subject:(RNA silencing suppressor)

University of Sydney

1. Naim, Fatima. Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins .

Degree: 2014, University of Sydney

URL: http://hdl.handle.net/2123/12072

► The use of transgenic pathways is a cornerstone of basic and applied research into plant biology. However, transgenes can fail over time and obtaining elite… (more)

▼ The use of transgenic pathways is a cornerstone of basic and applied research into plant biology. However, transgenes can fail over time and obtaining elite plant materials that perform well over numerous generations is an intensive process. Such failures in transgene performance are associated with the generation of small RNA (sRNA) in the host plant that trigger silencing. This mechanism is related to host defence pathways against invading nucleic acids including those from viral genomes. To counteract this silencing mechanism, plant viruses have evolved and encode for viral silencing-suppressor proteins (VSP) to block the silencing machinery of the host. This thesis tests the hypothesis that VSPs are also capable of enhancing transgene performance in stably-transformed plants. The effects of a number of VSPs on transgenic pathways were assessed transiently in Nicotiana benthamiana leaves and in long-term population studies spanning five and four generations in Arabidopsis thaliana and Brassica napus seeds, respectively. Overall this study shows that VSPs are able to enhance the performance of transgenic pathways in both leaves and seeds. The transient leaf assay in N.benthamiana leaves is a well-established tool and allows a rapid examination of transgenic pathways in a short period of time. One limitation of the assay format is an inability to both silence endogenous pathways and permit maximal overexpression of transgenes. This study demonstrates extensive manipulation of lipid pathways in N.benthamiana leaves by introducing an alternative VSP, V2, which stops the co-suppression of transgenes and allows simultaneous silencing of endogenes. A combination of V2, silencing of NbFAD2 and overexpression of GhCPFAS and AtDGAT1 resulted in high levels of a novel fatty acid, dihydrosterculic acid, in leaf oil. The V2-based assay was used to silence NbFAD7 and shunt linoleic acid into a three step transgenic pathway to synthesise arachidonic acid (AA), an ω-6 long chain polyunsaturated fatty acid (LCPUFA). Lipid head group fractionations of infiltrated leaf extracts showed that leaf cells rapidly shuffle novel fatty acids between various soluble and membrane-bound lipid pools. The assay was also used to investigate the effect of silencing a number of key lipid biosynthesis genes which included NbSAD1, NbFATA, NbFATB, NbFAD3, NbFAD6, NbLPCAT, NbGPAT9, NbLPAAT4 and NbLPAAT6 on lipid fluxes in N.benthamiana leaves. Various VSPs were co-expressed with a three step transgenic pathway for the synthesis of AA in A.thaliana and B.napus seeds. The expression of the VSP was limited to oil synthesis in the seed and in A.thaliana the results showed that transgenic populations co-expressing V2 or p19 contained higher levels of AA. A p19 line contained 40% of AA in T3 seeds although such high levels came at the expense of oil content. Similar constructs were also transformed into B.napus. Unlike A.thaliana, B.napus displayed a bottleneck in AA biosynthesis at an intermediate step, indicating differences in the biochemical capacity of…

Subjects/Keywords: Viral silencing-suppressor protein; Metabolic engineering; Plant lipids; Small RNA; RNA silencing

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APA (6^th Edition):

Naim, F. (2014). Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/12072

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Naim, Fatima. “Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins .” 2014. Thesis, University of Sydney. Accessed March 01, 2021. http://hdl.handle.net/2123/12072.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Naim, Fatima. “Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins .” 2014. Web. 01 Mar 2021.

Vancouver:

Naim F. Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins . [Internet] [Thesis]. University of Sydney; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2123/12072.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Naim F. Enhanced metabolic engineering of lipid biosynthesis in leaves and seeds with the use of viral silencing-suppressor proteins . [Thesis]. University of Sydney; 2014. Available from: http://hdl.handle.net/2123/12072

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

2. Incarbone, Marco. In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus.

Degree: Docteur es, Aspects moléculaires et cellulaires de la biologie, 2016, Université de Strasbourg

URL: http://www.theses.fr/2016STRAJ090

►

Chez les plantes, le RNA silencing (RNAi) est le principal mécanisme de défense antivirale. Il est opéré par de petites molécules d’ARN (siRNA), de 21-22nt… (more)

▼

Chez les plantes, le RNA silencing (RNAi) est le principal mécanisme de défense antivirale. Il est opéré par de petites molécules d’ARN (siRNA), de 21-22nt de long, générées à partir de l’ARN viral par DCL4 et DCL2, respectivement. Ces siRNA confèrent la séquence-spécificité des réactions de défense intracellulaire et peuvent se déplacer à longue distance pour immuniser les cellules saines. En conséquence, les virus ont développé des protéines (VSRs) capables de supprimer ces deux aspects du RNAi. Au cours de cette thèse, j’ai pu démontrer in vivo que la protéine P15 du Peanut clump virus (PCV) est capable de séquestrer les siRNA de 21 et 22nt et qu’elle bloque le mouvement de ces derniers plus efficacement que ceux de 21nt. Pour compenser cette faiblesse, au cours de l’infection par le PCV, P15 est transportée à l’intérieur des peroxisomes en association avec les siRNA qu’elle séquestre. Le confinement des siRNA mobiles de 21nt à l’intérieur de ces organelles conduit à une inhibition du RNAi systémique et stimule fortement la propagation du PCV à travers la plante. Ces travaux définissent une nouvelle stratégie de pathogénèse virale au cours de laquelle une organelle est utilisé pour neutraliser des molécules de défense produites par l’hôte.

In plants, RNA interference (RNAi) is the main antiviral defense mechanism. It is initiated through the processing of viral RNA into 21-22nt long siRNA by DCL4 and DCL2, respectively. These siRNA can mediate sequence-specific local defense reactions (cell-autonomous RNAi) or move to distant tissues to prime defenses in naive cells (systemic RNAi). Consequently, viruses have evolved proteins (VSRs) to suppress both aspects of RNAi. In this in vivo study, I show that P15, the VSR of Peanut clump virus (PCV), binds and sequesters both 21nt and 22nt siRNA. Importantly, it stops the movement of 22nt siRNA more efficiently than 21nt siRNA. During infection, P15 is shuttled into peroxisomes, and is able to « piggyback » siRNA into these organelles. By confining mobile DCL4-dependent antiviral 21nt siRNA within peroxisomes, P15 is able to shut down systemic RNAi and strongly promote PCV movement. This work describes a novel pathogenic strategy in which an organelle is used to neutralize host defensive molecules.

Advisors/Committee Members: Dunoyer, Patrice (thesis director).

Subjects/Keywords: Virus; SiRNA; RNA silencing systémique; Suppresseur de RNA silencing; Peroxisome; Virus; SiRNA; Non-cell autonomous RNAi; Suppressor of RNA silencing; Peroxisome; Piggyback; 572.8; 581

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Incarbone, M. (2016). In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus. (Doctoral Dissertation). Université de Strasbourg. Retrieved from http://www.theses.fr/2016STRAJ090

Chicago Manual of Style (16^th Edition):

Incarbone, Marco. “In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus.” 2016. Doctoral Dissertation, Université de Strasbourg. Accessed March 01, 2021. http://www.theses.fr/2016STRAJ090.

MLA Handbook (7^th Edition):

Incarbone, Marco. “In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus.” 2016. Web. 01 Mar 2021.

Vancouver:

Incarbone M. In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus. [Internet] [Doctoral dissertation]. Université de Strasbourg; 2016. [cited 2021 Mar 01]. Available from: http://www.theses.fr/2016STRAJ090.

Council of Science Editors:

Incarbone M. In vivo study of the suppression of cell-autonomous and systemic RNA silencing by the Peanut clump virus protein P15 : Caractérisation in vivo de la suppression du RNA silencing intracellulaire et systémique par la protéine P15 du Peanut clump virus. [Doctoral Dissertation]. Université de Strasbourg; 2016. Available from: http://www.theses.fr/2016STRAJ090

University of California – Riverside

3. Kuan, Tung. Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis.

Degree: Microbiology, 2018, University of California – Riverside

URL: http://www.escholarship.org/uc/item/2d70k8c7

► Phytophthora belong to a group of fungus-like and zoospore-forming microorganisms, which are important plant pathogens that cause diseases on a broad range of crop and… (more)

▼ Phytophthora belong to a group of fungus-like and zoospore-forming microorganisms, which are important plant pathogens that cause diseases on a broad range of crop and tree species worldwide. However, the control of Phytophthora diseases remains challenging due to the lack of understanding of their pathogenesis. Phytophthora are successful plant pathogens since they encode hundreds of effectors to suppress plant immune responses. Among them, the PSR2 family effectors are evolutionarily conserved among several Phytophthora species. Both PSR2 (encoded by Phytophthora sojae) and PiPSR2 (encoded by Phytophthora infestans) function as RNA silencing suppressors and are able to promote Phytophthora infection in plants. To understand the molecular mechanisms by which PSR2 suppresses RNA silencing and increase disease susceptibility in plants, I identified serine/threonine protein phosphatase 2A (PP2A) as a PSR2-associating protein in plants. PP2A is a heterotrimeric enzyme consisting of scaffold A, regulatory B, and catalytic C subunits, where each subunit is encoded by gene families with multiple members. PSR2 has stronger associations with A subunits, weaker associations with C subunits, and no association with B subunits. Arabidopsis transgenic plant expressing PSR2 showed reduced production of phasiRNAs, which might be one of the underlying mechanisms suppressing plant immunity. To determine the functional involvement of PP2A subunits in PSR2-mediated RNA silencing suppression, I examined small RNA accumulation in transgenic Arabidopsis with PSR2-expressed in pp2a mutation backgrounds. Interestingly, the reduction of the phasiRNAs caused by PSR2 was rescued by the scaffold subunit rcn1 and pdf1 mutations, while these rcn1 and pdf1 mutants alone did not alter small RNA biogenesis. In addition, PSR2 deletion mutants that had reduced interaction with PP2A partially lost the phasiRNA suppression activity, suggesting the functional involvement of PP2A in PSR2-mediated small RNA suppression.Lastly, mass spectrometry analyses revealed plenty of PP2A B subunits in RCN1-, but not PSR2-, associated protein complexes. Thus, PSR2 may serve as a regulatory B subunit to modulate the function of PP2A core enzyme (consisting of A and C subunits). This hypothesis was further supported by that PSR2 structurally mimicked PP2A B family subunits and it also shared similar binding sites to the scaffold with B family subunits. Furthermore, PSR2 was able to compete out a B subunit from the PP2A by an initial replacement pull-down assay. Together, my thesis research provides novel mechanistic insights into the pathogenesis of Phytophthora PSR2 effector by hijacking PP2A core enzyme in plants to suppress plant RNA silencing.

Subjects/Keywords: Plant pathology; Microbiology; Molecular biology; Effector; Phytophthora; Plant immunity; Protein phsphatase; RNA silencing suppressor; Small RNA

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APA (6^th Edition):

Kuan, T. (2018). Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/2d70k8c7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kuan, Tung. “Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis.” 2018. Thesis, University of California – Riverside. Accessed March 01, 2021. http://www.escholarship.org/uc/item/2d70k8c7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kuan, Tung. “Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis.” 2018. Web. 01 Mar 2021.

Vancouver:

Kuan T. Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis. [Internet] [Thesis]. University of California – Riverside; 2018. [cited 2021 Mar 01]. Available from: http://www.escholarship.org/uc/item/2d70k8c7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kuan T. Molecular and Mechanistic Study of Phytophthora RxLR Effector PSR2 in Arabidopsis. [Thesis]. University of California – Riverside; 2018. Available from: http://www.escholarship.org/uc/item/2d70k8c7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Euskal Herriko Unibertsitatea / Universidad del País Vasco

4. Katorcha, Elizaveta. Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 .

Degree: 2014, Euskal Herriko Unibertsitatea / Universidad del País Vasco

URL: http://hdl.handle.net/10810/11643

► The study is focused on structural aspects of interaction between silencing suppressor p19 and CUG-repeating small RNAs. The work involves crystal structure determination of a… (more)

Subjects/Keywords: RNA; protein-RNA complex; X-ray crystallography; siRNA; trinucleotide repeats; silencing; mismatch base pair; viral suppressor; p19; CTG/CUG repeats; structural biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Katorcha, E. (2014). Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 . (Doctoral Dissertation). Euskal Herriko Unibertsitatea / Universidad del País Vasco. Retrieved from http://hdl.handle.net/10810/11643

Chicago Manual of Style (16^th Edition):

Katorcha, Elizaveta. “Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 .” 2014. Doctoral Dissertation, Euskal Herriko Unibertsitatea / Universidad del País Vasco. Accessed March 01, 2021. http://hdl.handle.net/10810/11643.

MLA Handbook (7^th Edition):

Katorcha, Elizaveta. “Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 .” 2014. Web. 01 Mar 2021.

Vancouver:

Katorcha E. Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 . [Internet] [Doctoral dissertation]. Euskal Herriko Unibertsitatea / Universidad del País Vasco; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10810/11643.

Council of Science Editors:

Katorcha E. Structural study of CUG-repeating small RNAs complexed with silencing suppressor P19 . [Doctoral Dissertation]. Euskal Herriko Unibertsitatea / Universidad del País Vasco; 2014. Available from: http://hdl.handle.net/10810/11643

Universitat Politècnica de València

5. Soler Calvo, Nuria. Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus.

Degree: 2013, Universitat Politècnica de València

URL: http://hdl.handle.net/10251/31631

► El virus de la tristeza de los cítricos (Citrus tristeza virus; CTV) es el agente causal de unas de las enfermedades virales de los árboles… (more)

▼ El virus de la tristeza de los cítricos (Citrus tristeza virus; CTV) es el agente causal de unas de las enfermedades virales de los árboles cítricos más devastadoras en el mundo. CTV está restringido al floema en su huésped cítrico natural, y ha desarrollado tres proteínas supresoras de silenciamiento que actúan a nivel intra-(p23 y p20) e intercelular (p20 y p25) para superar la fuerte defensa antiviral del huésped. La interferencia de RNA, una aproximación basada en el uso de dsRNA para desencadenar el silenciamiento de RNA, ha sido utilizada ampliamente para generar plantas transgénicas resistentes a virus. Considerando el importante papel de p23, p20 y p25 en la patogénesis de CTV, hemos transformado plantas de lima Mexicana con un vector intrón-horquilla que porta la secuencia completa en versión no traducible de los genes p25, p20, p23 y el extremo 3¿-UTR de la cepa T36 de CTV, para intentar silenciar su expresión en células infectadas. Se ha observado resistencia completa a la infección viral en tres líneas transgénicas, manteniéndose todas sus propagaciones asintomáticas y libres de virus tras ser inoculadas mediante injerto con CTV-T36, tanto en el portainjertos no transgénico como directamente sobre la variedad transgénica. La acumulación de siRNA derivados del transgén fue necesaria pero no suficiente para lograr resistencia frente a CTV en las plantas. Al inocular propagaciones de las líneas transgénicas inmunes con una cepa de CTV divergente, la resistencia fue parcialmente superada, destacando la importancia de la identidad de secuencia en el mecanismo subyacente a la interferencia de RNA. Este trabajo es el primero en que se consigue resistencia completa a CTV en un huésped cítrico muy sensible, actuando simultáneamente sobre los tres supresores virales de silenciamiento mediante interferencia de RNA. La proteína p23 codificada por el virus es además un importante factor de patogenicidad. La expresión ectópica de p23 en plantas de cítricos induce aberraciones fenológicas semejantes a síntomas de CTV. Para estudiar en más detalle el papel de p23 en la patogénesis de CTV, se ha sobre-expresado en lima Mexicana el gen p23 de CTV T36 y tres versiones truncadas del mismo bajo el control del promotor 35S del virus del mosaico de la coliflor (Cauliflower mosaic virus). Solo la versión truncada, que expresa los aminoácidos del 1 al 157 (p23-¿157) indujo síntomas similares a los producidos por CTV, aunque más suaves que los inducidos por la expresión de la proteína p23 entera (209 aminoácidos), permitiendo delimitar la región responsable de la patogénesis de p23 en cítricos a un fragmento de 157 aminoácidos que incluye el dedo de zinc y los motivos básicos flanqueantes de la proteína. La actividad de p23 como supresor de silenciamiento de RNA en N. benthamiana se perdía en todos los mutantes de p23 probados, lo cual indica que la supresión de silenciamiento implica a la mayoría de las regiones de la proteína. Para profundizar más en el papel de p23 en… Advisors/Committee Members: Fagoaga García, Carmen Concepción (advisor), PEÑA GARCIA, LEANDRO (advisor).

Subjects/Keywords: Transgenic citrus; RNA interference; RNA silencing suppressor; Antiviral defence; Virus resistance; Closterovirus; Intron-hairpin; Small interfering RNAs; Phloem-specific expression; Virus symptoms.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Soler Calvo, N. (2013). Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus. (Doctoral Dissertation). Universitat Politècnica de València. Retrieved from http://hdl.handle.net/10251/31631

Chicago Manual of Style (16^th Edition):

Soler Calvo, Nuria. “Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus. ” 2013. Doctoral Dissertation, Universitat Politècnica de València. Accessed March 01, 2021. http://hdl.handle.net/10251/31631.

MLA Handbook (7^th Edition):

Soler Calvo, Nuria. “Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus. ” 2013. Web. 01 Mar 2021.

Vancouver:

Soler Calvo N. Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus. [Internet] [Doctoral dissertation]. Universitat Politècnica de València; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10251/31631.

Council of Science Editors:

Soler Calvo N. Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus. [Doctoral Dissertation]. Universitat Politècnica de València; 2013. Available from: http://hdl.handle.net/10251/31631

Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ)

6. Mathioudakis, Matthaios. Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού.

Degree: 2012, Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ)

URL: http://hdl.handle.net/10442/hedi/29890

► (+)RNA viruses for a successful infection require except their RNA genome, viral-encoded proteins and also host machineries/pathways. By this way viruses can counteract host defenses… (more)

▼ (+)RNA viruses for a successful infection require except their RNA genome, viral-encoded proteins and also host machineries/pathways. By this way viruses can counteract host defenses and facilitating their vital functions, finally posing the plant under their control. The identification of host factors and the dissection of their roles in the viral replication cycle contributes to a better understanding of viral mechanisms during viral-host interactions, and indicate potential new control strategies against viral diseases. In the present work, three tomato proteins were identified to interact with Pepino mosaic virus (PepMV)-encoded proteins and their implication into viral replication and the suppression of RNA silencing was investigated. Of the three Hsc70 genes which were cloned in this study, only Hsc70.3 was shown to interact with CP in the cytoplasm, the nucleus, and as inclusion bodies. During PepMV infection in tomato plants, induction of Hsc70 mRNA and protein levels was observed, accumulation and its co-localization with PepMV-viroplasm as well as immunodetection together with purified PepMV-virions. The above data suggest an active role of Hsc70 in virus infection through its binding with CP, a protein also involved in potexviruses movement. The silence of Hsp70 in N. benthamiana plants had as a result a dramatic reduction in the systemic virus detection, and similar results were observed also in the approach using quercetin. Conclusively, these results demonstrate an important role of Ηsp70/CP interaction possibly in virus movement. p25 was verified as protein interactor of the catalase and their subcellular localization revealed their presence in the cytoplasm and the nucleus, in agreement with the identified sites of their interaction. The PepMV infection of tomato plants had no effect in the variation of mRNA and protein levels, but instead a specific induction of catalase activity was recorded and vice versa with the presence of H2O2. Further analysis showed that the increased enzyme activity was specifically due to the p25 interaction, probably mediated suppression of the plant oxidative stress defense mechanism in virus favour since catalase gene silencing studies in N. benthamiana plants showed that high catalase activity ensures high virus levels. Screening of four PepMV-proteins to study their role in the RNA silencing mechanism revealed that p25 and CP, exhibited different suppressing activities and mechanisms of action, and probably targeted different steps of the PTGS. These data constitute the first report of CP as a PTGS-suppressor in the Potexvirus genus, and also the dual role of p25 in the suppression of two different defense mechanisms, RNA silencing and oxidative stress. The multifunctional p25 protein was also demonstrated to interact with a tomato protein that includes a thioredoxin domain and this protein was phylogenetically related to the thioredoxin type z proteins, a category of proteins related with the oxidative stress as synergistic regulators of antioxidant enzymes functions.…

Subjects/Keywords: Τομάτα (Solanum lycopersicum); Ιός του μωσαϊκού του Solanum muricatum; Αλληλεπιδράσεις πρωτεϊνών; Σίγηση γονιδίων; Καταστολέας; Σίγηση του RNA; Καταλάση; Hsc70; Tomato (Solanum lycopersicum); Pepino mosaic virus; Protein interactions; Gene silencing; Suppressor; RNA silencing; Catalase; Hsc70

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APA (6^th Edition):

Mathioudakis, M. (2012). Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού. (Thesis). Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ). Retrieved from http://hdl.handle.net/10442/hedi/29890

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mathioudakis, Matthaios. “Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού.” 2012. Thesis, Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ). Accessed March 01, 2021. http://hdl.handle.net/10442/hedi/29890.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mathioudakis, Matthaios. “Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού.” 2012. Web. 01 Mar 2021.

Vancouver:

Mathioudakis M. Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού. [Internet] [Thesis]. Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ); 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10442/hedi/29890.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mathioudakis M. Αλληλεπιδράσεις πρωτεϊνών του ιού του μωσαϊκού του Solanum muricatum και της τομάτας και μελέτη του ρόλου ιικών-φυτικών πρωτεϊνών στην καταστολή σίγησης του RNA και την αναπαραγωγή του ιού. [Thesis]. Aristotle University Of Thessaloniki (AUTH); Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (ΑΠΘ); 2012. Available from: http://hdl.handle.net/10442/hedi/29890

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

7. Powers, Jason Gannon. Mapping Replication and Silencing Suppression Elements in the RCNMV Genome.

Degree: PhD, Genetics, 2009, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/3948

► Viruses infect all Kingdoms of life on Earth. Their life cycle represents a constant struggle for survival in hostile cellular environments. To survive the virus… (more)

Subjects/Keywords: Virus; RNA Silencing; Suppressor; VSR; TCV-sGFP; RCNMV; Viral Replication

…Second Suppressor of RNA Silencing… …Green Fluorescent Protein Sub-genomic RNA Suppressor of Gene Silencing 3 Short-interfering RNA… …rattle virus Vaccinia virus Viral suppressor(s) of RNA silencing Chapter 1 A… …protein SUPPRESSOR OF GENE SILENCING 3 (SGS3) uses the single-stranded RNA fragment to… …providing some valuable insight into RNA silencing and viruses, as does Robert Franks for agreeing…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Powers, J. G. (2009). Mapping Replication and Silencing Suppression Elements in the RCNMV Genome. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/3948

Chicago Manual of Style (16^th Edition):

Powers, Jason Gannon. “Mapping Replication and Silencing Suppression Elements in the RCNMV Genome.” 2009. Doctoral Dissertation, North Carolina State University. Accessed March 01, 2021. http://www.lib.ncsu.edu/resolver/1840.16/3948.

MLA Handbook (7^th Edition):

Powers, Jason Gannon. “Mapping Replication and Silencing Suppression Elements in the RCNMV Genome.” 2009. Web. 01 Mar 2021.

Vancouver:

Powers JG. Mapping Replication and Silencing Suppression Elements in the RCNMV Genome. [Internet] [Doctoral dissertation]. North Carolina State University; 2009. [cited 2021 Mar 01]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3948.

Council of Science Editors:

Powers JG. Mapping Replication and Silencing Suppression Elements in the RCNMV Genome. [Doctoral Dissertation]. North Carolina State University; 2009. Available from: http://www.lib.ncsu.edu/resolver/1840.16/3948

Virginia Tech

8. Allen, William Joseph. Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease.

Degree: PhD, Biochemistry, 2011, Virginia Tech

URL: http://hdl.handle.net/10919/78000

► Molecular modeling is a term referring to the study of proteins, nucleic acids, lipids, and other bio- or macro- or small molecules at the atomistic… (more)

▼ Molecular modeling is a term referring to the study of proteins, nucleic acids, lipids, and other bio- or macro- or small molecules at the atomistic level using a combination of computational methods, physico-chemical principles, and mathematical functions. It can be generally sub-divided into two areas: molecular mechanics, which is the treatment of atoms and bonds as Newtonian particles and springs, and quantum mechanics, which models electronic behaviors using the Schrödinger equation and wavefunctions. Each technique is a powerful tool that, when used alone or in combination with wet lab experiments, can yield useful results, the products of which have broad applications in studying human disease models, oxidative damage, and other biomolecular processes that are otherwise not easily observed by experiment alone. Within this document, we study seven different such systems. This includes the mode of inhibitor binding to the enzyme monoamine oxidase B, the active site mechanism of that same enzyme, the dynamics of the unstructured p53 C-terminal domain in complex with globular, structured proteins, the process of the viral protein B2 unbinding from double-stranded RNA, and a focus on the dynamics of a variable loop in the antigenic peanut protein Ara h 2. In addition to those conventional molecular modeling studies, several of which were done in tandem with wet lab experiment, we also discuss the validation of charges and charge group parameters for small molecules used in molecular mechanics, and the development of software for the analysis of lipid bilayer systems in molecular mechanics simulations. As computational resources continue to evolve, and as more structural information becomes available, these methods are becoming an integral part of the study of biomolecules in the context of disease. Advisors/Committee Members: Bevan, David R. (committeechair), Li, Jianyong (committee member), Smith, Edward J. (committee member), Tanko, James M. (committee member), Helm, Richard Frederick (committee member).

Subjects/Keywords: Arachis Ara h 2 protein; molecular modeling; monoamine oxidase B; p53 C-terminal domain; B2 suppressor of RNA silencing; lipid bilayer analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Allen, W. J. (2011). Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/78000

Chicago Manual of Style (16^th Edition):

Allen, William Joseph. “Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease.” 2011. Doctoral Dissertation, Virginia Tech. Accessed March 01, 2021. http://hdl.handle.net/10919/78000.

MLA Handbook (7^th Edition):

Allen, William Joseph. “Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease.” 2011. Web. 01 Mar 2021.

Vancouver:

Allen WJ. Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease. [Internet] [Doctoral dissertation]. Virginia Tech; 2011. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/10919/78000.

Council of Science Editors:

Allen WJ. Practical Applications of Molecular Modeling Pertaining to Oxidative Damage and Disease. [Doctoral Dissertation]. Virginia Tech; 2011. Available from: http://hdl.handle.net/10919/78000

Queensland University of Technology

9. Tsao, Theresa Tsun-Hui. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.

Degree: 2008, Queensland University of Technology

URL: https://eprints.qut.edu.au/17031/

► Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising… (more)

▼ Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising strategies to control BBTV. Pathogen-derived resistance (PDR) strategies have been applied successfully to generate plants that are resistant to numerous different viruses, primarily against those viruses with RNA genomes. BBTV is a circular, single-stranded (css) DNA virus of the family Nanoviridae, which is closely related to the family Geminiviridae. Although there are some successful examples of PDR against geminiviruses, PDR against the nanoviruses has not been reported. Therefore, the aim of this thesis was to investigate the potential of BBTV genes to interfere with virus replication when used as transgenes for engineering banana plants resistance to BBTV. The replication initiation protein (Rep) of nanoviruses is the only viral protein essential for viral replication and represents an ideal target for PDR. Therefore, this thesis focused on the effect of wild-type or mutated Rep genes from BBTV satellite DNAs or the BBTV integral genome on the replication of BBTV in banana embryogenic cell suspensions. A new Rep-encoding satellite DNA, designated BBTV DNA-S4, was isolated from a Vietnamese BBTV isolate and characterised. When the effect of DNA-S4 on the replication of BBTV was examined, it was found that DNA-S4 enhanced the replication of BBTV. When the replicative capabilities of DNA-S4 and the previously characterised Rep-encoding BBTV satellite, DNA-S1, were compared, it was found that the amount of DNA-S4 accumulated to higher levels than DNA-S1. The interaction between BBTV and DNA-S1 was also examined. It was found that over-expression of the Rep encoded by DNA-S1 using ubi1 maize polyubiquitin promoter enhanced replication of BBTV. However, when the Rep-encoded by DNA-S1 was expressed by the native S1 promoter (in plasmid pBT1.1-S1), it suppressed the replication of BBTV. Based on this result, the use of DNA-S1 as a possible transgene to generate PDR against BBTV was investigated. The roles of the Rep-encoding and U5 genes of BBTV DNA-R, and the effects of over-expression of these two genes on BBTV replication were also investigated. Three mutants of BBTV DNA-R were constructed; plasmid pUbi-RepOnly-nos contained the ubi1 promoter driving Rep expression from DNA-R, plasmid pUbi-IntOnly-nos contained the ubi1 promoter driving expression of the DNA-R internal gene product (U5), while plasmid pUbi-R.ORF-nos contained the ubi1 promoter driving the expression of both Rep and the internal U5 gene product. The replication of BBTV was found to be significantly suppressed by pUbi-RepOnly-nos, weakly suppressed by pUbi-IntOnly-nos, but strongly enhanced by pUbi-R.ORF-nos. The effect of mutations in three conserved residues within the BBTV Rep on BBTV replication was also assessed. These mutations were all made in the regions in the ATPase motifs and resulted in changes from hydrophilic to hydrophobic residues (i.e. K187→M, D224→I and N268→L). None of…

Subjects/Keywords: banana bunchy top virus; nanoviruses; replication initiation protein (Rep); pathogen-derived resistance; BBTV DNA-R; BBTV DNA-S1; BBTV DNA-S3; BBTV DNA-S4; satellite DNA; ATPase; post-transcriptional gene silencing; RNA silencing suppressor

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tsao, T. T. (2008). Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Thesis, Queensland University of Technology. Accessed March 01, 2021. https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Web. 01 Mar 2021.

Vancouver:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Internet] [Thesis]. Queensland University of Technology; 2008. [cited 2021 Mar 01]. Available from: https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Thesis]. Queensland University of Technology; 2008. Available from: https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

The Ohio State University

10. Jackel, Jamie Nicole. GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION.

Degree: PhD, Molecular Genetics, 2013, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1367494030

► RNA silencing refers to a set of mechanistically related and evolutionarily conserved processes including post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). In plants,… (more)

▼ RNA silencing refers to a set of mechanistically related and evolutionarily conserved processes including post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). In plants, TGS is often accompanied by RNA-directed DNA methylation (RdDM). Both PTGS and TGS use specialized double stranded RNA binding proteins (DRBs) in conjunction with specific ribonucleases (Dicer-like proteins; DCL) to cleave 21, 22, or 24 nucleotide (nt) small interfering RNAs (siRNAs) from large double stranded RNAs (dsRNA). Cytoplasmic PTGS utilizes 21 and 22 nt siRNAs to target mRNA for degradation. The current model for TGS/RdDM involves a complex nuclear pathway where evolutionarily related forms of RNA polymerase II (Pol II), known as Pol IV and Pol V, transcribe DNA and work together with RNA dependent RNA polymerase 2 (RDR2) to produce long dsRNAs that are cleaved into 24 nt siRNAs by Dicer-like 3 (DCL3). These siRNAs associate with a complex that contains the ribonuclease argonaute 4 (AGO4) to recruit histone and DNA methyltransferases that subsequently target homologous DNA for methylation-mediated silencing. A feature that enhances PTGS and TGS defense is the ability of the silencing signal to spread from cell-to-cell and systemically throughout the plant. An antiviral role is well established, and the importance of PTGS as a host defense is clear from the fact that virtually all plant viruses encode proteins that target and suppress different aspects of this pathway. By contrast, while TGS has long been known to suppress potentially damaging DNA such as transposons, it has only recently been shown to target geminivirus DNA for repressive methylation. Geminiviruses are circular single-stranded DNA (ssDNA) viruses that replicate in the nucleus through a double-stranded DNA (dsDNA) intermediate that associates with histones to form minichromosomes. Geminiviruses depend on host cellular machinery for both replication and transcription, thus providing excellent models to study the epigenetic regulation of these processes. Unlike most plant viruses (which have RNA genomes) geminiviruses must combat both PTGS and TGS defense pathways in order to be successful. We have shown that two related geminivirus-encoded silencing suppressors, AL2 and L2, suppress both PTGS and TGS by interacting with and inhibiting adenosine kinase (ADK), a methyl cycle co-factor. However, recent work has identified an additional suppression function of AL2 that is independent of ADK inhibition and requires AL2ߣs ability to activate transcription of host genes. Chapter 2 of this thesis characterizes the transcription activation-dependent suppressor function of AL2 in TGS reversal and the inhibition of systemic spread of silencing. Using ADK knock-down, it was determined that methyl cycle inhibition has no impact on systemic spread and that AL2, but not L2 or AL2 lacking its transcriptional activation domain (AL2 1-114), can prevent the spread of the silencing signal. Thus inhibition of systemic silencing likely depends on the ability of… Advisors/Committee Members: Bisaro, David (Advisor), Parris, Deborah (Advisor).

Subjects/Keywords: Molecular Biology; Plant Biology; Virology; RNA polymerase IV; RNA polymerase V; DNA methylation; histone methylation; geminivirus; DRB proteins; Dicer-like proteins; Argonaute proteins; silencing suppressor; AL2; L2; Adenosine Kinase; methyl cycle

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jackel, J. N. (2013). GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1367494030

Chicago Manual of Style (16^th Edition):

Jackel, Jamie Nicole. “GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION.” 2013. Doctoral Dissertation, The Ohio State University. Accessed March 01, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1367494030.

MLA Handbook (7^th Edition):

Jackel, Jamie Nicole. “GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION.” 2013. Web. 01 Mar 2021.

Vancouver:

Jackel JN. GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION. [Internet] [Doctoral dissertation]. The Ohio State University; 2013. [cited 2021 Mar 01]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1367494030.

Council of Science Editors:

Jackel JN. GEMINIVIRUSES AS MODELS TO STUDY THE ESTABLISHMENT AND MAINTENANCE OF DNA METHYLATION. [Doctoral Dissertation]. The Ohio State University; 2013. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1367494030

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