The latest model of tertiary structure of capsid protein of potato virus X (PVX CP) was used as a template to design new insertion sites suitable for the preparation of PVX-based antigen presentation system. Based on this model, seven insertion sites (A-G) located in putative surface loops were tested. As an antigen inserted into these sites was used 17 amino acids long epitope derived from human papillomavirus type 16 E7 oncoprotein (E7 epitope) fused with either 6xHis tag or StrepII tag in both possible orientations (6xHis-E7 and E7-6xHis, StrepII-E7 and E7-StrepII). Prior to plant expression, modified PVX CPs were expressed in Escherichia coli MC1061. The results showed that only PVX CP carrying StrepII-E7 or E7-StrepII in the insertion site A formed virus particles. The results from transient expression experiments with modified PVX CPs in Nicotiana benthamiana showed that only the insertion site A (located between 24th and 25th amino acid in the PVX CP) could tolerate all tested inserts. Importantly, viral particles were detected only in the presence of StrepII tag and their stability was affected by the insert orientation (StrepII-E7 vs. E7-StrepII) as only the viral particles presenting E7-StrepII could be purified. Besides the preparation of PVX-based antigen presentation system, an...

A movement protein Potato virus X (PVX) chimera virus (PVX.GFP(CH3)) bearing the grapevine virus Grapevine rupestris stem pitting-associated virus (GRSPaV) triple gene block proteins (TGB) (denoted P1, P2 and P3) instead of the PVX TGB was delivered into N. benthamiana and other related species by agro-inoculation. This movement protein PVX chimera virus was found to be unable to support the local and systemic movement of PVX in cis. Local and systemic movement of this PVX chimera virus was restored in trans by the dianthovirus Red clover necrotic mosaic virus (RCNMV) movement protein and by a PVX TGB rescue virus that replaced the GRSPaV TGB with the PVX TGB (PVX.GFP(Rescue)). However, a PVX TGB hybrid chimera virus (PVX.GFP(HY2)) containing PVX P1 and the GRSPaV TGB had limited cell-to-cell, but not systemic, movement.

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No description available.

Plants have developed a number of ways how to minimise negative influence of the environment. As a consequence of stress action, plants carbohydrate metabolism is quite often influenced, esp. on the level of expression and activities of different enzymes and also several metabolites concentration. One of key enzymes of carbohydrate metabolism is invertase. The aim of this work was to find out, whether the activity of its isoforms (cytoplasmic, vacuolar and extracellular) in tobacco plants is influenced by Potato virus Y (PVY). It was shown, that activity of cytoplasmic invertase was not affected, but the activity of vacuolar and extracellular isoform was enhanced during potyviral infection. Hence, it is likely, that vacuolar and extracellular invertases are related to plant antiviral defence. The effect of PVY on other enzymes of carbohydrate metabolism and several metabolites content was studied. Activity of α-amylase and phosphorylase, starch-degrading enzymes, was strongly enhanced during potyviral infection. That is probably how plant cells get glucose, which is a key source of energy and metabolites for biosynthesis of different compounds. It may also serve as a signal molecule. Activity of other hydrolytic enzymes, β-glucosidase and β-hexosaminidase, was also slightly increased. There was no...

Pepper (Capsicum annuum L.) is an important vegetable crop grown and consumed worldwide. Potato virus Y (PVY) is a globally economically important pathogen which significantly reduces the yield and quality of cultivated pepper. The virus is considered as a major limiting factor to the economic production of pepper in the province of KwaZulu-Natal (KZN) in the Republic of South Africa (RSA). Many applied practices to control the spread of PVY are ineffective to mitigate the losses incurred by many farming communities across the KZN province. Therefore, the objectives of this study was to determine the full genome sequence of a PVY isolate from KZN, to identify resistance alleles in commercially available pepper varieties in KZN and to develop a pepper hybrid variety with resistance to PVY using a molecular breeding strategy The first part of the study was conducted to determine the first full genome sequence of a PVY isolate (JVW-186) infecting pepper from KZN. The complete genome sequence of JVW-186 was assembled from overlapping RT-PCR clones using MEGA 5 software. Individual ORFs were identified using the nucleotide data base NCBI and aligned using CLUSTALW. RDP4 software was used to identify recombination junctions in the sequence alignment of JVW-186. CLC Main Workbench 6 software was used to determine the nucleotide sequence similarity of recombinant and non-recombinant fragments of JVW-186 in conjunction with ten PVY parental isolates. Based on sequence data, virus morphology and the coat protein size as determined by SDS-PAGE analysis, the identity of the isolate JVW-186 was confirmed as PVY. Phylogenetic trees were constructed from all recombinant and non-recombinant segments of the sequence by the maximum likelihood method using MEGA 5 software. The full length sequence of JVW-186 consisted of 9700bp. Two ORF’s were identified at position 186 and 2915 of the sequence alignment encoding the viral polyprotein and the frameshift translated protein P3N-PIPO, respectively. RDP4 software confirmed two recombination breakpoints at position 343 and 9308 of the sequence resulting in four segments of the genome. At each recombination event, a 1021-bp fragment at the 5’ end in the region of the P1/HC-Pro protein and a 392-bp fragment in the region of the coat protein shared a high sequence similarity of 91.8 % and 98.89 % to the potato borne PVYC parental isolate PRI-509 and the PVYO parental isolate SASA-110 respectively. The non-recombinant fragment 1 clustered within the C clade of PVY isolates; however the large 7942-bp fragment 3 did not cluster within any of the clades although it shared > 80% nucleotide sequence similarity to other PVY isolates used in this study. Our results suggest that isolate JVW-186 is a novel recombinant strain of PVY that could have evolved due to the dynamics of selection. The second part of the study aimed to evaluate different pepper lines for resistance to PVY. Two recessive alleles (pvr21 and pvr22) located on the pvr2-elF4E locus are known to confer resistance to the virus. To this end, six pepper lines were challenged with PVY infected Nicotiana tabacum cv. Xanthi leaf material using mechanical inoculation under greenhouse conditions. Each line was assessed for resistance to PVY by visual screening for disease severity and quantitative enzyme linked immunosorbent assay (ELISA) for virus load. Pepper lines were further characterized using tetra-primer ARMS-PCR (amplification refractory mutation system polymerase chain reaction) to identify and differentiate the presence of homozygous/heterozygous resistance alleles that confer PVY resistance. Evaluations revealed two resistant pepper lines (Double Up and Cecelia) and varying levels of susceptibility in the other four pepper lines challenged with PVY. The most susceptible pepper line was Benno, although high levels of susceptibility were observed in three other lines (IP, Mantenga and Excellence). The pvr2+ allele was positively identified in all the susceptible pepper lines using the T200A tetra-primer which confirms that the presence of this allele is dominant for PVY susceptibility. Double Up and Cecelia were genotyped homozygous pvr21/pvr21 and pvr22/pvr22 respectively, and remained asymptomatic throughout the trial which indicates that these alleles confer resistance to the isolate of PVY used in this study. The information generated in this study can be incorporated into breeding programs intended to control PVY on pepper in KZN. The final part of the study focused on the development of resistant varieties as the best alternative to manage PVY diseases on pepper. Homozygous F2 pepper lines were developed from local germplasm carrying PVY resistance genes (pvr21 and pvr22) using marker assisted selection (MAS). The F1 progeny was obtained by crossing a homozygous pvr21 (resistant) ‘Double Up’ cultivar with a heterozygous susceptible (pvr2+/pvr22) ‘Benno’ cultivar. F1 and F2 generations were assessed for the presence of PVY resistance/susceptibility alleles (pvr2+/pvr21/pvr22) at the pvr2-elF4e locus using the tetra primer amplification refractory mutation system – polymerase chain reaction (ARMS-PCR) procedure. Negative selection was carried out using the tetra-primer T200A marker to detect the pvr2+ (susceptible) allele. All F1 progeny displaying the pvr2+ allele were eliminated from further study. All 302 plants belonging to 29 F2 families expressing homozygous recessive traits were tested via mechanical inoculation for their response to PVY infection and resistance to PVY was confirmed in all selected families based on symptomatology in greenhouse house screens using double antibody sandwich enzyme linked immunosorbent assay (DAS-ELISA). These results show that ARMS-PCR can be used to successfully screen pepper genotypes for alleles that confer PVY resistance thereby contributing to the improvement of pepper production using molecular breeding approaches. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Whithin their natural environment, plants are subjected to a combination of stress conditions. Since potential interactions between signal pathways, plants respond to multiple stresses differently from how they do to individual stresses, activating a specific programme. Heat shock proteins (HSP70) overexpressed after heat shock influence the viral infection. On one side HSP70 can participate on refolding of aggregated or partially denaturated proteins, on the other side HSP70 can interact with viral proteins and facilitate propagation of viral replication complexes. In this work the effect of heat shock (42řC, 2. hours) applied before or after the inoculation of plants Nicotiana tabacum L. cv. Petit Havana SR1 with Potato virus Y on viral infection was detected. This effect was studied in two biological experiments. The amount of coat protein of PVYNTN and protein HSP70 were detected simultaneously with the activity assays of Hatch-Slack cycle enzymes, glycosidases and peroxidase. Both experimental approaches (heat shock applied before or after the inoculation by PVYNTN ) enhanced amount of the virus and in the 2nd experiment it accelerated infection development. Immediately after application of heat shock the amount of HSP70 was increased. The enhancement of HSP70 by viral infection occurred...

Tesis por compendio / [ES] En el contexto actual de cambio climático, resulta urgente desarrollar nuevas tecnologías de fitomejoramiento que garanticen el suministro de alimentos a una población en rápido crecimiento. La reciente aparición de herramientas basadas en las repeticiones palindrómicas cortas agrupadas y regularmente interespaciadas (del acrónimo CRISPR en inglés) y sus proteínas asociadas (Cas) ha revolucionado la edición genómica dirigida, resultando muy prometedora tanto para la biología vegetal básica como para la mejora de cultivos. Los sistemas CRISPR-Cas más comunes incluyen una endonucleasa Cas y un ARN guía que determina específicamente la secuencia diana a editar en el genoma. El suministro de los componentes de reacción CRISPR-Cas a una célula vegetal es un paso crucial que influye notablemente en la velocidad y la eficiencia de edición. Los enfoques convencionales se basan en el suministro de dichos componentes mediante tecnologías de transformación o la expresión transitoria en protoplastos, siendo ambos procesos laboriosos que pueden acarrear problemas legales. Alternativamente, estudios recientes han destacado el potencial de virus de ARN para ser utilizados como vectores de expresión transitoria de los componentes de reacción CRISPR-Cas en plantas, también conocido como edición genómica inducida por virus (VIGE en inglés). Puesto que la aplicabilidad de cada vector viral se encuentra limitada por sus propiedades moleculares y un rango específico de plantas huésped, esta Tesis ha tenido como objetivo principal expandir y mejorar las herramientas disponibles para el VIGE. En primer lugar, diseñamos un vector derivado del Virus X de la patata (PVX; género Potexvirus; familia Alphaflexiviridae) para suministrar múltiples ARNs guía a una línea transformada de Nicotiana benthamiana que expresaba constitutivamente la nucleasa Cas9 de Streptococcus pyogenes. Mediante el vector derivado de PVX, conseguimos editar genes endógenos de la planta huésped de manera eficiente, IV produciendo casi un 80% de modificaciones en tejidos de plantas adultas. Curiosamente, PVX permitió la expresión simultánea de matrices de ARNs guía no espaciados, lo cual resultó en la edición de múltiples genes en pocos días. Obtuvimos progenies editadas con una alta tasa de mutaciones bialélicas hereditarias tanto de plantas regeneradas a partir de tejido infectado como de semillas de plantas infectadas; en este último caso, el ARN guía fue previamente fusionado a un módulo de ARN móvil. Dado que PVX no se transmite por semillas, todas las plántulas editadas estaban libres de virus. A fin de expandir las estrategias basadas en virus de plantas para una edición genómica sin transformación, seguidamente desarrollamos un sistema de dos vectores virales compatibles para el suministro simultáneo de todos los componentes de reacción CRISPR-Cas en la planta. Modificamos el Virus del grabado del tabaco (TEV; género Potyvirus; familia Potyviridae) para que expresase una nucleasa Cas12a y, en combinación con el envío de ARN guía mediante PVX, logramos la edición sin transformación de una línea de N. benthamiana que expresaba constitutivamente la NIb del potyvirus. Además, demostramos que un único vector PVX era capaz de proporcionar la actividad de NIb, así como de suministrar el ARN guía para la edición genómica en plantas silvestres. En conjunto, el trabajo realizado en esta Tesis contribuye a la expansión de las herramientas actuales para VIGE. La amplia gama de huéspedes que poseen tanto PVX como TEV, particularmente entre solanáceas, postula a ambos virus como candidatos muy prometedores para futuras aplicaciones en genómica funcional y mejora de cultivos. / [CA] En el context actual de canvi climàtic, resulta urgent desenvolupar noves tecnologies de fitomillorament que garantisquen el subministrament d'aliments a una població en ràpid creixement. La recent aparició d'eines basades en les repeticions palindròmiques curtes agrupades i regularment interespaiades (de l'acrònim CRISPR en anglés) i les seues proteïnes associades (Cas) ha revolucionat l'edició genòmica dirigida, resultant molt prometedora tant per a la biologia vegetal bàsica com per a la millora de cultius. Els sistemes CRISPR-Cas més comuns inclouen una endonucleasa Cas i un ARN guia que determina específicament la seqüència diana a editar en el genoma. El subministrament dels components de reacció CRISPR-Cas a una cèl·lula vegetal és un pas crucial que influeix notablement en la velocitat i l'eficiència d'edició. Els enfocaments convencionals es basen en el subministrament d'aquests components mitjançant tecnologies de transformació o l'expressió transitòria en protoplasts, sent tots dos processos laboriosos que poden implicar problemes legals. Alternativament, estudis recents han destacat el potencial de virus d'ARN per a ser utilitzats com a vectors d'expressió transitòria dels components de reacció CRISPR-Cas en plantes, també conegut com a edició genòmica induïda per virus (VIGE en anglés). Com que l'aplicabilitat de cada vector viral es troba limitada per les seues propietats mol·leculars i un rang específic de plantes hoste, aquesta Tesi ha tingut com a objectiu principal expandir i millorar les eines disponibles per al VIGE. En primer lloc, dissenyem un vector derivat del Virus X de la creïlla (PVX; gènere Potexvirus; família Alphaflexiviridae) per a subministrar múltiples ARNs guia a una línia transformada de Nicotiana benthamiana que expressava constitutivament la nucleasa Cas9 de Streptococcus pyogenes. Mitjançant el vector derivat de PVX, aconseguim editar gens endògens de la planta hoste de manera eficient, produint quasi un 80% de modificacions en teixits de plantes adultes. Curiosament, PVX va permetre l'expressió VI simultània de matrius d'ARNs guia no espaiats, la qual cosa va resultar en l'edició de múltiples gens en pocs dies. Vam obtindre progènies editades amb una alta taxa de mutacions bial·lèliques hereditàries tant de plantes regenerades a partir de teixit infectat com de llavors de plantes infectades; en aquest últim cas, l'ARN guia va ser prèviament fusionat a un mòdul d'ARN mòbil. Atés que PVX no es transmet per llavors, totes les plàntules editades estaven lliures de virus. A fi d'expandir les estratègies basades en virus de plantes per a una edició genòmica sense transformació, seguidament desenvolupem un sistema de dos vectors virals compatibles per al subministrament simultani de tots els components de reacció CRISPR-Cas en la planta. Modifiquem el Virus del gravat del tabac (TEV; gènere Potyvirus; família Potyviridae) perquè expressara una nucleasa Cas12a i, en combinació amb l'enviament d'ARN guia mitjançant PVX, aconseguim l'edició sense transformació d'una línia de N. benthamiana que expressava constitutivament la NIb del potyvirus. A més, vam demostrar que un únic vector PVX era capaç de proporcionar l'activitat de NIb, així com de subministrar l'ARN guia per a l'edició genòmica en plantes silvestres. En conjunt, el treball realitzat en aquesta Tesi contribueix a l'expansió de les eines actuals per a VIGE. L'àmplia gamma d'hostes que posseeixen tant PVX com TEV, particularment entre solanàcies, postula a tots dos virus com a candidats molt prometedors per a futures aplicacions en genòmica funcional i millora de cultius. / [EN] Innovative breeding technologies are urgently needed to ensure food supply to a rapidly growing population in the face of climate change. The recent emergence of tools based on the clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins has revolutionized targeted genome editing, thus holding great promise to both basic plant science and precision crop breeding. Most common CRISPR-Cas arrangements include a Cas endonuclease and a single guide RNA (sgRNA) that determines the specific target sequence to edit in the genome. The delivery of CRISPR-Cas reaction components within a plant cell is a crucial step that greatly influences editing speed and efficiency. Conventional approaches rely on supplying editing reaction components by transformation technologies or transient delivery to protoplasts, both of which are laborious processes that can raise legal concerns. Alternatively, recent studies have highlighted the potential of plant RNA viruses as transient delivery vectors of CRISPR-Cas reaction components, following the so-called virus-induced genome editing (VIGE). Since the applicability of each viral vector is limited to its molecular biology properties and a specific host range, the main objective of this Thesis has been to expand and improve the available toolbox for VIGE. First, we engineered a vector derived from Potato virus X (PVX; genus Potexvirus; family Alphaflexiviridae) to deliver multiple sgRNAs in a Nicotiana benthamiana transformed line constitutively expressing Streptococcus pyogenes Cas9. Using the PVX derived vector, host endogenous genes were efficiently targeted, producing nearly 80% indels in the tissues of adult plants. Interestingly, PVX allowed the simultaneous expression of unspaced sgRNA arrays, achieving highly efficient multiplex editing in a few days. We obtained edited progeny with a high rate of heritable bi-allelic mutations either from plants regenerated from infected tissue or infected plant seeds; in the latter II case, the sgRNA was previously fused to a mobile RNA module. Hence, since PVX is not seed-transmitted, all edited seedlings were virus-free. Aiming to expand the virus-based toolbox for transformation-free editing, we next developed a two-compatible virus vector system for the simultaneous delivery of all CRISPR-Cas reaction components in the plant. Tobacco etch virus (TEV; genus Potyvirus; family Potyviridae) was engineered to express a Cas12a nuclease, and in combination with PVX-assisted sgRNA delivery, we achieved successful transformation-free genome editing in a N. benthamiana line constitutively expressing potyviral NIb. Moreover, we demonstrated that a single PVX vector can supply the potyviral NIb activity as well as perform sgRNA delivery for genome editing in wild-type plants. Altogether, the work performed in this Thesis contributes to the enrichment of the current VIGE toolbox. The wide host range that both PVX and TEV possess, particularly among solanaceous species, postulates them as promising candidates for future applications in VIGE-mediated functional genomics and precision breeding. / Uranga Ruiz De Eguino, M. (2022). Engineering Viral Vectors for CRISPR-Cas Mediated Genome Editing in Plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/183374 / Compendio

Potato virus Y (PVY) is an economically important virus worldwide. In South Africa, PVY has been shown to be a major limiting factor in the production of important solanaceous crops, including potato (Solanum tuberosum L.), pepper (Capsicum annuum L.), tomato (Lycopersicon esculentum Mill.) and tobacco (Nicotiana spp). The variability that PVY displays, wherever the virus occurs, merits the study of the isolates occurring in KwaZulu-Natal (KZN) in the Republic of South Africa (RSA). This characterization will provide a clear understanding of strains/isolates from local vegetables and how they relate to the other PVY strains already identified, as well as information that can be used to manage the diseases they cause. Hence, the aim of this project was to study the biological and genetic properties of PVY isolates infecting potato, tomato and pepper in KZN. Enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies and reverse transcription polymerase chain reaction (RT-PCR) using primers specific to all PVY strains were used to detect the virus in plant material showing PVY-like symptoms collected from various locations in KZN. A total of 39 isolates (18 isolates infecting tomato, 12 infecting potato and 9 infecting pepper) were further differentiated into strains by means of ELISA using strain specific antibodies and RT-PCR using primers specific to the different strains of PVY identified around the world. All PVY isolates infecting tomato and pepper tested positive for the ordinary PVYO strain with both ELISA and RT-PCR. PVY isolates infecting potato were more diverse and comprised the PVYN, PVYNTN and PVYNWilga strains, with mixed infections noted in some cases. The biological properties were studied by mechanically inoculating Chenopodium quinoa, Nicotiana tabacum cv Xanthi, N. tabacum cv Samsun, N. glutinosa, and N. rustica with leaf extracts from plants infected with the different PVY strains detected in this study. All inoculated C. quinoa plants did not show symptoms. All tobacco plants showing symptoms were tested for the presence of PVY by means of ELISA using monoclonal antibodies targeting all strains and electron microscopy using the leaf dip technique. Not all the inoculated tobacco tested positive with ELISA. The symptoms observed were therefore divided into PVY-related and PVY non- related. PVY-related symptoms included vein clearing, mosaic chlorosis, stunting, and vein necrosis. PVY non-related symptoms included wrinkles and leaf distortions. Potyvirus-like particles of about 700 nm were observed under the transmission electron microscope (TEM) from plants showing PVY-related symptoms while rod shaped viral particles of sizes varying between 70 and 400 nm were observed from plants showing non-PVY related symptoms. A portion of the virus genome (1067 bp) covering part of the coat protein gene and the 3’ non-translated region (NTR) of three PVYO isolates infecting tomato, one PVYO isolate infecting pepper and one PVYNWilga isolate infecting potato were amplified, cloned and sequenced. The 5’ NTR, P1, HC-Pro and part of P3 regions (2559 bp) of a PVYN isolate infecting potato were also amplified, cloned and sequenced. Sequence data was compared with selected PVY sequences from different geographical locations around the world. These were available on the NCBI website and subsequently used for phylogenic analyses. The sequenced genomic regions of the PVYN isolate were found to be 99% similar to the New Zealand PVYN isolate (GenBank accession number: AM268435), the Swiss PVYN isolate CH605 (X97895) and the American PVYN isolate Mont (AY884983). Moreover, the deduced amino acid sequence comparison of the genomic regions of the PVYN isolate revealed the presence of five distinct amino acids residues. The three amino acid residues (D205, K400, and E419), which determine the vein necrosis phenotype in tobacco, were also identified. The coat protein and 3’ NTR sequences of all KZN PVYO isolates infecting pepper and tomato were closely similar to each other than to KZN PVYNWilga isolate infecting potato. The phylogenic analysis clustered the KZN PVYN isolate with the European sublineage N, PVYNWilga isolate infecting potato with the American PVYO isolate Oz (EF026074) in the O lineage and all PVYO isolates infecting tomato and pepper in a new sublineage within the O lineage. Taken together, these results point to the presence of PVY in solanaceous vegetables cultivated in KZN and they lay the foundation for the formulation of effective control measure against PVY diseases in KZN. / Thesis (M.Sc.) - University of KwaZulu-Natal, Pietermaritzburg, 2009.