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Proteins that bind to both DNA and RNA embody the ability to perform multiple functions by a single gene product. These nucleic acid binding proteins in prokaryotes can play a vital role in many cellular processes, including replication, transcription, gene expression, recombination, and repair, to name a few. Nucleic acid binding proteins have unique functional characteristics that stem from their structural attributes that have evolved in a widely-conserved manner. In Escherichia coli (E. coli), the highly-conserved histone-like protein, HU, which predominates as a heterodimer of HUα and HUβ, has been found to bind to both dsDNA and ssDNA. Likewise, RNA-binding proteins contain various structural motifs, many of which are also conserved amongst many bacterial species like the RNA recognition motif. However, in Porphyromonas gingivalis, a periodontal pathogen, the histone-like, HU proteins and the RNA-binding protein (RBP) are not well characterized compared to their respective structures in E. coli. In our study, we sought to characterize and compare the HU proteins and RBP in order to gain a better understanding of their structure and function in the cell. Our data showed the HU proteins predominate as homo-tetramers and RBP as a monomer. We demonstrated single-stranded DNA binding with all three proteins. We found both P. gingivalis HU subunits bind non-specifically to ssDNA but show preferential binding to poly(dG) content, while binding to poly(dA) the weakest. These results show that HUα, HUβ and RBP are novel ssDNA binding proteins in P. gingivalis, indicating an expanded role and function within the cell.

Porphyromonas gingivalis (P. gingivalis) is a gram-negative, anaerobic bacterium recognized as a major player in progression of periodontal disease. P. gingivalis survives in the oral cavity while being exposed to dynamic environmental conditions such as pH, temperature, nutrient availability and host immune responses such as oxygen tension and nitrosative stress. Survival and pathogenesis of P. gingivalis in the oral cavity require mechanisms to regulate gene expression in response to the extracellular signals. Little is known about the regulatory mechanisms of P. gingivalis in the oral cavity, so it is important to investigate and characterize these regulatory mechanisms. Adaptation to environmental cues using riboregulation is a significant mechanism for post-transcriptional regulation in bacteria. Using bioinformatics, we have identified a putative RNA-binding protein in P. gingivalis: RBP. Bioinformatic studies have led to the selection of HUβ and HUα nucleoid associated proteins as controls for RNA binding. I hypothesize that the candidate proteins RBP, HUβ and HUα bind RNA in P. gingivalis. The first aim is to show that RBP, HUβ and HUα bind RNA. Using electrophoretic mobility shift assays with IRE RNA and synthesized RNA motifs, I have confirmed that the proteins do bind RNA. The second aim is to isolate and sequence the P. gingivalis RNA that bind to RBP, HUβ and HUα. I have isolated the RNAs that bound the proteins and determined identity of the RNA using high throughput sequencing. Finally, I have identified an antibody that specifically binds RBP to use for in vivo immunoprecipitation of RNA-protein complexes from P. gingivalis. In conclusion RBP, HUβ and HUα are novel RNA binding proteins in P. gingivalis, and further investigation of these proteins is necessary to understand the mechanisms of gene regulation in P. gingivalis.

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is a major etiological agent in the initiation and progression of severe forms of periodontal disease. Oral bacteria like P. gingivalis are subject to continually changing conditions as a consequence of host eating, oral hygiene patterns and subgingival temperatures. As such survival requires an adaptive response to environmental cues, but little is known about the mechanism by which P. gingivalis controls co- and post-transcriptional regulation of RNA levels and potentially protein expression. RNA-binding proteins (RBPs) are evolutionarily conserved across species and are involved in such regulatory mechanisms. However, P. gingivalis currently has no identified RBP. Recently, PG0627 has become an ideal candidate for a putative RBP due to its sequence homology to RBPs across various species. By characterizing PG0627, we can gain better insight into the function of this hypothetical protein and determine if it indeed behaves like an RNA-binding protein. A host of studies were done on a PG0627-deficient P. gingivalis mutant, V3139, in order to determine the biological role of the protein encoded by the gene. Our bioinformatics analysis indicated that PG0627 had sequence homology to several RNA recognition motifs or RBPs. Furthermore, our PG0627-deficient mutant, when compared to W83, exhibited decreased cell-associated iron content, decreased total interactions and invasions with eukaryotic cells, and decreased protease activity. Conversely, our PG0627-deficient mutant displayed slightly increased growth in the presence of nitrosative stress, and in hemin-depleted conditions. In conclusion, our results support that PG0627 is a valid candidate for an RNA-binding protein in P. gingivalis.

<p>mRNA localization is emerging as a critical cellular mechanism for the spatiotemporal regulation of protein expression and serves important roles in oogenesis, embryogenesis, cell fate specification, and synapse formation. Signal sequence-encoding mRNAs are localized to the endoplasmic reticulum (ER) membrane by either of two mechanisms, a canonical mechanism of translation on ER-bound ribosomes (signal recognition particle pathway), or a poorly understood direct ER anchoring mechanism. In this study, we identify that the ER integral membrane proteins function as RNA-binding proteins and play important roles in the direct mRNA anchoring to the ER. We report that one of the ER integral membrane RNA-binding protein, AEG-1 (astrocyte elevated gene-1), functions in the direct ER anchoring and translational regulation of mRNAs encoding endomembrane transmembrane proteins. HITS-CLIP and PAR-CLIP analyses of the AEG-1 mRNA interactome of human hepatocellular carcinoma cells revealed a high enrichment for mRNAs encoding endomembrane organelle proteins, most notably encoding transmembrane proteins. AEG-1 binding sites were highly enriched in the coding sequence and displayed a signature cluster enrichment downstream of encoded transmembrane domains. In overexpression and knockdown models, AEG-1 expression markedly regulates translational efficiency and protein functions of two of its bound transcripts, MDR1 and NPC1. This study reveals a molecular mechanism for the selective localization of mRNAs to the ER and identifies a novel post-transcriptional gene regulation function for AEG-1 in membrane protein expression.</p> / Dissertation

The eukaryotic stress response involves translational suppression of non-housekeeping proteins, and the sequestration of unnecessary mRNA transcripts into stress granules (SGs). This process is dependent on mRNA binding proteins (RBPs), such as T- cell intracellular antigen (TIA-1). RBPs interact with unnecessary mRNA transcripts through prion and poly-glutamine like domains, and their aggregation mirrors proteins linked to neurodegenerative diseases. Recent advances in molecular genetics emphasize the importance of SG biology in disease by associating multiple RBPs linked to SGs with neurodegenerative disease. The major difference between SG proteins and aggregation prone proteins in neurodegeneration is that aggregation of SGs is transient and rapidly reverses when the stress is removed. In contrast, aggregates associated with disease are stable and accumulate over time. This study identifies overabundant SGs as a novel pathology in Alzheimer's disease and related tauopathies. The data suggest that TIA-1 is intimately linked to tau pathogenesis, acting as a modifier of tau aggregation and associated toxicity. TIA-1 is present in a protein complex with tau protein including hyper-phosphorylated and misfolded tau. The expression of WT or P301L mutant tau increases the formation and size of TIA-1 positive SGs, and the localization and dynamics of these SGs are altered. Conversely, the expression of TIA-1 increases the formation and stabilization of phospho- and misfolded tau inclusions, as well as visible alterations in microtubule morphology, perhaps reflecting a loss of tau function. The data further show that co-expression of TIA-1 and tau leads to dendrite shortening, increases in caspase cleavage, and apoptosis in primary neurons, suggesting that an interaction between TIA-1 and tau results in neurotoxicity. This toxicity is SG-dependent and is rescued by microtubule stabilizing drugs. The results of this thesis research suggest that the aggregation of tau may proceed through the SG pathway, with SG formation accelerating the pathophysiology of tau aggregation. These studies propose that these tau aggregates serve as a nidus for further accelerated aggregation of SGs, leading to formation of long-lived pathological SG.

Fetal germ cell development is a key stage of female reproductive life. The DAZ family proteins (DAZ, DAZL and BOLL) are RNA-binding proteins with critical roles in murine germ cell development but their expression and potential targets in the human are largely unknown. The studies in this Thesis investigated the expression and function of DAZL and BOLL in human fetal ovary. Both DAZL and BOLL mRNA are increased dramatically at the time of entry into meiosis. Immunohistochemical analysis with specific meiotic markers suggested that DAZL and BOLL have distinct spatial-temporal expression patterns, with minimal co-expression – BOLL expression was transient prior to follicle formation. This pattern was shown not to be present in the mouse fetal ovary, where Dazl and Boll are co-expressed, indicating a limitation of the mouse for exploring the function of Boll. Two human cell lines, embryonic kidney derived HEK293 cells and germ cell tumour derived TCam-2 cells were used as models to identify the mRNA targets of DAZL and BOLL after transfection of DAZL or BOLL vectors. In HEK293 cells, TEX19 and TEX14 were confirmed as potential targets of both DAZL and BOLL, and CDC25A as a potential DAZL target. Further experiments indicated that DAZL and BOLL did not increase target mRNA transcription but increased stabilisation. A DAZL/GFP co-transfection-FACS system for TCam-2 cells was established as this cell line has very low transfection efficiency. TEX14 and SYCP3 significantly increased in GFP+ve-DAZL+ve cells when compare to the GFP-ve-DAZL-ve cells, whilst SOX17 and DNMT3L significantly decreased in the GFP+ve-DAZL+ve cells. A 3'-UTR luciferase assay confirmed regulation of TEX14 and SOX17 by DAZL through their 3'-UTR. RNA immunoprecipitation further demonstrated direct binding between human TEX14, TEX19, SYCP3, SOX17 mRNA and DAZL protein, and that TEX14 binding is through its 3'-UTR. Dual fluorescence immunohistochemistry showed that SOX17 and DMNT3L are expressed in early germ cells with DAZL, and are later down-regulated co-incident with that of DAZL, consistent with the novel repressive effect of human DAZL on these two potential targets. These studies indicate that DAZL and BOLL are associated with different key meiotic stages of germ cell development in human fetal ovary. Several potential mRNA targets of DAZL and BOLL, and a novel repression function of human DAZL on its mRNA targets were identified giving further insight into the role of these factors in human ovarian development.

Le glioblastome multiforme (GBM) est une tumeur cérébrale extrêmement agressive associée à un mauvais pronostic. C'est pourquoi, il apparaît nécessaire d'identifier les mécanismes moléculaires participant au développement des GBM ainsi qu'à leurs résistances aux traitements afin de développer de nouvelles approches thérapeutiques. Récemment, il a été montré que les régulations traductionnelles jouent un rôle fondamental dans les propriétés agressives du GBM. Les protéines de liaison à l'ARN (RBP) sont des acteurs majeurs de ces régulations dont l'expression/activité est altérée dans les GBM. Les RBP hnRNP HF (HF) font partie des RBP les plus surexprimées dans les GBM et leur contribution dans la régulation traductionnelle des GBM n'a encore jamais été investiguée. Nous avons émis l'hypothèse que hnRNP H et hnRNP F soient au centre d'un réseau de régulations post-transcriptionnelles impactant la machinerie traductionnelle qui contrôle le développement tumoral et la résistance aux traitements des GBM. Nos résultats montrent qu'HF régulent la prolifération et la réponse aux traitements car leur perte d'expression (i) diminue la prolifération des GBM (modèle cellulaire, sphéroïde et xénogreffes in vivo), (ii) active les voies de réponse aux dommages à l'ADN et (iii) sensibilise les cellules de GBM aux irradiations. De plus, nous avons identifié un nouveau rôle pour HF en tant que régulateurs de la traduction. En effet, nos données montrent que les hnRNP HF contrôlent la traduction d'un ensemble d'ARNm en régulant l'expression et l'activité de facteurs d'initiation ainsi qu'en collaborant avec des ARN hélicases partenaires en ciblant des ARNm impliqués dans des processus reliés au développement tumoral et la résistance aux traitements possédant des structures secondaires G-quadruplexe dans leurs 5'UTR. Les données que nous avons générées suggèrent que hnRNP H et hnRNP F sont des régulateurs traductionnels essentiels au développement tumoral et à la résistance aux traitements des GBM. / Glioblastoma multiforme (GBM) is one of the most aggressive brain tumors with poor prognosis. Understanding the molecular mechanisms involved in the development and resistance to treatments of gliomas could improve treatment efficiency. Recently, it has been demonstrated that translational regulations play a key role in the GBM aggressivity. RNA binding proteins (RBP) are major regulators of these processes and have altered expression / activity in GBM. The RBP hnRNP H and hnRNP F (HF) are among the most overexpressed RBP in GBM and their role in GBM translational regulation has never been investigated yet. We hypothesize that HF are at the core of a post-transcriptional regulation network which impacts the translational machinery that controls GBM tumor development and resistance to treatment. We have demonstrated that hnRNP H and hnRNP F regulate proliferation and response to treatment because their depletion (i) decreases the GBM proliferation (cell line model, spheroid and in vivo xenografts), (ii) activates the DNA damage response pathways and (iii) sensitizes the GBM cells to irradiation. We have identified HF as new regulators of GBM translation. Indeed, our data show that hnRNP H and hnRNP F control mRNA translation by regulating expression/activity of initiation factors and in collaboration with RNA helicases by targeting mRNA involved in oncogenic processes and containing secondary structures called G-quadruplex in their 5'UTR. The data that we have generated suggest that HF are essential translational regulators involved in tumor development and resistance to treatment in GBM.

[Truncated abstract] Regulation of mRNA stability is an important posttranscriptional mechanism involved in the control of gene expression. The rate of mRNA decay can differ greatly from one mRNA to another and may be regulated by RNA-protein interactions. A key determinant of mRNA decay are sequence instability (cis) elements often located in the 3' untranslated region (UTR) of many mRNAs. For example, the AU rich elements (AREs), are such well characterized elements, and most commonly involved in promoting mRNA degradation, and specific binding of proteins to these elements leading to the stabilization of some mRNAs. Other cis-elements have been described for mRNA in which mRNA stability is a critical component of gene regulation. This includes the androgen receptor (AR) UC-rich cis element in its 3'UTR. The AR is a key target for therapeutics in human prostate cancer and thus understanding the mechanism involved in regulating its expression is an important goal. The [alpha]CP1 protein, a KH-domain containing RNA-binding protein has been found to bind this UC-rich region of the AR and is thought to play an important role in regulating AR mRNA expression. [alpha]CP1 protein is a triple KH (hnRNP K homology) domain protein with specificity for Crich tracts of RNA and ssDNA (single stranded DNA). Relatively little is known about the structural interaction of [alpha]CP1 with target RNA cis elements, thus the present study aimed to better understand the nature of interaction between 30 nt 3'UTR UC-rich AR mRNA and [alpha]CP1 protein using various biophysical techniques, in an attempt to determine which [alpha]CP1 domain or combination of domains is involved in RNA-binding. These studies could ultimately provide novel targets for drugs aimed to regulate AR mRNA expression in prostate cancer cells. At the commencement of this study little was known about the structure of the [alpha]CP1- KH domains and their basis for poly (C) binding specificity. ... Additional studies addressed the significance of the four core recognition nucleotides (TCCC) using a series of cytosine to thymine mutants. The findings verified some of the results predicted from structural studies, especially the need for maximum KH binding to a core tetranucleotide recognition sequence. Our mutational studies of the four core bases confirmed the importance of cytosine in positions two and three as no binding was observed, while some binding was observed when the fourth base was mutated. In summary, the work presented in this thesis provides new detailed insight into the molecular interactions between the [alpha]CP1-KH domain and AR mRNA. Furthermore, these studies shed light on the nature of protein/mRNA interactions in general, as well as the specific complex that forms on AR mRNA. These studies have provided new understanding into the mode of [alpha]CP1 binding at a target oligonucleotide binding site and, provide a foundation for future studies to define structure of multiprotein/oligonucleotide complexes involved in AR mRNA gene regulation. Understanding the detailed interaction between the AR mRNA and [alpha]CP1 could provide possible targets for drug development at reducing AR expression in prostate cancer cells by interfering with the interaction of [alpha]CP1 and AR-mRNA.

Spinal muscular atrophy is an autosomal recessive genetic disease that results from the loss and/or degeneration of alpha motor neurons in the lower part of the spinal cord. With ~ 1 in 6000 live births per year being affected, this disease is the second leading cause of infant death and is caused by the loss or decrease of the Survival of Motor Neuron protein (SMN). While a lot is known about the role that SMN plays in the cytoplasmic assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs), it remains a crucial question in the field to gain a better understanding of what specific/distinct function(s) SMN might have in motor neurons. We have identified novel interactions between SMN and two RNA-binding proteins (RBPs) known to be components of axonal RNA granules. More specifically, we demonstrated that SMN interacts with HuD and SERBP1 in a direct fashion in foci-like structures along neurites of motor neuron-derived cells. We have also demonstrated that the SMN/HuD interaction is required for the localization of HuD into RNA granules in neurites of motor neuron-derived cells. Furthermore, I have shown that SERBP1 is down-regulated in the absence of normal levels of SMN and, most importantly, that over-expression of SERBP1 can rescue SMA-like neuronal defects using a cell culture model of the disease. These findings may help shed light on the non-canonical molecular pathway(s) involving SMN and RBPs in motor neurons and underscores the possible therapeutic benefits of targeting these RBPs in the treatment of SMA.