Techn. Universiẗat, Diss., 2004--Berlin.

A subset of mitochondrial group II introns of flowering plants has, over evolutionary time, lost characteristic features and employs unconventional splicing pathways. Given the potential impact of cold treatment on RNA folding, as well as on enzymatic activity and import of nuclear-encoded splicing machinery, I have examined the physical excised forms of aberrant introns from wheat embryos subjected to 4oC. My findings suggest a shift in biochemistry with cold treatment to novel splicing pathways that generate heterogeneous in vivo circularized forms for nad1 intron 2, nad2 intron 1 and the cox2 intron, in contrast to predominantly linear excised intron forms at room temperature. Interestingly, the highly degenerate nad1 intron 1, which due to DNA rearrangement has been broken into two halves that interact for splicing in trans, is excised exclusively by first-step hydrolysis at room temperature and under cold treatment. In this case, splicing culminates in two distinct linear half introns that appears correlated with an unusual 5’ terminal insert. This represents the first in vivo demonstration of hydrolytic trans-splicing. Based on northern analysis, cold treatment was further associated with reduced splicing efficiency for all introns surveyed. Moreover, study of precursor transcripts of the nad1a-intron 1a locus suggests the efficiency of end-maturation, including processing of the cotranscribed tRNA-Pro gene, is also reduced in the cold. My findings demonstrate a temperature-sensitivity of transcript maturation, particularly for RNA splicing, providing new insight into the impact of cold growth conditions on plant mitochondrial gene expression.

Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

Indiana University-Purdue University Indianapolis (IUPUI) / Alternative RNA splicing is an important means of genetic control and transcriptome diversity. Alternative splicing events are frequently studied independently, and coordinated splicing controlled by common factors is often overlooked: The molecular mechanisms by which splicing regulators promote or repress specific pre-mRNA processing are still not yet well understood. It is well known that splicing factors can regulate splicing in a context-dependent manner, and the search for modulation of splicing factor activity via direct or indirect mechanisms is a worthwhile pursuit towards explaining context-dependent activity. We hypothesized that the combined analysis of hundreds of consortium RNA-seq datasets could identify trans-acting “modulators” whose expression is correlated with differential effects of a splicing factor on its target splice events in mRNAs. We first tested a genome-wide approach to identify relationships between RNA-binding proteins and their inferred modulators in kidney cancer. We then applied a more targeted approach to identify novel modulators of splicing factor SRSF1 function over dozens of its intron retention splicing targets in a neurological context using hundreds of dorsolateral prefrontal cortex samples. Our hypothesized model was further strengthened with the incorporation of genetic variants to impute gene expression in a Mendelian randomization-based approach. The modulators of intron retention splicing we identified may be associated with risk variants linked to Alzheimer’s Disease, among other neurological disorders, to explain disease-causing splicing mechanisms. Our strategy can be widely used to identify modulators of RNA-binding proteins involved in tissue-specific alternative splicing.

Os genes eucarióticos, em sua maioria, são divididos em exons e introns, requerendo processamento do RNAm para remover as sequências intrônicas e juntar os exons (splicing). As bordas exon/intron são definidas por sítios de splice que normalmente são reconhecidos com alta fidelidade, gerando os mesmos RNAms processados a cada vez. Apesar desse reconhecimento preciso, tem sido observada a junção de exons de maneiras alternativas (splicing alternativo), foco de muitos estudos recentes devido à sua importância em vários processos biológicos. Este processamento alternativo do RNAm pode ser principalmente de três tipos: exclusão de exon, no qual um exon pode ser incluído ou não no RNAm maduro; uso alternativo de sítios de splice, resultando em exons mais longos ou mais curtos e retenção de intron, o tipo menos estudado, no qual uma sequência intrônica é mantida no RNAm maduro. Um dos aspectos cruciais no entendimento de splicing alternativo é conhecer os mecanismos que levam à geração de diferentes transcritos. Coerente com a importância dos sítios de splice no splicing de RNAms, a retenção de intron parece ser causada por falha no reconhecimento daqueles que são sub-ótimos. Como os sítios de splice são reconhecidos aos pares ao se estabelecer uma ponte através de exons ou introns, dependendo de qual é mais curto, uma falha no reconhecimento de um exon ou de um intron leva a diferentes tipos de splicing alternativo (exclusão de exon ou retenção de intron, respectivamente). Desta forma, acredita-se que a ocorrência de retenção de intron esteja também associada a uma falha no reconhecimento de introns curtos. Embora estudos de introns retidos individuais tenham abordado estas questões, poucas análises sistemáticas de grandes quantidades de dados foram conduzidas sobre as características gerais que levam à retenção de intron. Para este fim, realizamos uma análise de bioinformática de sequências do genoma e transcriptoma (RNAm) humanos armazenadas em formato de computador. Para realizar as análises computacionais, desenvolvemos um sistema de anotação de splicing alternativo completo. Particionamos os eventos de retenção de intron identificados em sequências expressas pelo nosso sistema de anotação em dois grupos, com base na abundância relativa das duas isoformas (um grupo de eventos com <50% e outro com >50% de transcritos retendo o intron) e comparamos características relevantes. Verificamos que uma maior frequência de retenção de intron em humano está associada a sítios de splice mais fracos, genes com introns mais curtos e maior nível de expressão gênica, e menor densidade de um conjunto de elementos inibitórios exônicos e do promotor de splicing intrônico GGG. Os dois grupos apresentaram eventos conservados em camundongo, nos quais os introns retidos também eram curtos e apresentavam sítios de splice mais fracos. Embora nossos resultados tenham confirmado que sítios de splice mais fracos estão associados à retenção de intron, eles mostram que uma fração não-desprezível dos eventos não pode ser explicada apenas por esta característica. Nossa análise sugere que elementos reguladores em cis provavelmente têm um papel na regulação da retenção de intron e também revelou características previamente desconhecidas que parecem influenciar sua ocorrência. Estes resultados salientam a importância de considerar o compromisso entre estas características na regulação da frequência relativa de retenção de intron. / Most eukaryotic genes are split in exons and introns, requiring mRNA processing to remove intervening sequences and join exons (splicing). Exon/intron borders are defined by splice sites that are normally recognized with high fidelity, yielding the same processed mRNA each time. Notwithstanding such precise recognition, alternative joining of exons has been observed (alternative splicing) and is the focus of many recent studies, due to its importance in several biological processes. This alternative mRNA processing can be mainly of three types: exon skipping, whereby an exon may be included or not in the mature mRNA; alternative use of splice sites, resulting in longer or shorter exons and intron retention, the least studied type whereby an intronic sequence is maintained in the mature mRNA. One of the key aspects in understanding alternative splicing is to know the mechanisms that lead to the generation of different transcripts. Coherent with the importance of splice sites in mRNA splicing, intron retention seems to be caused by failure in the recognition of those that are sub-optimal. As splice sites are recognized in pairs by bridging either exons or introns, depending on which is the shortest, failure to recognize an exon or an intron leads to different types of alternative splicing (exon skipping or intron retention, respectively). This way, the occurrence of intron retention is believed to be associated to failure in recognition of short introns also. Although studies on individual retained introns have addressed such issues, few systematic surveys of large amounts of data have been conducted on the general features leading to intron retention. To this end, we performed a bioinformatics analysis of human genome and transcriptome (mRNA) sequences stored in computer format. To perform the computational analyses we developed a complete alternative splicing annotation system. We partitioned intron retention events identified in expressed sequences by our annotation system in two groups based on the relative abundance of both isoforms (one group of events with <50% and another with >50% of transcripts retaining the intron) and compared relevant features. We found that a higher frequency of intron retention in human is associated to weaker splice sites, genes with shorter intron lengths and higher expression level, and lower density of a set of exonic inhibitory elements and the intronic splicing enhancer GGG. Both groups of events presented conserved events in mouse, in which the retained introns were also short and presented weaker splice sites. Although our results confirmed that weaker splice sites are associated to intron retention, they showed that a non-negligible fraction of events can not be explained by this feature alone. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating intron retention and also revealed previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of intron retention.

Os genes eucarióticos, em sua maioria, são divididos em exons e introns, requerendo processamento do RNAm para remover as sequências intrônicas e juntar os exons (splicing). As bordas exon/intron são definidas por sítios de splice que normalmente são reconhecidos com alta fidelidade, gerando os mesmos RNAms processados a cada vez. Apesar desse reconhecimento preciso, tem sido observada a junção de exons de maneiras alternativas (splicing alternativo), foco de muitos estudos recentes devido à sua importância em vários processos biológicos. Este processamento alternativo do RNAm pode ser principalmente de três tipos: exclusão de exon, no qual um exon pode ser incluído ou não no RNAm maduro; uso alternativo de sítios de splice, resultando em exons mais longos ou mais curtos e retenção de intron, o tipo menos estudado, no qual uma sequência intrônica é mantida no RNAm maduro. Um dos aspectos cruciais no entendimento de splicing alternativo é conhecer os mecanismos que levam à geração de diferentes transcritos. Coerente com a importância dos sítios de splice no splicing de RNAms, a retenção de intron parece ser causada por falha no reconhecimento daqueles que são sub-ótimos. Como os sítios de splice são reconhecidos aos pares ao se estabelecer uma ponte através de exons ou introns, dependendo de qual é mais curto, uma falha no reconhecimento de um exon ou de um intron leva a diferentes tipos de splicing alternativo (exclusão de exon ou retenção de intron, respectivamente). Desta forma, acredita-se que a ocorrência de retenção de intron esteja também associada a uma falha no reconhecimento de introns curtos. Embora estudos de introns retidos individuais tenham abordado estas questões, poucas análises sistemáticas de grandes quantidades de dados foram conduzidas sobre as características gerais que levam à retenção de intron. Para este fim, realizamos uma análise de bioinformática de sequências do genoma e transcriptoma (RNAm) humanos armazenadas em formato de computador. Para realizar as análises computacionais, desenvolvemos um sistema de anotação de splicing alternativo completo. Particionamos os eventos de retenção de intron identificados em sequências expressas pelo nosso sistema de anotação em dois grupos, com base na abundância relativa das duas isoformas (um grupo de eventos com <50% e outro com >50% de transcritos retendo o intron) e comparamos características relevantes. Verificamos que uma maior frequência de retenção de intron em humano está associada a sítios de splice mais fracos, genes com introns mais curtos e maior nível de expressão gênica, e menor densidade de um conjunto de elementos inibitórios exônicos e do promotor de splicing intrônico GGG. Os dois grupos apresentaram eventos conservados em camundongo, nos quais os introns retidos também eram curtos e apresentavam sítios de splice mais fracos. Embora nossos resultados tenham confirmado que sítios de splice mais fracos estão associados à retenção de intron, eles mostram que uma fração não-desprezível dos eventos não pode ser explicada apenas por esta característica. Nossa análise sugere que elementos reguladores em cis provavelmente têm um papel na regulação da retenção de intron e também revelou características previamente desconhecidas que parecem influenciar sua ocorrência. Estes resultados salientam a importância de considerar o compromisso entre estas características na regulação da frequência relativa de retenção de intron. / Most eukaryotic genes are split in exons and introns, requiring mRNA processing to remove intervening sequences and join exons (splicing). Exon/intron borders are defined by splice sites that are normally recognized with high fidelity, yielding the same processed mRNA each time. Notwithstanding such precise recognition, alternative joining of exons has been observed (alternative splicing) and is the focus of many recent studies, due to its importance in several biological processes. This alternative mRNA processing can be mainly of three types: exon skipping, whereby an exon may be included or not in the mature mRNA; alternative use of splice sites, resulting in longer or shorter exons and intron retention, the least studied type whereby an intronic sequence is maintained in the mature mRNA. One of the key aspects in understanding alternative splicing is to know the mechanisms that lead to the generation of different transcripts. Coherent with the importance of splice sites in mRNA splicing, intron retention seems to be caused by failure in the recognition of those that are sub-optimal. As splice sites are recognized in pairs by bridging either exons or introns, depending on which is the shortest, failure to recognize an exon or an intron leads to different types of alternative splicing (exon skipping or intron retention, respectively). This way, the occurrence of intron retention is believed to be associated to failure in recognition of short introns also. Although studies on individual retained introns have addressed such issues, few systematic surveys of large amounts of data have been conducted on the general features leading to intron retention. To this end, we performed a bioinformatics analysis of human genome and transcriptome (mRNA) sequences stored in computer format. To perform the computational analyses we developed a complete alternative splicing annotation system. We partitioned intron retention events identified in expressed sequences by our annotation system in two groups based on the relative abundance of both isoforms (one group of events with <50% and another with >50% of transcripts retaining the intron) and compared relevant features. We found that a higher frequency of intron retention in human is associated to weaker splice sites, genes with shorter intron lengths and higher expression level, and lower density of a set of exonic inhibitory elements and the intronic splicing enhancer GGG. Both groups of events presented conserved events in mouse, in which the retained introns were also short and presented weaker splice sites. Although our results confirmed that weaker splice sites are associated to intron retention, they showed that a non-negligible fraction of events can not be explained by this feature alone. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating intron retention and also revealed previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of intron retention.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

Intragenic regions (introns) are found in all classes of organism. Transcription of such genes must undergo a splicing reaction to produce the mature, functional form of RNAs. Introns can be divided into four categories by their splicing mechanisms, namely Group I, Group II, spliceosomal, and nuclear tRNA introns. The former two are self-splicing introns. Group I introns are ubiquitous, however, most metazoan mitochondrial genomes lack introns. A novel group I intron in the mitochondrial cytochrome oxidase I gene (cox1) of Cinachyrella auctraliensis, which belongs to the IB2 subgroup, encodes a putative homing endonuclease with two amino acid motifs of the LAGLIDADG family. The homing endonuclease may perform intron translocation. Splicing in the cox1 of the sponge was demonstrated by comparing the length of DNA and RNA sequences. The intron was spliced in vivo or in vitro as revealed by RT-PCR and sequencing. Group I introns are classified as ribozymes. The pre-mRNAs fold into specific configurations that facilitate attacks of free guanosine followed by two consecutive trans-esterification steps to remove the introns. The excised cox1 intron was found to form a circle with the 5¡¦-end linked to the 3¡¦-end. Two other forms of lariats were also found with the 5¡¦-end linked to the inside sequence of the intron. Mutagenesis of a key nucleotide, which participates base pairing of RNA secondary structure, in P7 region decreased the splicing activity of the intron.

Structured RNAs are pervasive in biology, spanning a functional repertoire that includes messengers, regulators of gene expression and catalysts of translation and splicing. From the relatively simple tRNAs and riboswitches to the highly structured ribosomal RNAs, the ability of RNAs to function is dependent on well-defined secondary and tertiary structures. However, studies of RNA folding in vitro have revealed an extreme propensity to form alternative structures, which can be long-lived and interfere with function. In the cell, a diverse array of RNA binding proteins and RNA chaperones guide RNAs towards the correct structure and disrupt misfolded intermediates. Among these proteins, DEAD-box protein family stands out as one of the largest groups, with its members ubiquitously involved in RNA metabolism across all domains of life. DEAD-box proteins can function as both specific and general RNA chaperones by disrupting RNA structures in an ATP-dependent manner. Here I describe my work studying the general RNA chaperone mechanism of the Neurospora crassa protein CYT-19, a model DEAD-box protein and a biological RNA chaperone that is required for efficient folding of self-splicing group I intron RNAs in vivo. After an introduction to DEAD-box proteins and their mechanisms as RNA remodelers (Chapter 1), I will first describe studies of group I intron unfolding by CYT-19, focusing on the effects of RNA tertiary structure stability on CYT-19 activity and targeting to RNA substrates (Chapter 2). I will then describe the characterization of ATP-dependent mechanisms during CYT-19-mediated refolding of the misfolded group I intron (Chapter 3). In Chapter 4, I will present small-angle X-ray scattering (SAXS) studies of structural features of DEAD-box proteins that allow them to efficiently interact with large structured RNA substrates. Finally, I will turn to studies of DEAD-box protein involvement during early steps of RNA compaction and folding, using SAXS and activity-based approaches (Chapter 5). I will conclude with a general discussion of superfamily 2 RNA helicases, which include DEAD-box and related proteins, and their functions and mechanisms as remodelers of structured RNAs and RNPs. / text

Made available in DSpace on 2014-06-12T15:04:09Z (GMT). No. of bitstreams: 2 arquivo4416_1.pdf: 690757 bytes, checksum: 6e1d8fd2843b82ae7a0a60b516bd6c3c (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2002 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Foram analisadas vinte linhagens de Beauveria bassiana isoladas de diferentes regiões e hospedeiros, quanto ao perfil de DNA, através da análise da região ITS do rDNA, de RAPD e Intron, para avaliação da diversidade genética e auxílio na caracterização. A região ITS1-5.8s-ITS2 do rDNA foram digeridas com as enzimas Eco RI, Dra I, Msp I e Hae III, onde a Eco RI e Dra I não apresentaram sítio de restrição e a Hae III e Msp I não apresentaram polimorfismo entre as linhagens, confirmando a espécie estudada. Para RAPD foram selecionados cinco primers OPX17, OPW4, OPW7, OPW19, 0PW20, que produziram um total de 442 bandas. Os dados obtidos foram submetidos à análise estatística pelo programa NTSYS.PC e construída uma matriz de similaridade utilizando o coeficiente de Jaccard, que gerou um dendrograma através do método de agrupamento UPGMA. A similaridade foi em torno de 70%. A análise do dendrograma mostrou a formação de quatro grupos, onde não houve correlação com o hospedeiro ou origem geográfica, embora duas linhagens isoladas de Nezara viridula e duas de Deois flavopicta tenham mostrado maior nível de similaridade. Os dados obtidos pela análise de Intron, mostraram o aparecimento de cinco grupos