Positive-strand RNA viruses associate with specific organelle membranes of host cells to establish viral replication complexes. The replication protein 1a of brome mosaic virus associates strongly with the nuclear endoplasmic reticulum (ER) membranes, invaginates membranes into the lumen, and recruits various host proteins to establish replication complexes termed spherules. 1a has a strong affinity towards the perinuclear ER membrane, however, the structural features in 1a that dictate its membrane associations and thereby membrane remodeling activities are unclear. This study examined the possible role of an amphipathic α-helix, helix B, in BMV 1a's membrane association. Deletion or single substitution of multiple amino acids of helix B abolished BMV 1a's localization to nuclear ER membranes. Additional reporter-based, gain-of-function assays showed that helix B is sufficient in targeting several soluble proteins to the nuclear ER membranes. Furthermore, we found that the helix B-mediated organelle targeting is a functionally conserved feature among positive-strand RNA viruses of the alphavirus-like superfamily that includes notable human viruses such as Hepatitis E virus and Rubella virus as well as plant viruses such as cucumber mosaic virus and cowpea chlorotic mottle virus. Our results demonstrate a critical role for helix B across members of the alphavirus-like superfamily in anchoring viral replication complexes to the organelle membranes. We anticipate our findings to be a starting point for the development of sophisticated models to use helix B as a novel target for the development of antivirals for positive-strand RNA viruses that belong to the alphavirus-like superfamily. / Doctor of Philosophy / Among the seven classes of viruses, the positive-strand RNA viruses dominate the domain of viral diseases of the world. Brome mosaic virus (BMV) is a positive-strand RNA virus that infects cereal crops such as wheat, barley, and rice. BMV has a simple genome organization and serves as a suitable model virus to study and characterize positive-strand RNA viruses. The replication of all positive-strand RNA viruses occurs at the organelle membranes of the host. Membrane association of the replication is one of the early steps and a crucial event in the life cycle of positive-strand RNA viruses. One of the proteins produced early on during BMV infection is the replication protein 1a, which is also the master regulator of viral replication; 1a recruits viral factors in addition to hijacking the necessary host factors at the membranous sites to initiate replication. Upon reaching the organelle membranes, 1a induces membrane rearrangements to form viral replication complexes that safeguard the recruited factors from the deleterious effects of the host cell. The structural determinants within 1a that are responsible for such membrane association are unknown. This study explored the potential roles of a short helical motif within the 1a protein for its ability to dictate such site-specific membrane associations. We show here that this helical region is necessary and sufficient for 1a's membrane-binding activity. We also discovered it to be a functionally conserved feature that is responsible for membrane associations in various viruses of the alphavirus-like superfamily that includes some of the notable human viruses such as Hepatitis E virus and Rubella virus in addition to plant viruses such as cucumber mosaic virus and cowpea chlorotic mottle virus.

The Interferon (IFN) family of cytokines are produced in direct response to virus infection and they constitute the first line of defence against virus infection by inducing hundreds of interferon stimulated genes (ISGs) which act in concert to establish the so-called “antiviral state”. Influenza A viruses and parainfluenza virus type 5 (PIV5) are both small negative strand RNA viruses that must circumvent their hosts’ interferon (IFN) response for replication. However, the ways in which these viruses interact with the IFN system are very different. Although PIV5 replication is initially severely impaired in cells in a pre-existing IFN-induced antiviral state, it manages to overcome the antiviral state by targeting an essential component of type I IFN signalling, STAT1, for degradation. Thus the cells cannot maintain the antiviral state indefinitely without continuous signalling. Consequently, the virus resumes its normal replication pattern after 24-48 hours post-infection. In clear contrast, influenza virus fails to establish its replication in the majority of infected cells (90-95%) with a pre-existing IFN-induced antiviral state, although a few cells are still able to produce viral antigens. To further investigate how influenza virus interacts with cells in a pre-existing IFN-induced antiviral state, I have used in situ hybridization to follow the fate of input and progeny genomes in cells that have, or have not, been treated with IFN prior to infection. Here I show for the first time that IFN pre-treatment blocks the nuclear import of influenza A virus genome, which prevents the establishment of virus replication, but this can be overcome by increasing multiplicities of infection. Of those IFN-induced antiviral molecules, human MxA is an essential component of the IFN-induced antiviral state in blocking influenza virus genome import, as this block can be abolished by lentivirus-mediated knockdown of MxA. I also show that in cells constitutively expressing MxA the viral genome still manages to be transported into the nucleus, indicating that MxA might require an unidentified IFN-induced factor to block nuclear import of the influenza virus genome. These results reveal that IFN exerts its action at an early stage of virus infection by inducing MxA to interfere with the transport of viral genome into the nucleus, which is the factory for viral RNA production.

Positive-strand RNAviruses invariably assemble their viral replication complexes (VRCs) by remodeling host intracellular membranes. How viral replication proteins are targeted to specific organelle membranes to initiate VRC assembly remains elusive. Brome mosaic virus (BMV), whose replication can be recapitulated in Saccharomyces cerevisiae, assembles its VRCs by invaginating the outer perinuclear endoplasmic reticulum (ER) membrane. Remarkably, BMV replication protein 1a (BMV 1a) is the only viral protein required for such membrane remodeling. We show that ER-vesicle protein of 14 kD (Erv14), a cargo receptor of coat protein complex II (COPII), interacts with BMV 1a. Moreover, the perinuclear ER localization of BMV 1a is disrupted in cells lacking ERV14 or expressing dysfunctional COPII coat components (Sec13, Sec24 or Sec31). The requirement of Erv14 for the localization of BMV 1a is bypassed by addition of a Sec24-recognizable sorting signal to BMV 1a or by overexpressing Sec24, suggesting a coordinated effort by both Erv14 and Sec24 for the proper localization of BMV 1a. The COPII pathway is well known for being involved in protein secretion; our data suggest that a subset of COPII coat proteins have an unrecognized role in targeting proteins to the perinuclear ER membrane.

O Vírus Respiratório Sincicial Humano é um vírus envelopado de RNA negativo e considerado o patógeno mais importante do trato respiratório de bebês e crianças. As proteínas virais N e P foram expressas em bactérias, purificadas e usadas para a produção de anticorpos policlonais em camundongos. Estudos in silico permitiram a predição de regiões desordenadas da proteína P, as quais foram identificadas por espectrometria de massa como regiões hiper sensíveis a proteases. A otimização dos genes N e P permitiu uma forte e eficiente expressão das proteínas N e P em células humanas. Vacinas de DNA contendo os genes otimizados foram testadas em camundongos e geraram forte resposta imune humoral. As proteínas N e P expressas em células humanas foram imunoprecipitadas e analisadas quanto a interações com proteínas celulares, identificadas por espectrometria de massa. A proteína P mostrou ser capaz de interagir com a HSP70. Por fim, um sistema Minigenoma alternativo, usando o promotor da RNA polimerase II, foi construído para o HRSV mas pouca ou nula atividade foi detectada. / The Human Respiratory Syncytial Virus is a single stranded negative RNA enveloped virus and it is considered the most important pathogen of the respiratory tract of infants and neonates. The viral N and P proteins were expressed in bacteria, purified and used for the production of polyclonal antibodies in mice. In silico studies allowed the prediction of intrinsically disordered domains for P protein, which were identified by mass spectrometry as protease hyper sensible regions. The optimization of N and P genes allowed a robust expression of the N and P proteins in human cells. DNA vaccines containing the optimized genes were tested in mice and generated strong humoral imune response. The N and P proteins expressed in human cells were immunoprecipitated and their interactions with cellular proteins were identified by mass spectrometry. The P protein was able to interact with the HSP70 protein. Finally, an alternative Minigenome system, using an RNA polymerase II promoter, was developed for HRSV but low or no activity was detected.

Norovirus (NoV) is a leading causative agent of non-bacterial gastroenteritis in humans worldwide. NoV is genetically classified into five distinct genogroups in which genogroups I (GI), II, and rarely IV infect humans. Each genogroup is further subdivided into different genotypes. Previous local surveillance studies demonstrated that NoV GII, in particular the genotype 4 (GII/4) strain, is the predominant genogroup circulating in Hong Kong since 2001. Similar epidemiologic observations were also reported in the US, Europe, UK, Australia, and Japan, highlighting the enormous pandemic and epidemic potential of this genogroup. However, explanation for its predominance has been lacking. In this study, we demonstrated that NoV GII, comprised mostly of the GII/4 strain, showed an increased median viral RNA level in fecal specimens which was at least 100-fold higher than that of GI. The high level of viral shedding may confer greater opportunity for transmission of GII strains through the fecal-oral route. We also demonstrated that fecal viral RNA level correlated positively and independently with diarrhea duration in NoV GII/4 infections. The median fecal viral level in patients with protracted (last for ≥4 days) diarrhea was 100-fold higher than that in patients with only limited diarrhea. Longer infectivity period may also confer greater opportunity for virus transmission through the fecal-oral route. Higher chance of transmission may result in more efficient person-to-person transmission and rapid dissemination, maintaining a high level of NoV GII persistence in the community. In summer 2006, a territory-wide gastroenteritis outbreak attributed to NoV has occurred with more than 3,000 cases of laboratory-confirmed NoV infections in Hong Kong. Phylogenetic analysis showed that the virus causing this unprecedented outbreak was a novel NoV GII/4 variant distinct from all previously reported global pandemic and local epidemic strains. In this 2006 variant, we identified two hypervariable regions when compared with previous local epidemic strains in 2005: protruding domain 2 (P2 domain) of viral protein 1 (VP1) and VP1-binding domain of VP2. We mapped frequent amino acid substitutions to the modeled antigenic loop regions of P2 domain. We also identified in carboxyl-terminus of VP1 an epidemiologically important, putative conformational epitope that alternates between two 3-amino acid signatures during pandemic NoV GII/4 strains evolution since 1995. Our findings reflect the rapid evolution of NoV GII/4 under immunological pressure and suggest that immune evasion might be a potential mechanism for pandemic NoV GII/4 strains emergence. Taken together, high level of fecal viral shedding, longer infectivity period, and periodic emergence of novel variant may underlie the global predominance of NoV GII. Further investigations are warranted to better understand the public health and biological importance of NoV GII. / Chan, Chi Wai. / Adviser: Wai K. Leung. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0818. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 124-143). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / School code: 1307.

Les protéines sont des acteurs majeurs dans les processus moléculaires et cellulaires d’un organisme. La remise en question des modalités associées aux fonctions de ces macromolécules a récemment été apportée par le concept de désordre intrinsèque. Celui-ci définit l’absence (transitoire ou permanente) de structure tridimensionnelle de certaines protéines ou régions protéiques comme étant directement liée à leurs fonctions. Chez les virus à ARN, les propriétés des protéines ou régions désordonnées semblent associées aux capacités de ces micro-organismes à détourner la machinerie cellulaire de l’hôte en interagissant avec de multiples partenaires, et à s’adapter aux nombreuses contraintes auxquelles ils doivent faire face en tant que parasites obligatoires. Ce travail porte sur les potyvirus, figurant parmi les pathogènes de plantes les plus dommageables étudiés à ce jour. L'objectif de cette thèse a été d’explorer les fonctions associées au désordre intrinsèque dans le cycle infectieux des potyvirus ainsi que dans le processus d’adaptation. Notre approche a ainsi démontré que : i) le désordre est ubiquitaire chez le genre Potyvirus ; ii) les régions de désordre conservées chez plusieurs protéines de potyvirus semblent être associées à leur(s) fonction(s) pendant l'infection ; iii) les régions désordonnées sont généralement associées à moins de contraintes évolutives, suggérant ainsi leur implication dans les processus adaptatifs des potyvirus ; iv) les régions prédites comme désordonnées semblent privilégier l’apparition de mutations et donc la capacité d’un virus à accumuler de la diversité génétique au cours de l'évolution sur son hôte naturel ; v) ce travail a permis de corréler le taux en désordre de la protéine viral genome-linked (VPg) du Potato virus Y à sa capacité à s’adapter à la résistance récessive pvr23 du piment. / Proteins are essential actors involved in a majority of molecular and cellular processes. The features associated with the functions of these macromolecules have been recently questioned with the emergence of the intrinsic disorder concept. It defines the transitory or permanent lack of 3D structure in some proteins or regions as directly related to their functions. Among RNA viruses, the properties of disordered proteins may be linked to the ability of these microorganisms to hijack the host machinery by interacting with multiple partners, as well as to adapt to the multiple constraints they must face as obligatory parasites. This work focuses on the Potyvirus genus, which includes some of the most damaging plant pathogens studied to date. The goal of this thesis was to explore the functions associated with intrinsic disorder in the infectious cycle of this viral genus as well as in its process of adaptation. Our studies have shown that i) intrinsic disorder is ubiquitous in potyviruses; ii) intrinsically disordered regions (IDR) of some of potyviral proteins are likely to be associated with important functions for the viral cycle ; iii) IDR are generally less evolutionary constrained, suggesting an adaptive potential of these regions ; iv) predicted IDR seem to favor the appearance of mutations and therefore virus ability to accumulate genetic diversity during its evolution in natural host ; v) an experimental disorder modulation within the Viral genome-linked (VPg) protein has been demonstrated as positively correlated with the adaptive ability of the Potato virus Y to overcome the pvr23 recessive resistance in pepper.

Les éléments transposables (ET) sont des parasites génomiques présents dans tous les génomes, dont une partie présente une structure similaire à celle de certains virus. Dans les cellules ovariennes d'insecte, l'abondance des transcrits d’ET est contrôlée par ARN interférence (ARNi), et plus particulièrement par la voie piARN (Piwi-interacting RNA). Une autre voie d'ARNi, la voie siARN (Small interfering RNA), constitue l'une des principales réponses immunitaires des insectes contre les infections virales, et est aussi dédiée au contrôle somatique des ET. Ces deux voies d'ARNi sont dirigées par des effecteurs moléculaires distincts et décrites comme indépendantes. Cependant, des similitudes structurales et de mécanisme de contrôle entre les ET et les virus suggèrent la possibilité d’une interaction. Nous avons utilisé la drosophile comme modèle et infecté l'organisme avec le virus Sindbis (SINV), un arbovirus (Arthropod-Borne virus), ou le virus Sigma (SV), un virus spécifique de drosophile. À l'aide d'un séquençage à haut débit, nous avons caractérisé les répertoires d'ARN et de petits ARN interférents produits par les drosophiles infectées, à partir des tissus de carcasses ou d'ovaires. Globalement, nos résultats démontrent un impact de l'infection virale sur les quantités de transcrits d’ET via la modulation des répertoires piARN et siARN, et représentent la première démonstration des effets d’infections virales sur l’activité des ET. Plus précisément, l’infection par SINV favorise une diminution globale des quantités de transcrits d’ET alors que l’infection par SV réactive de nombreux ET. Nos données suggèrent que la modulation résulte de substrats d'ARN partagés et de trans-régulateurs communs des voies de l'ARNi. Ces résultats ouvrent un nouvel axe de recherche en génomique, suggérant que les épidémies virales ou les infections chroniques peuvent avoir un impact sur l'activité des ET, et donc sur le taux de diversification génétique ultérieure / Transposable elements (TEs) are genomic parasites that are found in all genomes, a part of which display structure similarity to some viruses. In insect ovarian cells, TE transcript abundance is controlled by RNA interference (RNAi) machinery and more particularly by the piRNA pathway (Piwi-interacting RNA). Another RNAi pathway, named siRNA pathway (Small interfering RNA), is one of the key insect immune responses against viral infections and is also dedicated to TE somatic control. These two interfering RNA pathways are led by distinct molecular effectors and described as independent. However, similarities in structure and control mechanisms across TEs and viruses suggest that an interplay may exist. We used Drosophila as a model, and infected the organism with Sindbis virus (SINV), an arbovirus (Arthropod-Borne virus), or Sigma virus (SV), a Drosophila-specific virus. Using high-throughput sequencing, we characterized the RNA and small-RNA repertoires produced by Drosophila flies from carcass or ovary tissues. Overall, our results demonstrate an impact of viral infection on TE transcript amounts via modulation of the piRNA and siRNA repertoires and represent the first demonstration of the effects of viral infection on TE activity. More precisely, SINV infection promotes a global decrease of TE transcript levels while SV infection reactivates many TEs. Our data suggest that the modulation results from shared RNA substrates and common trans-regulators of the small RNA pathways. These results open new avenue of research in genomics, suggesting that viral epidemics or chronic infections can impact TE activity and thus the rate of subsequent genetic diversification

The prediction of correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. Among the major obstacles is the fact that accurate calculations scale as O(n⁴), so the computational requirements become prohibitive as the length increases. We present a new parallel multicore and scalable program called GTfold, which is one to two orders of magnitude faster than the de facto standard programs mfold and RNAfold for folding large RNA viral sequences and achieves comparable accuracy of prediction. We analyze the algorithm's concurrency and describe the parallelism for a shared memory environment such as a symmetric multiprocessor or multicore chip. We are seeing a paradigm shift to multicore chips and parallelism must be explicitly addressed to continue gaining performance with each new generation of systems. We provide a rigorous proof of correctness of an optimized algorithm for internal loop calculations called internal loop speedup algorithm (ILSA), which reduces the time complexity of internal loop computations from O(n⁴) to O(n³) and show that the exact algorithms such as ILSA are executed with our method in affordable amount of time. The proof gives insight into solving these kinds of combinatorial problems. We have documented detailed pseudocode of the algorithm for predicting minimum free energy secondary structures which provides a base to implement future algorithmic improvements and improved thermodynamic model in GTfold. GTfold is written in C/C++ and freely available as open source from our website.

No description available.

O Vírus Respiratório Sincicial Humano é um vírus envelopado de RNA negativo e considerado o patógeno mais importante do trato respiratório de bebês e crianças. As proteínas virais N e P foram expressas em bactérias, purificadas e usadas para a produção de anticorpos policlonais em camundongos. Estudos in silico permitiram a predição de regiões desordenadas da proteína P, as quais foram identificadas por espectrometria de massa como regiões hiper sensíveis a proteases. A otimização dos genes N e P permitiu uma forte e eficiente expressão das proteínas N e P em células humanas. Vacinas de DNA contendo os genes otimizados foram testadas em camundongos e geraram forte resposta imune humoral. As proteínas N e P expressas em células humanas foram imunoprecipitadas e analisadas quanto a interações com proteínas celulares, identificadas por espectrometria de massa. A proteína P mostrou ser capaz de interagir com a HSP70. Por fim, um sistema Minigenoma alternativo, usando o promotor da RNA polimerase II, foi construído para o HRSV mas pouca ou nula atividade foi detectada. / The Human Respiratory Syncytial Virus is a single stranded negative RNA enveloped virus and it is considered the most important pathogen of the respiratory tract of infants and neonates. The viral N and P proteins were expressed in bacteria, purified and used for the production of polyclonal antibodies in mice. In silico studies allowed the prediction of intrinsically disordered domains for P protein, which were identified by mass spectrometry as protease hyper sensible regions. The optimization of N and P genes allowed a robust expression of the N and P proteins in human cells. DNA vaccines containing the optimized genes were tested in mice and generated strong humoral imune response. The N and P proteins expressed in human cells were immunoprecipitated and their interactions with cellular proteins were identified by mass spectrometry. The P protein was able to interact with the HSP70 protein. Finally, an alternative Minigenome system, using an RNA polymerase II promoter, was developed for HRSV but low or no activity was detected.