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 / TESIS / Compendio

A produção de proteínas e peptídeos heterólogos representa um dos mais importantes segmentos do setor biotecnológico. Apesar das diferentes tecnologias hoje disponíveis para a (bio) síntese de proteínas e peptídeos (como a síntese química ou o emprego de microrganismos, animais e plantas transgênicos), nenhuma destas é capaz de produzir uma quantidade suficiente de proteínas e peptídeos para suprir as necessidades do mercado por apresentarem altos custos de produção e comercialização. Diante disso, este projeto visou utilizar os sistemas genéticos alternativos ou não convencionais existentes nas células da levedura Saccharomyces cerevisiae para a produção de peptídeos e proteínas heterólogas em larga escala, com um alto grau de pureza necessário às aplicações clínicas e com um custo de produção relativamente baixo para uso comercial. Estes sistemas não convencionais, representados especialmente por partículas virais intracelulares de S. cerevisiae, são conhecidos há várias décadas por conferirem o fenótipo killer em diferentes linhagens de leveduras, tanto para os isolados ambientais quanto para as linhagens utilizadas industrialmente. As características moleculares destes sistemas virais são bem conhecidas, sendo que os genomas dos diferentes tipos de partículas virais de S. cerevisiae já foram completamente seqüenciados. Assim, este trabalho avaliou a capacidade de leveduras industriais e laboratoriais em produzir proteínas e peptídeos heterólogos funcionais utilizando para tanto, um sistema viral naturalmente presente na levedura, que compreende um mutante natural do vírus helper L-A denominado de sistema viral X de S. cerevisiae. / Submitted by Marcelo Teixeira (mvteixeira@ucs.br) on 2014-06-02T19:51:46Z No. of bitstreams: 1 Dissertacao Queli Defaveri Varela.pdf: 4371110 bytes, checksum: 9992e73e45f4352a46630f52b980c259 (MD5) / Made available in DSpace on 2014-06-02T19:51:46Z (GMT). No. of bitstreams: 1 Dissertacao Queli Defaveri Varela.pdf: 4371110 bytes, checksum: 9992e73e45f4352a46630f52b980c259 (MD5) / The production of heterologous proteins and peptides represents one of the most important segments of the biotechnology industry. Despite the different technologies available today for (bio) synthesis of proteins and peptides (such as chemical synthesis or the use of microorganisms, transgenic animals and plants), none of these are capable of producing sufficient quantities of proteins and peptides to the needs of the market because they present high costs of production and marketing. Thus, this project aims to use the alternative genetic systems or unconventional existing in the cells of the yeast Saccharomyces cerevisiae for the production of heterologous proteins and peptides on a large scale, with a high degree of purity needed for clinical applications and at a cost of production compared low for commercial use. These non-conventional systems, particularly represented by intracellular viral particles of S. cerevisiae, are known for several decades to give the killer phenotype in different strains of yeast, both for environmental isolates and to the strains used industrially. The molecular characteristics of these viral systems are well known, and the genomes of different types of viral particles from S. cerevisiae have been completely sequenced. Thus, this work assessed the capacity of industrial and laboratory yeasts to produce heterologous proteins and peptides using a viral system naturally present in yeast that is a natural mutant of the helper virus L-A, called X system of S. cerevisiae.

A produção de proteínas e peptídeos heterólogos representa um dos mais importantes segmentos do setor biotecnológico. Apesar das diferentes tecnologias hoje disponíveis para a (bio) síntese de proteínas e peptídeos (como a síntese química ou o emprego de microrganismos, animais e plantas transgênicos), nenhuma destas é capaz de produzir uma quantidade suficiente de proteínas e peptídeos para suprir as necessidades do mercado por apresentarem altos custos de produção e comercialização. Diante disso, este projeto visou utilizar os sistemas genéticos alternativos ou não convencionais existentes nas células da levedura Saccharomyces cerevisiae para a produção de peptídeos e proteínas heterólogas em larga escala, com um alto grau de pureza necessário às aplicações clínicas e com um custo de produção relativamente baixo para uso comercial. Estes sistemas não convencionais, representados especialmente por partículas virais intracelulares de S. cerevisiae, são conhecidos há várias décadas por conferirem o fenótipo killer em diferentes linhagens de leveduras, tanto para os isolados ambientais quanto para as linhagens utilizadas industrialmente. As características moleculares destes sistemas virais são bem conhecidas, sendo que os genomas dos diferentes tipos de partículas virais de S. cerevisiae já foram completamente seqüenciados. Assim, este trabalho avaliou a capacidade de leveduras industriais e laboratoriais em produzir proteínas e peptídeos heterólogos funcionais utilizando para tanto, um sistema viral naturalmente presente na levedura, que compreende um mutante natural do vírus helper L-A denominado de sistema viral X de S. cerevisiae. / The production of heterologous proteins and peptides represents one of the most important segments of the biotechnology industry. Despite the different technologies available today for (bio) synthesis of proteins and peptides (such as chemical synthesis or the use of microorganisms, transgenic animals and plants), none of these are capable of producing sufficient quantities of proteins and peptides to the needs of the market because they present high costs of production and marketing. Thus, this project aims to use the alternative genetic systems or unconventional existing in the cells of the yeast Saccharomyces cerevisiae for the production of heterologous proteins and peptides on a large scale, with a high degree of purity needed for clinical applications and at a cost of production compared low for commercial use. These non-conventional systems, particularly represented by intracellular viral particles of S. cerevisiae, are known for several decades to give the killer phenotype in different strains of yeast, both for environmental isolates and to the strains used industrially. The molecular characteristics of these viral systems are well known, and the genomes of different types of viral particles from S. cerevisiae have been completely sequenced. Thus, this work assessed the capacity of industrial and laboratory yeasts to produce heterologous proteins and peptides using a viral system naturally present in yeast that is a natural mutant of the helper virus L-A, called X system of S. cerevisiae.

Production of vaccines and pharmaceutical proteins in plants is a promising nascent technology with a great potential to provide high-quality, safe and non-expensive production and delivery platform. In this work we studied the experimental vaccine against human papillomavirus based on modified plant pathogen - Potato virus X (PVX). The experimental vaccine is based on PVX virus particles decorated with genetically fused HPV-E7 oncoprotein. These chimeric virus particles should be able to activate strong and specific cellular immune response. However the modification of the PVX coat protein with such relatively large fused protein might influence its ability to form particles. In this work we have characterized some properties of such chimeric virus particles like solubility or ability infect host plant. (In Czech)

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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