The essential protein Mtr4 is a conserved Ski2-like RNA helicase that maintains the integrity of nuclear RNA by promoting the 3' end decay of a wide variety of RNA substrates. Mtr4 activates the multi-protein exosome in RNA processing, surveillance, and turnover pathways by unwinding secondary structure and/or displacing associated proteins from RNA substrates. While Mtr4 may be able to promote decay independently, it is often associated with large multi-protein assemblies. Specifically, Mtr4 is the largest member of the TRAMP (Trf4/Air2/Mtr4 polyadenylation) complex which targets a plethora of RNA substrates for degradation by appending them with small (~5nt) poly(A) tails via the polymerase activity of Trf4. Mtr4 preferentially binds and unwinds RNAs with short poly(A) tails. Notably, the mechanism by which Mtr4 recognizes the length and identity of the RNA 3' end is coupled to the modulation of poly(A) polymerase activity of Trf4. The lack of structural data for Mtr4 and associated complexes severely limits the understanding of Mtr4 function. Particularly, it is unclear how Mtr4 senses RNA features, acts on RNA substrates, delivers RNA substrates to the exosome, and assembles into larger protein complexes. Presented here is the x-ray crystal structure of Mtr4 combined with detailed structural and biochemical analysis of the enzyme. The structure reveals that Mtr4 contains a four domain helicase core that is conserved in other RNA helicases and a unique arch-like RNA binding domain that is required for the in vivo processing of 5.8S rRNA. Furthermore, kinetic and in vivo analysis of conserved residues implicated in the poly(A) sensing mechanism demonstrates that ratchet helix residues regulate RNA unwinding and impact RNA sequence specificity. A comparison of the apo Mtr4 structure with the RNA/ADP bound structure (determined elsewhere) provides a view of the range of motion that individual domains of Mtr4 adopt upon substrate binding as well as the possible conformations that occur during RNA translocation. These studies provide an important framework for understanding the fundamental role of Mtr4 in exosome-mediated RNA decay, and more broadly describe common themes in architecture and function of the Ski2-like helicase family.

Homologous recombination is critical for generating genetic variation in living organisms by exchange and rearrangement of DNA. Most of our knowledge about homologous recombination is limited to processes in bacteria or in eukaryotic nuclei. In E. coli, homologous recombination is dependent on the RecA protein. Higher plant chloroplasts have RecA-like strand exchange activity. However, little is known about these mechanisms in higher plant mitochondria. I have detected a RecA-like strand exchange activity in soybean mitochondria. This activity forms joint molecules in the presence of ATP, Mg2+, and homologous DNA substrates. In addition, the E. coli single-stranded DNA binding (SSB) protein is a non-sequence-specific DNA binding protein that functions as an accessory factor for RecA protein-promoted strand exchange reactions. Our lab has identified an Arabidopsis homologue of E. coli SSB that is targeted to mitochondria (mtSSB). The results of my research shows the mtSSB protein has the same properties as the E. coli SSB protein and it can stimulate the E. coli RecA protein-promoted strand exchange reactions. DNA helicases utilize the energy of ATP to separate the two parental DNA strands at the replicating fork or during recombinational strand exchange. Although higher plant chloroplast helicase activity has been reported, no such activity has heretofore been identified in higher plant mitochondria. We report the characterization of a plant mitochondrial DNA helicase isolated from soybean leaves. ATP is required for this enzyme and this enzyme poorly utilizes any other NTPs or dNTPs. The enzyme requires Mg2+ for activity. This enzyme only has 3' to 5'unwinding activity. The optimal conditions for mitochondrial DNA helicase are 2 mM ATP, 8 to 10 mM Mg2+,100 to 200 mM NaCl and 37-42 oC incubation for one hour or longer time.

Yes / We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilises Rad51-DNA filaments and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although in such cells sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalised with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards interhomologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division. / Biotechnology and Biological Sciences Research Council (BB/K009346/1)

No description available.

POLQ is a unique multifunctional replication and repair gene that encodes a multidomain protein with a N-terminal superfamily 2 helicase and a C-terminal A-family polymerase. Although the function of the polymerase domain has been investigated, little is understood regarding the helicase domain. Multiple studies have reported that polymerase θ-helicase (Polθ-helicase) is unable to unwind DNA. However, it exhibits ATPase activity that is stimulated by single-stranded DNA, which presents a biochemical conundrum. In contrast to previous reports, we demonstrate that Polθ-helicase (residues 1– 894) efficiently unwinds DNA with 3'–5' polarity, including DNA with 3' or 5' overhangs, blunt- ended DNA, and replication forks. Polθ-helicase also efficiently unwinds RNA-DNA hybrids and exhibits a preference for unwinding the lagging strand at replication forks, similar to related HELQ helicase. Finally, we find that Polθ-helicase can facilitate strand displacement synthesis by Polθ-polymerase, suggesting a plausible function for the helicase domain. Taken together, these findings indicate nucleic acid unwinding as a relevant activity for Pol theta in replication repair. DNA polymerase theta is a unique polymerase-helicase fusion protein that promotes microhomology-mediated end-joining of DNA double-strand breaks. How full-length human DNA polymerase theta performs microhomology-mediated end-joining and is regulated by the helicase and disordered central domain remains unknown. We find that the helicase upregulates DNA polymerase theta microhomology-mediated end-joining activity in an ATPase-independent manner. Using single-particle microscopy, we find that DNA polymerase theta forms large multimeric complexes that promote DNA accumulation and end-joining. We further find that the disordered central domain regulates DNA polymerase theta multimerization and governs its DNA substrate requirements for end-joining. In summary, these studies identify major regulatory functions for the helicase and central domains in DNA end-joining and the structural organization of DNA polymerase theta. / Biomedical Sciences

O desenvolvimento de uma vacina para o controle da dengue é uma prioridade em todo o mundo. O domínio helicase da proteína NS3 (NS3H) viral alberga epítopos reconhecidos por linfócitos T citotóxicos, os quais tem papel importante na eliminação de células infectadas. Esse trabalho propôs a obtenção de uma forma recombinante, produzida em linhagens de Escherichia coli, da NS3H do DENV2 com características similares à proteína nativa e sua utilização como um potencial antígeno vacinal. A NS3H foi obtida na forma solúvel, foi reconhecida por anticorpos de camundongos e de humanos infectados e foi capaz de interagir com o RNA viral. Camundongos imunizados com NS3H coadministrada com diferentes adjuvantes desenvolveram respostas imunológicas específicas mas não foram protegidos após desafio. Em conjunto, os resultados indicam que a proteína NS3H recombinante preserva conformação e determinantes antigênicos da proteína viral nativa e pode ser útil em estudos sobre a biologia viral e na busca de estratégias anti-virais voltadas para o controle da dengue. / The development of a dengue vaccine is a worldwide priority. The helicase domain of viral NS3 protein (NS3H) preserves epitopes recognized by cytotoxic T lymphocytes, which plays an important role in the elimination of infected cells. This study aimed the generation of a recombinant NS3H form of a type 2 dengue virus (DENV2) lineage, in Escherichia coli strains, with properties similar to the native protein and its use as a potential vaccine antigen. The NS3H was obtained in soluble form, was recognized by antibodies from mice and human subjects and was able to interact with the viral RNA. Mice immunized with NS3H combined with different adjuvants developed specific immune responses but did not confer protection to a lethal challenge. Altogether, the results indicate that the recombinant NS3H protein preserves conformational and antigenic determinants of the native protein and may be a useful tool for studies dealing with the DENV biology and the search for anti-virus approaches.

O desenvolvimento de uma vacina para o controle da dengue é uma prioridade em todo o mundo. O domínio helicase da proteína NS3 (NS3H) viral alberga epítopos reconhecidos por linfócitos T citotóxicos, os quais tem papel importante na eliminação de células infectadas. Esse trabalho propôs a obtenção de uma forma recombinante, produzida em linhagens de Escherichia coli, da NS3H do DENV2 com características similares à proteína nativa e sua utilização como um potencial antígeno vacinal. A NS3H foi obtida na forma solúvel, foi reconhecida por anticorpos de camundongos e de humanos infectados e foi capaz de interagir com o RNA viral. Camundongos imunizados com NS3H coadministrada com diferentes adjuvantes desenvolveram respostas imunológicas específicas mas não foram protegidos após desafio. Em conjunto, os resultados indicam que a proteína NS3H recombinante preserva conformação e determinantes antigênicos da proteína viral nativa e pode ser útil em estudos sobre a biologia viral e na busca de estratégias anti-virais voltadas para o controle da dengue. / The development of a dengue vaccine is a worldwide priority. The helicase domain of viral NS3 protein (NS3H) preserves epitopes recognized by cytotoxic T lymphocytes, which plays an important role in the elimination of infected cells. This study aimed the generation of a recombinant NS3H form of a type 2 dengue virus (DENV2) lineage, in Escherichia coli strains, with properties similar to the native protein and its use as a potential vaccine antigen. The NS3H was obtained in soluble form, was recognized by antibodies from mice and human subjects and was able to interact with the viral RNA. Mice immunized with NS3H combined with different adjuvants developed specific immune responses but did not confer protection to a lethal challenge. Altogether, the results indicate that the recombinant NS3H protein preserves conformational and antigenic determinants of the native protein and may be a useful tool for studies dealing with the DENV biology and the search for anti-virus approaches.

CAG/CTG repeat instability is associated with at least 14 neurological disorders, including Huntington’s disease and Myotonic dystrophy type 1. In vitro and in vivo studies have showed that CAG/CTG repeats form a stable hairpin that is believed to be the intermediate for repeat expansion and contraction. Addition of extra DNA is essential for repeat expansion, so DNA synthesis is one of the keys for repeat expansion. In vivo studies reveal that 3’ CTG slippage with subsequent hairpin formation (henceforth called the 3’ CTG slippage hairpin) occurs during DNA synthesis. It is proposed that hairpin tolerance machinery is activated because prolonged stalling of DNA polymerase triggers severe DNA damage. As a means toward studying the hairpin-mediated expansion, we created a special hairpin substrate, mimicking the 3’ CTG slippage hairpin, to determine which polymerase promotes hairpin bypass. Our studies reveal polymerase β (pol β) is involved in the initial hairpin synthesis while polymerase δ (pol δ) is responsible for the resumption of DNA synthesis beyond the hairpin (extension step). Surprisingly, we also found that the pol δ can remove the short CTG hairpin by excision of the hairpin with its 3’ to 5’ exonuclease activity. Besides repairing the hairpin directly, resolving the hairpin is an alternative pathway to maintain CAG/CTG repeat stability. With limited understanding of which human helicase is responsible for resolving CAG/CTG hairpins, we conducted a screening approach to identify the human helicase involved. Werner Syndrome Protein (WRN) induces the hairpin repair activity when (CTG)35 hairpin is formed on the template strand. Primer extension assay reveals that WRN stimulates pol δ synthesis on (CAG)35/(CTG)35 template and such induction was still found in the presence of accessory factors. Helicase assay confirms that WRN unwinds CTG hairpin structures. Our studies provide a better understanding of how polymerases and helicases play a role in CAG/CTG repeat instability. Considering CAG/CTG repeat instability associated disorders are still incurable, our studies can provide several potential therapeutic targets for treating and/or preventing CAG/CTG repeat associated disorders.

DNA damage from both normal metabolic activities and environmental factors such as UV and radiation can cause as many as 1 million individual lesions to the DNA per cell per day (Lodish et al 2004). Cells respond to this continuous damage by employing many, highly efficient DNA repair mechanisms and undergo apoptosis when normal DNA repair fails. Of the many types of DNA damage that can occur, double strand breaks (DSBs) are the most toxic (Featherstone & Jackson 1999). A single unrepaired DSB is enough to induce cellular apoptosis and several mechanisms have developed to repair DSBs. The recognition, signalling and repair of DSBs involve large multi-­‐subunit complexes that bind to both the DNA and modified histone tails, which require modification of the chromatin in order to access their bind sites and function effectively (Allard et al 2004). Consequently several chromatin-­‐remodelling proteins have been implicated in DSB repair (van Attikum et al 2004, Chai et al 2005). LSH (Lymphoid specific helicase) is a putative chromatin-­‐remodelling enzyme that interacts with DNA methyltransferases and has been connected to DNA methylation (Myant & Stancheva, 2008). Knockouts of LSH or its homologues in A. thaliana and M. musculus show a reduction in DNA methylation of 60-­‐70% (Jeddeloh et al 1999, Dennis et al 2001). However in addition to this phenotype, knockout A. thaliana also have an increased sensitivity to DNA damage (Shaked et al 2006). A homologue of LSH has also been identified in S. cerevisiae, which interacts with known repair proteins (Collins et al 2007) and may be involved in DSB repair. Although the majority of Lsh-­‐/-­‐ mice die shortly after birth, 40% of the line produced by Sun et al survive and show unexplained premature aging (Sun et al 2004). As premature aging is a hallmark of increased acquisition of DNA damage there is the possibility of a conserved role for LSH in mammalian DNA damage repair. Here I show that LSH depleted mammalian cells have an increased sensitivity specifically to DSB inducing agents and show increased levels of apoptosis. Further analysis shows that cells lacking LSH repair DSBs slower, indicating a novel role for LSH in mammalian repair of DSB. I performed an in depth analysis of the DSB defects in LSH depleted cells in an attempt to elucidate the function of LSH in DSB repair. I found that LSH depleted cells can correctly recognise DSBs but recruit downstream signalling and repair factors, such as γH2AX, less efficiently. I show that reduced recruitment of downstream DSB repair factors is not accompanied by extended cell cycle checkpoint signalling. This suggests that LSH depleted cells continue through the mitosis with unrepaired DSBs, which most likely leads to apoptosis and the increased sensitivity to DSB inducing agents. These experiments also showed that recruitment of DSB signalling and repair factors is not impaired equally at all breaks, and I present a model system created to quantitatively compare individually breaks between WT and LSH depleted cells to identify DSB that require LSH for efficient repair. I also preformed an analysis of Lsh-­/-­ MEFs containing WT or catalytic null mutant LSH rescue constructs and I show that WT but not catalytic null LSH can restore efficient DSB repair. These studies identify a novel role for LSH in mammalian DSB repair and demonstrate the importance of its catalytic activity.

The initiation of cancer metastasis usually requires Epithelial-Mesenchymal Transition (EMT), by which tumor cells lose cell-cell interactions and gain the ability of migration and invasion. Previous study demonstrated that p68 RNA helicase, a prototypical member of the DEAD-box RNA helicases, functions as a mediator to promote platelet-derived growth factor (PDGF)-induced EMT through facilitating nuclear translocation of β-catenin in colon cancer cells. In this context, p68 RNA helicase was found to be phosphorylated at the tyrosine 593 residue (referred as phosphor-p68) by c-Abl kinase, and this phosphorylation is required for the activation of β-catenin signaling and the consequent EMT. The phosphor-p68 RNA helicase-mediated EMT was characterized by the repression of an epithelial marker, E-cadherin, and the upregulation of a mesenchymal marker, Vimentin. E-cadherin, a major cell-cell adhesion molecule that is involved in the formation of adherens junctions, has been shown to sequester β-catenin at the cell membrane and thus inhibit its transcriptional activity. The functional loss of E-cadherin is the fundamental event of EMT. Despite the role of phosphor-p68 RNA helicase in regulating nuclear translocation of β-catenin, whether phosphor-p68 is involved in the regulation of E-cadherin remains unknown. Here, our data indicated that phosphor-p68 RNA helicase initiated EMT by transcriptional upregulation of Snail1, a master transcriptional repressor of E-cadherin. The data suggest that phosphor-p68 RNA helicase displaced HDAC1 from the chromatin remodeling MBD3:Mi-2/NuRD complex at the Snail1 promoter, thereby activating the transcription of Snail1. In the xenograft tumor model, abolishing the phosphorylation of p68 RNA helicase by the expression of Y593F mutant resulted in a significant reduction of metastatic potential in human colon cancer cells. Analyses in the colon cancer tissues also revealed that the tyrosine 593 phosphorylation level of p68 RNA helicase is substantially enhanced in the tumor tissues comparing to that in the corresponding normal counterparts, suggesting a correlation of phosphor-p68 and tumor progression. In conclusion, we showed that tyrosine phosphorylation of p68 RNA helicase positively correlated to the malignant status of colon cancer progression. The molecular basis behind this correlation could be partly through the transcriptional regulation of Snail1.