Telomeres are critical for the integrity of eukaryotic genomes. They function to protect chromosome ends from DNA damage surveillance and inappropriate repair. Telomeres are maintained by the specialized ribonucleoprotein complex telomerase. Without telomerase, telomere shortening would ultimately lead to compromised genome stability and cellular senescence. Therefore, telomerase function is necessary for extension of the proliferative capacity of the cell. In this dissertation, we describe the characterization of core components of telomerase ribonucleoprotein complex in the flowering plant, Arabidopsis thaliana. We find that dyskerin, one of the core telomerase components in humans is also conserved in Arabidopsis telomerase. Arabidopsis dyskerin associates with the telomerase RNP in an RNA-dependent manner and is required for telomere length maintenance in this organism. We also describe the characterization of another core telomerase component, the telomerase RNA subunits (TERs). Unexpectedly, we uncovered two distinct TER subunits that share a region of high identity. The two TERs named TER1G7 and TER5G2, based on their chromosomal positions, display differences in their expression levels and their association with telomere-related proteins. Both TERs can serve as templates for telomerase in vitro. Through genetic analyses, we show a templating function for TER1G7 in vivo and a novel role for TER5G2 as a negative regulator of telomerase. Finally, the presence of TER genes in other plant species was investigated and evidence for duplication of TER genes in plants closely related to Arabidopsis was obtained. We also show evidence for a template mutation in Asparagus TER that could lead to variant repeats in this organism. In summary, the studies presented in this dissertation reveal that Arabidopsis telomerase shares both similarities and differences with other telomerase RNPs, making it an exciting model system for study of telomere biology.

Telomerase is a highly regulated ribonucleoprotein complex that stabilizes eukaryotic genomes by replenishing telomeric repeats on chromosome ends. Defects in telomerase RNP components involving the catalytic subunit TERT or the RNA template TER lead to stem cell-related diseases such as dyskeratosis congenita and idiopathic pulmonary fibrosis, while inappropriate telomerase expression is a rate-limiting step in carcinogenesis. In this study we report the discovery of a novel negative regulatory mechanism for telomerase that stems from duplication and diversification of key components of the telomerase RNP in the flowering plant Arabidopsis thaliana. We show that Arabidopsis encodes three distinct TERs: TER1, TER2 and a processed form of TER2 termed TER2S. Although all three RNAs can serve as templates for telomerase in vitro, in vivo they have different expression patterns, assemble into distinct RNPs with different protein binding partners, and play opposing roles in telomere maintenance. The TER1 RNP is analogous to the telomerase enzyme previously described in other eukaryotes, but the TER2 RNP is a negative regulator of telomerase activity and telomere maintenance in vivo. Furthermore, we demonstrate that the Protection Of Telomeres (POT1) paralogs in Arabidopsis (POT1a, POT1b and POT1c) are novel TER binding proteins. This finding is striking because in yeast and vertebrates, POT1 is an essential component of the telomere capping complex and functions to distinguish the chromosome terminus from a double-strand break. Thus, our data argue that Arabidopsis POT1 proteins have migrated off of the chromosome terminus and onto the telomerase RNP, indicating that duplication and diversification of Arabidopsis telomerase may be the end result of the co-evolution of the TER and POT1 RNP components. Additionally, given the dire consequences of misregulating telomerase in human cells, our discovery of a novel negative regulatory mechanism for telomerase in plants strongly suggests that additional modes of telomerase control remain to be elucidated in vertebrates.

abstract: The highly specialized telomerase ribonucleoprotein enzyme is composed minimally of telomerase reverse transcriptase (TERT) and telomerase RNA (TR) for catalytic activity. Telomerase is an RNA-dependent DNA polymerase that syntheizes DNA repeats at chromosome ends to maintain genome stability. While TERT is highly conserved among various groups of species, the TR subunit exhibits remarkable divergence in primary sequence, length, secondary structure and biogenesis, making TR identification extremely challenging even among closely related groups of organisms. A unique computational approach combined with in vitro telomerase activity reconstitution studies was used to identify 83 novel TRs from 10 animal kingdom phyla spanning 18 diverse classes from the most basal sponges to the late evolving vertebrates. This revealed that three structural domains, pseudoknot, a distal stem-loop moiety and box H/ACA, are conserved within TRs from basal groups to vertebrates, while group-specific elements emerge or disappear during animal TR evolution along different lineages. Next the corn-smut fungus Ustilago maydis TR was identified using an RNA-immunoprecipitation and next-generation sequencing approach followed by computational identification of TRs from 19 additional class Ustilaginomycetes fungi, leveraging conserved gene synteny among TR genes. Phylogenetic comparative analysis, in vitro telomerase activity and TR mutagenesis studies reveal a secondary structure of TRs from higher fungi, which is also conserved with vertebrates and filamentous fungi, providing a crucial link in TR evolution within the opisthokonta super-kingdom. Lastly, work by collabarotors from Texas A&M university and others identified the first bona fide TR from the model plant Arabidopsis thaliana. Computational analysis was performed to identify 85 novel AtTR orthologs from three major plant clades: angiosperms, gymnosperms and lycophytes, which facilitated phylogenetic comparative analysis to infer the first plant TR secondary structural model. This model was confirmed using site-specific mutagenesis and telomerase activity assays of in vitro reconstituted enzyme. The structures of plant TRs are conserved across land plants providing an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019

abstract: Telomerase is a specialized enzyme that adds telomeric DNA repeats to the chromosome ends to counterbalance the progressive telomere shortening over cell divisions. It has two essential core components, a catalytic telomerase reverse transcriptase protein (TERT), and a telomerase RNA (TR). TERT synthesizes telomeric DNA by reverse transcribing a short template sequence in TR. Unlike TERT, TR is extremely divergent in size, sequence and structure and has only been identified in three evolutionarily distant groups. The lack of knowledge on TR from important model organisms has been a roadblock for vigorous studies on telomerase regulation. To address this issue, a novel in vitro system combining deep-sequencing and bioinformatics search was developed to discover TR from new phylogenetic groups. The system has been validated by the successful identification of TR from echinoderm purple sea urchin Strongylocentrotus purpuratus. The sea urchin TR (spTR) is the first invertebrate TR that has been identified and can serve as a model for understanding how the vertebrate TR evolved with vertebrate-specific traits. By using phylogenetic comparative analysis, the secondary structure of spTR was determined. The spTR secondary structure reveals unique sea urchin specific structure elements as well as homologous structural features shared by TR from other organisms. This study enhanced the understanding of telomerase mechanism and the evolution of telomerase RNP. The system that was used to identity telomerase RNA can be employed for the discovery of other TR as well as the discovery of novel RNA from other RNP complex. / Dissertation/Thesis / Ph.D. Biochemistry 2011

Orientador: Maria Isabel Nogueira Cano / Resumo: Parasitos do gênero Leishmania pertencem à família Trypanosomatidae, os quais causam a leishmaniose, doença tropical negligenciada, que pode se apresentar em três formas clínicas: cutânea, mucocutânea e visceral. O Brasil é um dos países mais afetados pela doença, devido principalmente às condições socioeconômicas, às mudanças climáticas e ambientais. Pesquisas relacionadas à biologia da Leishmania contribuem para o entendimento dos mecanismos fisiológicos do parasito, e assim fornecem a possibilidade de encontrar novos alvos terapêuticos. O estudo dos telômeros de Leishmania se mostram promissores, já que estão relacionados com a estabilidade do genoma. Os telômeros estão localizados nas extremidades dos cromossomos e são responsáveis por proteger os cromossomos assegurando que a informação genética seja corretamente copiada durante a duplicação celular. Os telômeros são elongados por uma transcritase reversa especializada denominada telomerase. A telomerase é uma ribonucleoproteína, constituída por duas subunidades, uma proteína com função de transcriptase reversa denominada TERT, e um componente RNA (TER) que contém a sequência do molde da repetição telomérica copiado pela TERT. Estudos recentes mostram que o TER possui outras funções além de conter apenas um molde para elongamento dos telômeros. Sua estrutura secundária possui domínios com funções de controle da inserção de nucleotídeos pelo TERT, reconhecimento da sequência e ligação de proteínas acessórias. Recentemente... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Parasites of the Leishmania genus belong to the Trypanosomatide family, which present peculiar and particular characteristics. Among them are the species that cause leishmaniasis, a neglected tropical disease that can be expressed in three different clinical forms: cutaneous, mucocutaneous and visceral. Brazil is one of the most affected countries, due mainly to socioeconomic conditions, climate change and environmental alterations. Research related to the biology of Leishmania contributes to the understanding of the important physiological mechanisms of the parasite, and thus provide new therapeutic targets against the disease. The study of Leishmania telomeres appears promising since they related are to the genome stability. Telomeres are nucleoprotein structures located at the ends of the chromosomes and are responsible for protecting the chromosomes ensuring that the genetic information copied is correctly during cell duplication. DNA polymerase does not elongate telomeres as the rest of the genetic material, and thus maintained are by the action of a specialized reverse transcriptase named telomerase. Telomerase is a ribonucleoprotein minimally composed by two subunits, a protein with reverse transcriptase function TERT, and an RNA component (TER) that contains the telomeric repeat template sequence copied by TERT. Recent studies shown that TER has other functions besides being just a template for telomeres elongation. Its secondary structure has domains with control fun... (Complete abstract click electronic access below) / Mestre

abstract: Telomerase enzyme is a truly remarkable enzyme specialized for the addition of short, highly repetitive DNA sequences onto linear eukaryotic chromosome ends. The telomerase enzyme functions as a ribonucleoprotein, minimally composed of the highly conserved catalytic telomerase reverse transcriptase and essential telomerase RNA component containing an internalized short template region within the vastly larger non-coding RNA. Even among closely related groups of species, telomerase RNA is astonishingly divergent in sequence, length, and secondary structure. This massive disparity is highly prohibitive for telomerase RNA identification from previously unexplored groups of species, which is fundamental for secondary structure determination. Combined biochemical enrichment and computational screening methods were employed for the discovery of numerous telomerase RNAs from the poorly characterized echinoderm lineage. This resulted in the revelation that--while closely related to the vertebrate lineage and grossly resembling vertebrate telomerase RNA--the echinoderm telomerase RNA central domain varies extensively in structure and sequence, diverging even within echinoderms amongst sea urchins and brittle stars. Furthermore, the origins of telomerase RNA within the eukaryotic lineage have remained a persistent mystery. The ancient Trypanosoma telomerase RNA was previously identified, however, a functionally verified secondary structure remained elusive. Synthetic Trypanosoma telomerase was generated for molecular dissection of Trypanosoma telomerase RNA revealing two RNA domains functionally equivalent to those found in known telomerase RNAs, yet structurally distinct. This work demonstrates that telomerase RNA is uncommonly divergent in gross architecture, while retaining critical universal elements. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

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RNAs não codificantes (ncRNAs) têm ganho crescente prestígio nos últimos anos devido a recentes e contínuas descobertas revelando sua diversidade e importância. Porém, a identificação dessas moléculas ainda é um problema em aberto. Em particular, Plasmodium falciparum é um desafio para a pesquisa de ncRNAs, onde poucos foram identificados até o momento. P. falciparum é o parasita que causa uma malária humana letal. A descoberta de novos ncRNAs neste organismo pode auxiliar no desenvolvimento de novos tratamentos. Este trabalho faz um estudo sobre técnicas computacionais para a predição de ncRNAs e, utilizando como objeto de estudo P. falciparum, propõe uma metodologia de predição que seja aplicável inclusive a genomas com viés composicional. A ênfase deste estudo foi a predição de ncRNAs família-específicos, utilizando o componente RNA da telomerase como objeto de estudo. Este é um importante RNA que, devido à sua alta taxa de mutação, é de difícil identificação. Este RNA ainda não foi identificado em P. falciparum. No entanto, evidências biológicas indicam que este RNA é presente, funcional e deve ser essencial ao parasita, caracterizando-se como um alvo de drogas. Além disso, foi realizado um trabalho preliminar sobre a predição de ncRNAs em geral em P. falciparum utilizando uma abordagem comparativa. / Noncoding RNAs (ncRNAs) have been receiving increasing prestige in the last years due to recent and continuous discoveries revealing their diversity and importance. However, the identification of these molecules is still an open problem. In particular, Plasmodium falciparum is a challenge for the ncRNA research, in which few ncRNAs have been identified. P. falciparum is the parasite that causes a lethal human malaria. The discovery of new ncRNAs in this organism may help in the development of new treatments. This work does a research of computational techniques for the ncRNA prediction and, by using P. falciparum as target, proposes a prediction methodology which is also applicable to compositionally biased genomes. The emphasis of this study was the prediction of family-specific ncRNAs, by using the telomerase RNA component as target. This is an important RNA that has a high mutation rate, being difficult to predict. This RNA has not been identified in P. falciparum, yet. However, biological evidences indicate this RNA is present, functional and might be essential for the parasite, being a drug target. In addition, this work presents preliminary results about the prediction of general ncRNAs in P. falciparum by using a comparative approach.

RNAs não codificantes (ncRNAs) têm ganho crescente prestígio nos últimos anos devido a recentes e contínuas descobertas revelando sua diversidade e importância. Porém, a identificação dessas moléculas ainda é um problema em aberto. Em particular, Plasmodium falciparum é um desafio para a pesquisa de ncRNAs, onde poucos foram identificados até o momento. P. falciparum é o parasita que causa uma malária humana letal. A descoberta de novos ncRNAs neste organismo pode auxiliar no desenvolvimento de novos tratamentos. Este trabalho faz um estudo sobre técnicas computacionais para a predição de ncRNAs e, utilizando como objeto de estudo P. falciparum, propõe uma metodologia de predição que seja aplicável inclusive a genomas com viés composicional. A ênfase deste estudo foi a predição de ncRNAs família-específicos, utilizando o componente RNA da telomerase como objeto de estudo. Este é um importante RNA que, devido à sua alta taxa de mutação, é de difícil identificação. Este RNA ainda não foi identificado em P. falciparum. No entanto, evidências biológicas indicam que este RNA é presente, funcional e deve ser essencial ao parasita, caracterizando-se como um alvo de drogas. Além disso, foi realizado um trabalho preliminar sobre a predição de ncRNAs em geral em P. falciparum utilizando uma abordagem comparativa. / Noncoding RNAs (ncRNAs) have been receiving increasing prestige in the last years due to recent and continuous discoveries revealing their diversity and importance. However, the identification of these molecules is still an open problem. In particular, Plasmodium falciparum is a challenge for the ncRNA research, in which few ncRNAs have been identified. P. falciparum is the parasite that causes a lethal human malaria. The discovery of new ncRNAs in this organism may help in the development of new treatments. This work does a research of computational techniques for the ncRNA prediction and, by using P. falciparum as target, proposes a prediction methodology which is also applicable to compositionally biased genomes. The emphasis of this study was the prediction of family-specific ncRNAs, by using the telomerase RNA component as target. This is an important RNA that has a high mutation rate, being difficult to predict. This RNA has not been identified in P. falciparum, yet. However, biological evidences indicate this RNA is present, functional and might be essential for the parasite, being a drug target. In addition, this work presents preliminary results about the prediction of general ncRNAs in P. falciparum by using a comparative approach.