XPC complex that stimulates the nucleotide excision repair activity. Moreover, RAD23B participates as an adaptor protein in the process of protein degradation. Therefore, the interaction of DDI2 and RAD23B might have important implications for both known functions of DDI2. This work describes the DDI2 and RAD23B interaction on the structural level. Recombinant protein variants of both DDI2 and RAD23B proteins were prepared and the interaction was mapped by the affinity pull-down assay. Protein NMR titrations were further used to explore the interaction. Key words: ubiquitin-proteasome system, DNA damage repair, proteasome expression regulation, aspartyl protease, DDI2, NMR

Hepatitis B virus (HBV) is a Hepadnaviridae virus infecting mammals. Its infection can result in an acute or chronic infection. Chronic infection can result in hepatocellular carcinoma and liver cirrhosis, potentially leading to death of the patient. HBV is a small 42 nm virus with a genome length of 3.2 kb encoding seven viral proteins. HBV Core protein (HBc) is a capsid forming protein which is pleiotropic in function. We have identified two ubiquitin ligases which could interact with this protein: F-box only protein 3 (FBXO3; E3 ubiquitin ligase) and Ubiquitin conjugating enzyme E2 O (UBE2O; E2/E3 ubiquitin ligase). By employing multiple methods we have confirmed these interactions. Co- immunoprecipitation and further western blot analysis unveiled multiple new insights into the ligases′ impact on HBc: FBXO3-mediated HBc polyubiquitination stimulation and UBE2O-mediated HBc monoubiquitination promotion. FBXO3's and UBE2O's role in HBV life cycle was investigated as well. By silencing the expression of FBXO3 and UBE2O respectively, we have observed changes in HBV replication levels: FBXO3 serves as an inhibitor of HBV replication, while UBE2O stimulates the course of HBV life cycle. Further investigation of these newly-discovered understandings may lead to a whole new HBV - host interplay...

Human DDI2 protein is a dimeric aspartic protease that has been recently found to play an important role in DNA damage repair and transcriptional regulation of the proteasome expression. Current insights into the mechanistic details of both functions are still quite limited. We have previously identified the human RAD23B protein to interact with the DDI2 protein. RAD23B also functions in DNA damage repair as part of the XPC complex that stimulates the nucleotide excision repair activity. Moreover, RAD23B participates as an adaptor protein in the process of protein degradation. Therefore, the interaction of DDI2 and RAD23B might have important implications for both known functions of DDI2. This work describes the DDI2 and RAD23B interaction on the structural level. Recombinant protein variants of both DDI2 and RAD23B proteins were prepared and the interaction was mapped by the affinity pull-down assay. Protein NMR titrations were further used to explore the interaction. Key words: ubiquitin-proteasome system, DNA damage repair, proteasome expression regulation, aspartyl protease, DDI2, NMR

A atrofia está associada ao aumento da degradação protéica em doenças sistêmicas, sendo o sistema proteolítico ubiquitina proteassoma (SUP) uma das principais vias envolvidas. Contudo, pouco é conhecido sobre a contribuição do SUP à atrofia desencadeada pela insuficiência cardíaca (IC). Sabendo dos benefícios do treinamento físico aeróbico (TFA) e que os mecanismos moleculares envolvidos na atrofia na IC ainda não estão esclarecidos, nessa dissertação investigamos: 1) a contribuição do SUP para a atrofia associada à IC em 2 modelos experimentais: um modelo genético de camundongos com hiperatividade simpática (HS), e um modelo de infarto do miocárdio (IM) em ratos e 2) o efeito do TFA sobre a atrofia associada à IC e sobre o SUP. Na HS verificamos aumento da expressão das E3 ligases, da deubiquitinase USP28, das proteínas ubiquitinadas e da atividade do proteassoma no sítio quimiotripsina, sendo que o TFA reduziu a expressão dos componentes alterados. No IM, observamos disfunção cardíaca não associada à IC, porém, com aumento da expressão de Atrogin-1; enquanto o TFA não produziu efeitos significantes. Dessa forma, os dados sugerem a participação do SUP na atrofia desencadeada pela IC na HS e, que o TFA previne a atrofia por reduzir a expressão/atividade de alguns componentes do SUP; e, que no IM, o aumento da expressão de Atrogin-1 precedeu a perda de massa muscular / Skeletal muscle atrophy is associated with increased protein degradation in systemic diseases, which seems to be mainly related to ubiquitin-proteasome system (UPS). However, little is known about UPS contribution to the heart failure-induced muscle atrophy (HF-MA). Likewise, aerobic exercise training (AET) has been established as an adjuvant therapy for HF and molecular mechanisms underlying HF-MA has not been clarified yet. The objectives of the study were: 1) to verify UPS contribution for HF-MA in 2 experimental models: sympathetic hyperactivity-induced HF (α2A/α2CARKO) in mice, and myocardial infarction model (MI) in rats and 2) AET effects on HF-MA and UPS. In α2A/α2C ARKO mice, we observed activation of UPS characterized by increased mRNA levels of E3 ligases Atrogin-1 and E3-a, deubiquitinating enzyme USP28, increased levels of ubiquitinated proteins and chymotrypsin-like proteasome activity. AET prevented HF-MA in the α2A/α2C ARKO by reducing of UPS activity. In MI model, rats displayed cardiac dysfunction and exercise intolerance with no signs of atrophy. However, Atrogin-1 mRNA and protein levels were increased. Therefore, alterations in Atrogin-1expression might precede atrophy and HF in this model. In conclusion, our data provide evidence for skeletal muscle anti-atrophic effect upon AET in α2A/α2C ARKO that is related, at least in part, to a reduced UPS

A atrofia está associada ao aumento da degradação protéica em doenças sistêmicas, sendo o sistema proteolítico ubiquitina proteassoma (SUP) uma das principais vias envolvidas. Contudo, pouco é conhecido sobre a contribuição do SUP à atrofia desencadeada pela insuficiência cardíaca (IC). Sabendo dos benefícios do treinamento físico aeróbico (TFA) e que os mecanismos moleculares envolvidos na atrofia na IC ainda não estão esclarecidos, nessa dissertação investigamos: 1) a contribuição do SUP para a atrofia associada à IC em 2 modelos experimentais: um modelo genético de camundongos com hiperatividade simpática (HS), e um modelo de infarto do miocárdio (IM) em ratos e 2) o efeito do TFA sobre a atrofia associada à IC e sobre o SUP. Na HS verificamos aumento da expressão das E3 ligases, da deubiquitinase USP28, das proteínas ubiquitinadas e da atividade do proteassoma no sítio quimiotripsina, sendo que o TFA reduziu a expressão dos componentes alterados. No IM, observamos disfunção cardíaca não associada à IC, porém, com aumento da expressão de Atrogin-1; enquanto o TFA não produziu efeitos significantes. Dessa forma, os dados sugerem a participação do SUP na atrofia desencadeada pela IC na HS e, que o TFA previne a atrofia por reduzir a expressão/atividade de alguns componentes do SUP; e, que no IM, o aumento da expressão de Atrogin-1 precedeu a perda de massa muscular / Skeletal muscle atrophy is associated with increased protein degradation in systemic diseases, which seems to be mainly related to ubiquitin-proteasome system (UPS). However, little is known about UPS contribution to the heart failure-induced muscle atrophy (HF-MA). Likewise, aerobic exercise training (AET) has been established as an adjuvant therapy for HF and molecular mechanisms underlying HF-MA has not been clarified yet. The objectives of the study were: 1) to verify UPS contribution for HF-MA in 2 experimental models: sympathetic hyperactivity-induced HF (α2A/α2CARKO) in mice, and myocardial infarction model (MI) in rats and 2) AET effects on HF-MA and UPS. In α2A/α2C ARKO mice, we observed activation of UPS characterized by increased mRNA levels of E3 ligases Atrogin-1 and E3-a, deubiquitinating enzyme USP28, increased levels of ubiquitinated proteins and chymotrypsin-like proteasome activity. AET prevented HF-MA in the α2A/α2C ARKO by reducing of UPS activity. In MI model, rats displayed cardiac dysfunction and exercise intolerance with no signs of atrophy. However, Atrogin-1 mRNA and protein levels were increased. Therefore, alterations in Atrogin-1expression might precede atrophy and HF in this model. In conclusion, our data provide evidence for skeletal muscle anti-atrophic effect upon AET in α2A/α2C ARKO that is related, at least in part, to a reduced UPS

Les papillomavirus humains (HPV) constituent l’archétype des virus à ADN oncogènes. Les HPV muqueux à haut risque (principalement HPV16) sont les principaux agents étiologiques du cancer du col utérin. Les protéines virales E6 et E7 sont des acteurs cruciaux de la cancérogenèse induite par HPV. Nous avons construit une ressource composée de 600 ADNc codant les effecteurs humains du système ubiquitine-protéasome (UPS) et identifié de nouvelles cibles potentielles des protéines E6 et E7 en utilisant une méthode basée sur la complémentation protéique de la Gaussia princeps luciférase (GPCA). HPV16 E6 lie les motifs LxxLL présents dans E6AP et IRF3. Nous avons résolu la structure cristallographique des complexes E6/LxxLL de E6AP/p53 et E6/LxxLL de IRF3. Par ailleurs, nous avons montré que les HPV ciblent une nouvelle voie suppresseur de tumeurs, la voie Hippo, avec ses deux médiateurs clef YAP et TAZ. Nous avons généré une banque d’ADNc codant 265 domaines PDZ humains et identifié de nouveaux partenaires potentiels des protéines YAP/TAZ en utilisant la méthode GPCA. Les résultats obtenus permettent de mieux comprendre la biologie des HPV et leur pouvoir oncogène. / The human papillomavirus (HPVs) are the archetype of DNA oncogenic viruses. High-risk mucosal HPVs (mainly HPV16) are the main causative agents of cervical cancer and are also involved in other cancers. HPV oncogenic properties are mainly due to the expression of E6 and E7 proteins. We built a resource composed of 600 cDNA encoding the human ubiquitin-proteasome system (UPS) effectors and identified novel E6 and E7 potential targets by using a method based on the complementation of the Gaussia princeps luciferase (GPCA). HPV16 E6 binds to specific LxxLL motifs present in E6AP and IRF3. We have solved the crystallographic structure of the E6/E6AP LxxLL/p53 and E6/IRF3 LxxLL complexes. Furthermore, HPV may target a novel tumour suppressor pathway, the Hippo signalling pathway with its two main mediators YAP and TAZ. We have built a cDNA library dedicated to the 265 human PDZ domains and identified news potential partners of YAP and TAZ proteins by using the GPCA. The results provide novel insights on HPV biology and their oncogenic property.