The Escherichia coli small RNA (sRNA) MicA was identified recently in a genomewide search for sRNAs. It is encoded between the genes gshA and luxS in E. coli and its close relatives. The function of sRNAs in bacteria is generally believed to be in maintenance of homeostasis via stress-induced modulation of gene expression. Our studies on MicA have been aimed at attributing function(s) to this molecule. We carried out high throughput assays aimed at identifying genes that are differentially regulated upon knocking out or overexpressing MicA. Among the protein candidates identified was the outer membrane protein, OmpA. Subsequent analysis allowed us to show this regulation to be antisense in nature with MicA binding within the translation initiation region of ompA mRNA. Furthermore, blocking the ribosome from loading caused a translational decoupling that instigates degradation of the mRNA. The regulation was apparent in early stationary phase and seen to be dependent on the RNA chaperone Hfq. We went on to characterize the regulation of MicA, looking at its own transcription. Testing various stress conditions, we were able to identify putative promoter elements that we confirmed using transcriptional fusions. The results showed MicA to be dependent on the extracytoplasmic function ECF sigma E (σE) and could not detect MicA in mutants deleted for this factor. Lastly, we identified an additional target for MicA being the adjacently encoded luxS mRNA. The LuxS protein is essential for the synthesis of the quorum sensing AI-2 molecule. Transcription of the luxS mRNA is commences within the gshA gene, on the other side of MicA coding region. We were able to show that MicA interacts with luxS mRNA and is recognized by RNase III which processes this complex leading to a shorter luxS mRNA isoform. The significance of this processing event is as yet undetermined. Our data elucidated a new promoter driving transcription of luxS, and we demonstrated this promoter to be stationary phase responsive. In summary, the work presented here characterizes the sRNA MicA as a dual regulatory sRNA molecule, moonlighting between its cis-encoded target and its trans-encoded target. .

RNA is the only biological molecule that can function both as a repository of information and as a catalyst. This, together with the ability to self-replicate, led to recognition of RNA as ‘prelude to life’. My work highlights some of the important features of RNA as a catalyst, exemplified by RNase P. It addresses questions of evolutionary preservations of residues and structure, involvement of metal ions and finally structure evolution towards minimal catalytically competent RNA motifs. RNase P is the only enzyme involved in 5’ end processing of all pre-tRNAs. Until recently, it was believed that the RNA moiety of RNase P is responsible for mediating catalysis only in Bacteria. However, my recent study conclusively demonstrated that eukaryotic RNase P RNA is catalytically competent in vitro in absence of proteins. These findings evidenced evolutionary preservation of RNA-mediated catalysis in RNase P. RNase P RNA is a metalloeznyme. In my studies I analyzed the contributions of individual chemical groups at the cleavage site to catalysis. My findings suggested that the 2’OH of N-1 and the exocyclic amine of G+1 are involved in positioning of functionally important metal ions. Additionally, data appointed the function of Pb2+ as both structural metal ion and important in generating the nucleophile. My studies further indicate a conformational change upon RNase P RNA -substrate complex formation in keeping with an induced fit mechanism. Studying the effects of reducing the ribozyme size upon dissection of bacterial RNase P RNAs, we defined the smallest catalytically competent domain i.e. P15-loop. Derivatives of this autonomous metal ion binding domain, (the smallest being 31nt-s), are able to cleave both whole-length pre-tRNAs as well as hairpin substrates, though with severely reduced rates relative to their parent ribozymes. The study has inferred that partite ES interactions at the cleavage site prove sufficient for catalysis.

The potential application of a hydrogel-based strong anion-exchange (Q) membrane to purify plasmid DNAs was evaluated. The maximum binding capacity of plasmid DNA was estimated to be 12.4 mg/ml of membrane volume with a plasmid DNA recovery of ~ 90%, which is superior to other commercially available anion-exchange resins and membranes. The membrane was able to retain its structural integrity and performance after multiple cycles of usage (> 30 cycles). The inherent properties of plasmid DNA, membrane adsorbent, and the ionic environment on membrane performance were identified as the factors affecting membrane performance and their effects were systematically investigated. Plasmid DNAs with smaller tertiary structure have shorter dynamic radius and/or lowersurface charge densities, which tended to have a better adsorption and recovery than those with larger tertiary structure. Environmental Scanning Electron Microscopy (ESEM) revealed that the hydrogel structure is more porous on one side of membrane than the other, and higher plasmid DNA adsorption and recovery capacities were observed if the more porous side of the membrane was installed upward of flow in the chromatographic unit. ESEM also revealed improved pore distribution and increased membrane porosity if membrane was pre-equilibrated in the buffer solution for 16 hours. The development of better flow through channel in the hydrogel membrane upon extensive soaking further improved plasmid DNA adsorption and recovery capacities. The ionic environment affects the tertiary size of plasmid DNA; and the optimal operating pH of membrane chromatography was different for the plasmid DNAs investigated in this study. The relative contribution of these factors to improve membrane chromatography of plasmid DNAs was analyzed using statistical modeling. It was found that the adsorption of plasmid DNA was mainly affected by the available adsorptive area associated with membrane porosity, whereas the recovery of plasmid DNAs was mainly affected by the environmental pH. A novel, RNase-free, and potentially scalable bioprocess was synthesized using the hydrogel membrane as the technology platform for the manufacturing of pharmaceutical-grade plasmid DNA. High bioprocess recovery and product quality were primarily associated with the optimal integration of impurity removal by calcium chloride precipitation and anion-exchange membrane chromatography and the implementation of isopropanol precipitation as a coupling step between the two impurity-removing steps. Complete removal of total cellular RNA impurity was demonstrated without the use of animal-derived RNase. High-molecular-weight (HMW) RNA and genomic DNA (gDNA) were removed by selective precipitation using calcium chloride at an optimal concentration. Complete removal of the remaining low-molecular-weight (LMW) RNA was achieved by membrane chromatography using the high-capacity and high-productive hydrogel membrane. The simultaneous achievement of desalting, concentrating and buffer exchange by the coupling step of isopropanol precipitation and the high efficiency and resolution of DNA-RNA separation by anion-exchange membrane chromatography significantly reduced the operating complexity of the overall bioprocess, increased the overall recovery of plasmid DNA, and enhanced product quality by removing trace amounts of impurities of major concern for biomedical applications, such as gDNA, proteins, and endotoxin.

Η ριβονουκλεάση Ρ (RNase P) είναι μια πανταχού παρούσα ενδονουκλεάση, και σε πολλές περιπτώσεις αποτελεί ένα ριβοένζυμο, η οποία συμμετέχει στον μηχανισμό ωρίμανσης των πρόδρομων tRNAs. Στην πλειοψηφία των περιπτώσεων είναι ένα ριβονουκλεοπρωτεϊνικό σύμπλοκο που αποτελείται από μια RNA υπομονάδα και τουλάχιστον μια πρωτεϊνική υπομονάδα. Όσον αφορά τα ευκαρυωτικά κύτταρα, πιστεύεται πως υπάρχουν δυο διακριτές μορφές του ολοενζύμου, μια πυρηνική και μια μιτοχονδριακή. Στο Saccharomyces cerevisiae η μιτοχονδριακή RNase P διαθέτει μια RNA και μια πρωτεϊνική υπομονάδα που κωδικοποιούνται από ένα μιτοχονδριακό (rnpB) και ένα πυρηνικό γονίδιο, αντίστοιχα. Σε αυτήν την εργασία απομονώσαμε και μερικώς καθαρίσαμε την μιτοχονδριακή RNase P από τον Schizosaccharomyces pombe. Κλωνοποιήθηκε, επίσης, το γονίδιο που κωδικοποιεί την RNA υπομονάδα της μιτοχονδριακής RNase P. Αυτό το ένζυμο παρουσιάζει διαφορετική εξειδίκευση για τα υποστρώματα SupS1 (pre-tRNASer) και pre-tRNATyr και δεν απενεργοποιείται από την μικροκοκκική νουκλεάση. / Ribonuclease P is a universally conserved ribozyme that it is involved in the 5΄ maturation of precursors tRNAs. It is in most cases a ribonucleoprotein complex which comprises an RNA subunit and at least one protein subunit. Concerning the eukaruotic cells, it is expected that distinctive nuclear and mitochondrial RNase P activities exist. In Saccharomyces cerevisiae the mitochondrial RNase P consists of an RNA and a protein subunit encoded by a mitochondrial (rnpB) and a nuclear gene, respectively. In the present study we isolated and partially purified mitochondrial RNase P from Schizosaccharomyces pombe and we cloned the gene that encodes the mitochondrial RNase P RNA subunit. This enzyme exhibits different specificity on SupS1 and pre-tRNATyr substrates and is not inactivated by micrococcal nuclease.

L’auto-incompatibilité (AI) est la capacité génétiquement déterminée d’une plante fertile de rejeter son propre pollen. Chez les Solanacées l’AI dépend des éléments d’un locus fort complexe (locus S) multigénique. L’élément du locus-S exprimé dans le pistil est une ribonucléase (S-RNase) dont le rôle est de dégrader l’ARN chez le pollen self, tandis que l’élément du locus S exprimé dans le pollen est un ensemble de protéines du type F-box, qui sont normalement impliquées dans la dégradation des protéines. Cependant, comment les S-RNases self restent actives lors des croisements incompatibles et comment les S-RNases non-self sont inactivées lors des croisements compatibles ce n’est encore pas clair. Un modèle propose que les S-RNases non-self soient dégradées lors des croisements compatibles. Un autre modèle propose que toutes les S-RNases, self et non-self, soient d'abord séquestrées à l’intérieur d’une vacuole, et elles y resteraient lors des croisements compatibles. Lors de croisements incompatibles, par contre, elles seraient relâchées dans le cytoplasme, où elles pourront exercer leur action cytotoxique. Notre étude tente de répondre à ces questions. Notamment, nous cherchons à mettre en évidence la localisation vacuolaire et/ou cytoplasmique des S-RNases et leur concentration par immunolocalisation, en utilisant un anticorps ciblant la S11-RNase de Solanum chacoense et la microcopie électronique à transmission. Nos résultats montrent que la densité de marquage observée pour les S-RNases cytoplasmiques est significativement plus haute dans les tubes incompatibles que dans ceux compatibles ce qui nous indique que pour qu’un tube pollinique soit compatible il doit contenir une faible densité de S-RNase cytoplasmique. / Self-incompatibility (SI) is a widespread genetic device used by flowering plants to reject their own pollen, and thus to avoid inbreeding. This cell-cell recognition mechanism is mediated by molecular interactions between gene products expressed in the pollen and those expressed in specialized cells of the pistil. The genetic determinants of the system are produced from a highly complex multigenic S-locus with multiple S-haplotypes, although other genes outside the S-locus also contribute to the phenomenon in a non-allele specific manner. SI discriminates between self and non-self pollen, as the former will be rejected (incompatible cross), whereas the latter will be allowed to accomplish fertilization (compatible cross). In the Solanaceae (to which Solanum chacoense belongs) the pistillar determinant to SI is an extremely polymorphic stylar extracellular S-RNase, whereas the pollen determinant involves the collaborative action of several members of the F-box family (SLF or S-locus F-box). This has led to the hypothesis that during compatible crosses, ubiquitin-mediated degradation of non-self S-RNases takes place (degradation model). However, it has also been found that non-self S-RNases appear to be sequestered in the vacuole during compatible crosses (sequestration model). The objective of our study was to discriminate between these two models by using immunolocalization techniques and transmission electron microscopy. We have found that the concentration of S-RNases is significantly higher in incompatible pollen tubes than in compatible ones.

The potential application of a hydrogel-based strong anion-exchange (Q) membrane to purify plasmid DNAs was evaluated. The maximum binding capacity of plasmid DNA was estimated to be 12.4 mg/ml of membrane volume with a plasmid DNA recovery of ~ 90%, which is superior to other commercially available anion-exchange resins and membranes. The membrane was able to retain its structural integrity and performance after multiple cycles of usage (> 30 cycles). The inherent properties of plasmid DNA, membrane adsorbent, and the ionic environment on membrane performance were identified as the factors affecting membrane performance and their effects were systematically investigated. Plasmid DNAs with smaller tertiary structure have shorter dynamic radius and/or lowersurface charge densities, which tended to have a better adsorption and recovery than those with larger tertiary structure. Environmental Scanning Electron Microscopy (ESEM) revealed that the hydrogel structure is more porous on one side of membrane than the other, and higher plasmid DNA adsorption and recovery capacities were observed if the more porous side of the membrane was installed upward of flow in the chromatographic unit. ESEM also revealed improved pore distribution and increased membrane porosity if membrane was pre-equilibrated in the buffer solution for 16 hours. The development of better flow through channel in the hydrogel membrane upon extensive soaking further improved plasmid DNA adsorption and recovery capacities. The ionic environment affects the tertiary size of plasmid DNA; and the optimal operating pH of membrane chromatography was different for the plasmid DNAs investigated in this study. The relative contribution of these factors to improve membrane chromatography of plasmid DNAs was analyzed using statistical modeling. It was found that the adsorption of plasmid DNA was mainly affected by the available adsorptive area associated with membrane porosity, whereas the recovery of plasmid DNAs was mainly affected by the environmental pH. A novel, RNase-free, and potentially scalable bioprocess was synthesized using the hydrogel membrane as the technology platform for the manufacturing of pharmaceutical-grade plasmid DNA. High bioprocess recovery and product quality were primarily associated with the optimal integration of impurity removal by calcium chloride precipitation and anion-exchange membrane chromatography and the implementation of isopropanol precipitation as a coupling step between the two impurity-removing steps. Complete removal of total cellular RNA impurity was demonstrated without the use of animal-derived RNase. High-molecular-weight (HMW) RNA and genomic DNA (gDNA) were removed by selective precipitation using calcium chloride at an optimal concentration. Complete removal of the remaining low-molecular-weight (LMW) RNA was achieved by membrane chromatography using the high-capacity and high-productive hydrogel membrane. The simultaneous achievement of desalting, concentrating and buffer exchange by the coupling step of isopropanol precipitation and the high efficiency and resolution of DNA-RNA separation by anion-exchange membrane chromatography significantly reduced the operating complexity of the overall bioprocess, increased the overall recovery of plasmid DNA, and enhanced product quality by removing trace amounts of impurities of major concern for biomedical applications, such as gDNA, proteins, and endotoxin.

A short oligonucleotide sequence as in a single-stranded antisense oligo nucleotides (AON) or in double-stranded small interfering RNAs (siRNA) can modulate the gene expression by targeting against the cellular mRNA, which can be potentially exploited for therapeutic purposes in the treatment of different diseases. In order to improve the efficacy of oligonucleotide-based drugs, the problem of target affinity, nuclease stability and delivery needs to be addressed. Chemical modifications of oligonucleotides have been proved to be an effective strategy to counter some of these problems. In this thesis, chemical synthesis of conformationally constrained nucleosides such as 7′-Me-carba-LNA-A, -G, -MeC and -T as well as 6′, 7′-substituted α-L-carba-LNA-T (Papers I-III) was achieved through a key free-radical cyclization. 1D and 2D NMR techniques were employed to prove the formation of bicyclic ring system by free-radical ring closure as well as to identify the specific constrained conformations in sugar moieties. These sugar-locked nucleosides were transformed to the corresponding phosphoramidites and incorporated into antisense oligonucleotides in different sequences, to evaluate their physicochemical and biochemical properties for potential antisense-based therapeutic application. AONs modified with 7′-Me-carba-LNA analogues exhibited higher RNA affinities (plus 1-4°C/modification) (Papers I & III), but AONs containing α-L-carba-LNA analogues showed decreased affinities (minus 2-3°C/ modification) (Paper II) towards complementary RNA compared to the native counterpart.  It has been demonstrated in Papers I-III that 7′-methyl substitution in α-L-carba-LNA caused the Tm drop due to a steric clash of the R-configured methyl group in the major groove of the duplex, whereas 7′-methyl group of carba-LNA locating in the minor groove of the duplex exerted no obviously negative effect on Tms, regardless of its orientation. Moreover, AONs containing 7′-Me-carba-LNA and α-L-carba-LNA derivatives were found to be nucleolytically more stable than native AONs, LNA modified AONs as well as α-L-LNA modified ones (Papers I-III). We also found in Paper II & III that the orientations of OH group in C6′ of α-L-carba-LNAs and methyl group in C7′ of 7′-Me-carba-LNAs can significantly influence the nuclease stabilities of modified AONs. It was proved that the methyl substitution in cLNAs which points towards the vicinal 3′-phosphate were more resistant to nuclease degradation than that caused by the methyl group pointing away from 3′-phosphate. Additionally, AONs modified with 7′-Me-carba-LNAs and α-L-carba-LNAs were found to elicit the RNase H mediated RNA degradation with comparable or higher rates (from 2-fold to 8-fold higher dependent upon the modification sites) as compared to the native counterpart. We also found that the cleavage patterns and rates by E. coli RNase H1 were highly dependent upon the modification sites in the AON sequences, regardless of the structural features of modifications (Papers II & III). Furthermore, we have shown that the modulations of Tms of AON/RNA duplexes are directly correlated with the aqueous solvation (Paper III).

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