Academic literature on the topic 'Partner proteins'
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Journal articles on the topic "Partner proteins"
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Sahin, Umut, Omar Ferhi, Marion Jeanne, Shirine Benhenda, Caroline Berthier, Florence Jollivet, Michiko Niwa-Kawakita, et al. "Oxidative stress–induced assembly of PML nuclear bodies controls sumoylation of partner proteins." Journal of Cell Biology 204, no. 6 (March 17, 2014): 931–45. http://dx.doi.org/10.1083/jcb.201305148.
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The promyelocytic leukemia (PML) protein organizes PML nuclear bodies (NBs), which are stress-responsive domains where many partner proteins accumulate. Here, we clarify the basis for NB formation and identify stress-induced partner sumoylation as the primary NB function. NB nucleation does not rely primarily on intermolecular interactions between the PML SUMO-interacting motif (SIM) and SUMO, but instead results from oxidation-mediated PML multimerization. Oxidized PML spherical meshes recruit UBC9, which enhances PML sumoylation, allow partner recruitment through SIM interactions, and ultimately enhance partner sumoylation. Intermolecular SUMO–SIM interactions then enforce partner sequestration within the NB inner core. Accordingly, oxidative stress enhances NB formation and global sumoylation in vivo. Some NB-associated sumoylated partners also become polyubiquitinated by RNF4, precipitating their proteasomal degradation. As several partners are protein-modifying enzymes, NBs could act as sensors that facilitate and confer oxidative stress sensitivity not only to sumoylation but also to other post-translational modifications, thereby explaining alterations of stress response upon PML or NB loss.
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Di, Han, Husni Elbahesh, and Margo A. Brinton. "Characteristics of Human OAS1 Isoform Proteins." Viruses 12, no. 2 (January 29, 2020): 152. http://dx.doi.org/10.3390/v12020152.
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The human OAS1 (hOAS1) gene produces multiple possible isoforms due to alternative splicing events and sequence variation among individuals, some of which affect splicing. The unique C-terminal sequences of the hOAS1 isoforms could differentially affect synthetase activity, protein stability, protein partner interactions and/or cellular localization. Recombinant p41, p42, p44, p46, p48, p49 and p52 hOAS1 isoform proteins expressed in bacteria were each able to synthesize trimer and higher order 2′-5′ linked oligoadenylates in vitro in response to poly(I:C). The p42, p44, p46, p48 and p52 isoform proteins were each able to induce RNase-mediated rRNA cleavage in response to poly(I:C) when overexpressed in HEK293 cells. The expressed levels of the p42 and p46 isoform proteins were higher than those of the other isoforms, suggesting increased stability in mammalian cells. In a yeast two-hybrid screen, Fibrillin1 (FBN1) was identified as a binding partner for hOAS1 p42 isoform, and Supervillin (SVIL) as a binding partner for the p44 isoform. The p44-SVIL interaction was supported by co-immunoprecipitation data from mammalian cells. The data suggest that the unique C-terminal regions of hOAS1 isoforms may mediate the recruitment of different partners, alternative functional capacities and/or different cellular localization.
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Krishna, Priti. "Plant Hsp90 and Its Partner Proteins." Journal of Plant Biochemistry and Biotechnology 9, no. 2 (July 2000): 53–56. http://dx.doi.org/10.1007/bf03263085.
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Rassow, J. "Partner proteins determine multiple functions of Hsp70." Trends in Cell Biology 5, no. 5 (May 1995): 207–12. http://dx.doi.org/10.1016/s0962-8924(00)89001-7.
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Rassow, Joachim, Wolfgang Voos, and Nikolaus Pfanner. "Partner proteins determine multiple functions of Hsp70." Trends in Cell Biology 5, no. 5 (May 1995): 207–12. http://dx.doi.org/10.1016/0962-8924(95)80013-7.
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Stower, Hannah. "Proteins partner up in a vigorous relationship." Nature Reviews Genetics 14, no. 12 (October 29, 2013): 822. http://dx.doi.org/10.1038/nrg3617.
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Pancsa, Rita, Fruzsina Zsolyomi, and Peter Tompa. "Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings." International Journal of Molecular Sciences 19, no. 11 (October 25, 2018): 3315. http://dx.doi.org/10.3390/ijms19113315.
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Although improved strategies for the detection and analysis of evolutionary couplings (ECs) between protein residues already enable the prediction of protein structures and interactions, they are mostly restricted to conserved and well-folded proteins. Whereas intrinsically disordered proteins (IDPs) are central to cellular interaction networks, due to the lack of strict structural constraints, they undergo faster evolutionary changes than folded domains. This makes the reliable identification and alignment of IDP homologs difficult, which led to IDPs being omitted in most large-scale residue co-variation analyses. By preforming a dedicated analysis of phylogenetically widespread bacterial IDP–partner interactions, here we demonstrate that partner binding imposes constraints on IDP sequences that manifest in detectable interprotein ECs. These ECs were not detected for interactions mediated by short motifs, rather for those with larger IDP–partner interfaces. Most identified coupled residue pairs reside close (<10 Å) to each other on the interface, with a third of them forming multiple direct atomic contacts. EC-carrying interfaces of IDPs are enriched in negatively charged residues, and the EC residues of both IDPs and partners preferentially reside in helices. Our analysis brings hope that IDP–partner interactions difficult to study could soon be successfully dissected through residue co-variation analysis.
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Cerveira, Nuno, Susana Bizarro, and Manuel R. Teixeira. "MLL-SEPTIN gene fusions in hematological malignancies." Biological Chemistry 392, no. 8-9 (August 1, 2011): 713–24. http://dx.doi.org/10.1515/bc.2011.072.
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AbstractThe mixed lineage leukemia (MLL) locus is involved in more than 60 different rearrangements with a remarkably diverse group of fusion partners in approximately 10% of human leukemias.MLLrearrangements include chromosomal translocations, gene internal duplications, chromosome 11q deletions or inversions andMLLgene insertions into other chromosomes, or vice versa. MLL fusion partners can be classified into four distinct categories: nuclear proteins, cytoplasmatic proteins, histone acetyltransferases and septins. Five different septin genes (SEPT2,SEPT5,SEPT6,SEPT9, andSEPT11) have been identified asMLLfusion partners, giving rise to chimeric fusion proteins in which the N terminus of MLL is fused, in frame, to almost the entire open reading frame of the septin partner gene. The rearranged alleles result from heterogeneous breaks in distinct introns of bothMLLand its septin fusion partner, originating distinct gene fusion variants.MLL-SEPTIN rearrangements have been repeatedly identified inde novoand therapy related myeloid neoplasia in both children and adults, and some clinicopathogenetic associations are being uncovered. The fundamental roles of septins in cytokinesis, membrane remodeling and compartmentalization can provide some clues on how abnormalities in the septin cytoskeleton and MLL deregulation could be involved in the pathogenesis of hematological malignancies.
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Siahaan, Riana Friska, and Erli Mutiara. "TURNING DISASTER INTO BUSINESS OPPORTUNITY THROUGH PROCESSING OF POTATO STICK IN SIOSAR VILLAGE KARO DISTRICT." Journal of Community Research and Service 1, no. 2 (March 29, 2018): 59. http://dx.doi.org/10.24114/jcrs.v1i2.9338.
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AbstractThe purpose of this activity is to empower the potential owned by the partner community. The activities are conducted from July to November 2017. Activity partners are Ati Rohati and home industries Wahyuni. Location of activity in Suka Meriah Village Siosar Kec. Brand Kab. Karo. This village is an area where the relocation of people affected by eruption of Mount Sinabung. Located 110 km from Unimed. Methods of implementation of activities are education, production training, business management training, machine use and mentoring. Output t of this activity is 1) Potato Sticker Machine and 2) Potato Stick. Specifications of potato sticks are: 1) Have nutritional content: Carbohydrates, Proteins, fats, iron, and fiber; 2) Durable and hygienic. Results of activities obtained are partners have knowledge of potato stick processing, actively participating partners, skilled partners using potato sticker printing machine. Partner production is getting better and partner income is also increasing.Keywords: Stick, Potato, Disaster, Karo
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Berthelsen, J. "Prep1, a novel functional partner of Pbx proteins." EMBO Journal 17, no. 5 (March 2, 1998): 1423–33. http://dx.doi.org/10.1093/emboj/17.5.1423.
Full textDissertations / Theses on the topic "Partner proteins"
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Tattersall, Daniel. "The identification of retromer partner proteins." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615241.
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Njunge, James Mwangi. "Characterization of the Hsp40 partner proteins of Plasmodium falciparum Hsp70." Thesis, Rhodes University, 2014. http://hdl.handle.net/10962/d1013186.
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Human malaria is an economically important disease caused by single-celled parasites of the Plasmodium genus whose biology displays great evolutionary adaptation to both its mammalian host and transmitting vectors. This thesis details the 70 kDa heat shock protein (Hsp70) and J protein chaperone complements in malaria parasites affecting humans, primates and rodents. Heat shock proteins comprise a family of evolutionary conserved and structurally related proteins that play a crucial role in maintaining the structural integrity of proteins during normal and stress conditions. They are considered future therapeutic targets in various cellular systems including Plasmodium falciparum. J proteins (Hsp40) canonically partner with Hsp70s during protein synthesis and folding, trafficking or targeting of proteins for degradation. However, in P. falciparum, these classes of proteins have also been implicated in aiding the active transport of parasite proteins to the erythrocyte cytosol following erythrocyte entry by the parasite. This host-parasite “cross-talk” results in tremendous modifications of the infected erythrocyte, imparting properties that allow it to adhere to the endothelium, preventing splenic clearance. The genome of P. falciparum encodes six Hsp70 homologues and a large number of J proteins that localize to the various intracellular compartments or are exported to the infected erythrocyte cytosol. Understanding the Hsp70-J protein interactions and/or partnerships is an essential step for drug target validation and illumination of parasite biology. A review of these chaperone complements across the Plasmodium species shows that P. falciparum possesses an expanded Hsp70-J protein complement compared to the rodent and primate infecting species. It further highlights how unique the P. falciparum chaperone complement is compared to the other Plasmodium species included in the analysis. In silico analysis showed that the genome of P. falciparum encodes approximately 49 J proteins, 19 of which contain a PEXEL motif that has been implicated in routing proteins to the infected erythrocyte. Most of these PEXEL containing J proteins are unique with no homologues in the human system and are considered as attractive drug targets. Very few of the predicted J proteins in P. falciparum have been experimentally characterized. To this end, cell biological and biochemical approaches were employed to characterize PFB0595w and PFD0462w (Pfj1) J proteins. The uniqueness of Pfj1 and the controversy in literature regarding its localization formed the basis for the experimental work. This is the first study showing that Pfj1 localizes to the mitochondrion in the intraerythrocytic stage of development of P. falciparum and has further proposed PfHsp70-3 as a potential Hsp70 partner. Indeed, attempts to heterologously express and purify Pfj1 for its characterization are described. It is also the first study that details the successful expression and purification of PfHsp70-3. Further, research findings have described for the first time the expression and localization of PFB0595w in the intraerythrocytic stages of P. falciparum development. Based on the cytosolic localization of both PFB0595w and PfHsp70-1, a chaperone – cochaperone partnership was proposed that formed the basis for the in vitro experiments. PFB0595w was shown for the first time to stimulate the ATPase activity of PfHsp70-1 pointing to a functional interaction. Preliminary surface plasmon spectroscopy analysis has revealed a potential interaction between PFB0595w and PfHsp70-1 but highlights the need for further related experiments to support the findings. Gel filtration analysis showed that PFB0595w exists as a dimer thereby confirming in silico predictions. Based on these observations, we conclude that PFB0595w may regulate the chaperone activity of PfHsp70-1 in the cytosol while Pfj1 may play a co-chaperoning role for PfHsp70-3 in the mitochondrion. Overall, this data is expected to increase the knowledge of the Hsp70-J protein partnerships in the erythrocytic stage of P. falciparum development, thereby enhancing the understanding of parasite biology.
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Krishnan, Kadalmani. "Characterisation of the G protein controlled tyrosine kinase, ACK1 and its interaction with nucleolar partner proteins." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610698.
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Chan, Pui Wai. "Fhit : a novel interacting partner of G[alpha][subscript q] proteins /." View abstract or full-text, 2008. http://library.ust.hk/cgi/db/thesis.pl?BICH%202008%20CHAN.
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Mohamad, Nada. "The RNA binding protein Mip6, a novel cellular partner of Mex67 export factor with implications in mRNA export." Doctoral thesis, Universitat Politècnica de València, 2017. http://hdl.handle.net/10251/90397.
Full textAbstract:
Nuclear export of messenger ribonucleic acid (mRNA) is a complex and essential process for a correct gene expression in all eukaryotic cells. The export of mRNA through the nuclear pore complex depends mostly on the crosstalk and coordination of several proteins forming what is known as mRNPs (messenger ribonucleoproteins) that play dynamic, interconnecting roles in the different mRNA biogenesis steps such as pre-mRNA processing, stability, and export.
One key protein in this process is Mex67, conserved from yeast to humans, is the major messenger RNA exporter also involved in ribosomal RNA export. Mex67 interacts with Mtr2 to form an evolutionary conserved heterodimer essential for proper mRNA export and subsequently the survival of the cell. Mex67 have been studied for many years, however due to the complexity and interconnectivity of the different processes in mRNA biogenesis, there is yet to uncover many details on the dynamics of the process and the crosstalk between Mex67 and its many partners.
In this study, using a combination of biochemical, biophysical, and structural analysis, we characterize the interaction between Mex67 and a novel partner protein called Mip6 (Mex67 interacting protein 6). We were able to reconstitute a stable complex in vitro, and extensively study the mechanism in which the two proteins interact. We also solved the crystal structure of the C-terminal region of Mex67 that interacts with Mip6 and identified the UBA domain of Mex67, known to bind FG nucleoporins and Hpr1 protein as also the site where Mip6 binds. However, little was known about the structure or function of Mip6 and its paralogue Pes4. Here we proved that Mip6 is an RNA binding protein with four RNA recognition motifs that binds RNA in vitro with high affinity. Additionally, its fourth RNA recognition motif was also the site of binding of Mex67. Furthermore, we showed that the Mex67 complex formation with Mip6 RRM4 compromises its ability to bind RNA or vice versa. We also designed a point mutation on Mip6 RRM4 that disrupts its interaction with Mex67 but not with RNA. Subsequent in vivo yeast assays led us to hypothesize a role of Mip6 as an adaptor protein for Mex67 in nuclear export especially upon stress. Additional function of Mip6 was the localization of its bound mRNA to cytoplasmic stress granules in cellular stress conditions.
Moreover, the crystal structures of Mip6 RRM3, Pes4 RRM3, Pes4 RRM4, and Pes4 RRM3/4 were also solved. All RRMs adopted a canonical RRM fold with conserved RNP1 and RNP2 sequences normally involved in RNA binding, except Mip6 RRM3 that was missing the aromatic ring in RNP2. In the structure of RNA-free Pes4 RRM3/4, the tandem RRM domains were connected with a flexible disordered linker and no inter-domain contact between them. Finally, although Pes4 RRM4 was binding RNA in vitro, it did not have the ability to interact with Mex67 thus suggesting a separate evolutionary function for Mip6 and Pes4.La exportación nuclear de ácido ribonucleico mensajero (ARNm) es un proceso complejo y esencial para una expresión correcta de los genes en todas las células eucariotas. La exportación de ARNm a través del complejo del poro nuclear depende principalmente de la interacción y coordinación de varias proteínas, que forman lo que se conoce como mRNPs (ribonucleoproteínas mensajeras), que tienen un papel dinámico e interconectado en las diferentes etapas de la biogénesis de ARNm, tales como el procesamiento del pre-ARNm, estabilidad, y exportación. Una proteína clave en este proceso es Mex67, conservada de levaduras a humanos, que es la principal exportadora de ARN mensajero y también está implicada en la exportación de ARN ribosomal. Mex67 interacciona con Mtr2 para formar un heterodímero conservado evolutivamente esencial para una exportación adecuada de ARNm y la consiguiente supervivencia de la célula. Se ha estudiado Mex67 durante muchos años, sin embargo, debido a la complejidad e interconectividad de los diferentes procesos de biogénesis de ARNm, todavía quedan por descubrir muchos detalles de la dinámica del proceso y las interacciones entre Mex67 y sus muchas proteínas asociadas. En este estudio, combinando un análisis bioquímico, biofísico y estructural, hemos caracterizado la interacción entre Mex67 y una nueva proteína asociada denominada Mip6 (proteína 6 que interacciona con Mex67). Hemos podido reconstituir un complejo estable in vitro y estudiar extensivamente el mecanismo por el cual interaccionan estas dos proteínas. También hemos resuelto la estructura cristalográfica de la región C-terminal de Mex67 que interacciona con Mip6 e identificado el dominio UBA de Mex67, conocido por unirse a nucleoporinas FG y a la proteína Hpr1, así como el sitio por el que se une Mip6. No obstante, se sabía muy poco sobre la estructura o la función de Mip6 y su parálogo Pes4. Hemos probado que Mip6 es una proteína de unión a ARN con cuatro motivos de reconocimiento de ARN que se unen a ARN in vitro con una afinidad alta. Además, su cuarto motivo de reconocimiento de ARN es también el sitio de unión a Mex67. Posteriormente, demostramos que la formación del complejo de Mex67 con el dominio RRM4 de Mip6 compromete su capacidad para unir ARN o viceversa. También diseñamos una mutación puntual en el RRM4 de Mip6 que rompe la interacción con Mex67 pero no con el ARN. Los ensayos posteriores in vivo en levaduras nos permitieron establecer una hipótesis sobre el papel de Mip6 como proteína adaptadora para Mex67 en la exportación nuclear, especialmente en condiciones de estrés. Una función adicional de Mip6 era la localización del ARNm que se unía a ella en gránulos de estrés en condiciones de estrés celular. Además, hemos resuelto las estructuras cristalográficas del RRM3 de Mip6, RRM3 de Pes4, RRM4 de Pes4 y los RRM3 y 4 de Pes4. Todos los RRMs adoptaron una conformación canónica RRM con secuencias RNP1 y RNP2 conservadas generalmente implicadas en la unión a ARN, excepto el RRM3 de Mip6 que carecía del anillo aromático en RNP2. En la estructura sin ARN de los RRM3 y 4 de Pes4, los dominios RRM tándem estaban conectados por una región flexible desordenada y no había un contacto inter-dominio entre ellos. Finalmente, aunque el RRM4 de Pes4 se unía a ARN in vitro, no presentaba la capacidad de interaccionar con Mex67 lo cual sugiere una divergencia evolutiva de la función de Mip6 y Pes4.
L¿exportació nuclear d¿àcid ribonucleic missatger (mRNA) es un procés complex i essencial per a una correcta expresió gènica en totes cèl¿lules eucariotes. L¿exportació del mRNA a través del complex del porus nuclear depén principalment de la interacció i coordinació de diverses proteïnes, que formen el que es coneix com mRNPs (ribonucleoproteïnes missatgeres), que tenen un paper dinàmic i interconnectat en les diferents etapes de la biogènesi d¿ARNm, com el processament del pre-ARNm, estabilitat, localització i exportació. Una proteïna clau en aquest procés és MEX67, conservada de llevats fins a humans, que és la principal exportadora de ARN missatger i també està implicada en l¿exportació de ARN ribosomal. Mex67 interacciona amb Mtr2 per a formar un heterodímer conservat evolutivament essencial per a una exportació adequada d¿ARNm i la consegüent supervivència de la cèl¿lula. S¿ha estudiat Mex67 durant molts anys, però degut a la complexitat i interconectivitat dels diferents processos de biogènesi d¿ARNm, encara queden per descobrir molts detalls de la dinàmica del procés i les interaccions entre Mex67 i les seues moltes proteïnes associades. En aquest estudi, combinant l¿anàlisi bioquímic, biofísic i estructural, hem caracteritzat la interacció entre Mex67 i una nova proteïna associada anomenada Mip6 (proteïna 6 que interacciona amb Mex67). Hem pogut reconstituir un complex estable in vitro i estudiar extensivament el mecanisme pel qual interaccionen estes dos proteïnes. També hem resolt l¿estructura cristal¿logràfica de la regió C-terminal de Mex67 que interacciona amb Mip6 i identificat el domini UBA de Mex67, conegut per unir-se a nucleoporines FG i a la proteïna Hpr1, així com ser el lloc pel que s¿uneix Mip6. No obstant, se sabia molt poc sobre l¿estructura o la funció de Mip6 i el seu paràleg Pes4. Hem comprobat que Mip6 es una proteïna d¿unió a ARN amb quatre motius de reconeixement d¿ARN que s¿uneixen a ARN in vitro amb una afinitat alta. A més, el seu quart motiu de reconeixement d¿ARN és també el lloc d¿unió a Mex67. Posteriorment, demostràrem que la formació del complex de Mex67 amb el domini RRM4 de Mip6 compromet la seua capacitat per a unir ARN o viceversa. També vam dissenyar una mutació puntual en el RRM4 de Mip6 que trenca la interacció amb Mex67 però no amb l¿ARN. Els assajos posteriors in vivo en llevats ens van permetre establir una hipòtesi sobre el paper de Mip6 com a proteïna adaptadora per a Mex67 en l¿exportació nuclear, especialment en condicions d¿estrès. Una funció adicional de Mip6 era la localització de l¿ARNm que s¿unia a ella en grànuls d¿estrès en condicions d¿estrès cel¿lular. A més, hem resolt les estructures cristal¿logràfiques del RRM3 de Mip6, RRM3 de Pes4, RRM4 de Pes4 i els RRM3 i 4 de Pes4. Tots els RRMs adoptaren una conformació canònica RRM amb seqüències RNP1 i RNP2 conservades generalment implicades en la unió a ARN, excepte el RRM3 de Mip6 que mancava del anell aromàtic en RNP2. En la estructura sense ARN dels RRM3 i 4 de Pes4, els dominis RRM tàndem estàven conectats per una regió flexible desordenada i no hi havia un contacte interdomini entre ells. Finalment, encara que el RRM4 de Pes4 es unia a ARN in vitro, no presentava la capacitat d¿interaccionar amb Mex67, la cual cosa sugerix una divergencia evolutiva de la funció de Mip6 y Pes4.
Mohamad, N. (2017). The RNA binding protein Mip6, a novel cellular partner of Mex67 export factor with implications in mRNA export [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90397
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Ekiert, Robert. "Analysis of partner proteins of MeCP2 and their relevance to Rett syndrome." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/9901.
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Methyl-CpG binding protein 2 (MeCP2) was discovered as a protein binding to methylated DNA more than 20 years ago. It is very abundant in the brain and was shown to be able to repress transcription. The mutations in MeCP2 cause Rett syndrome, an autism-spectrum neurological disorder affecting girls. Yet, the exact role of MeCP2 in Rett disease, its function and mechanism of action are not fully elucidated. In order to shed some light on its role in the disease the aim of this project was to identify proteins interacting with MeCP2. Affinity purification of MeCP2 from mouse brains and mass spectrometry analysis revealed new interactions between MeCP2 and protein complexes. Detailed analysis confirmed the findings and narrowed down the top interactions to distinct regions of MeCP2. One of the domains interacts with identified NCoR/SMRT co-repressor complex and is mutated in many patients with Rett syndrome. In vitro assays proved that these mutations abolish the putative transcriptional repressor function of MeCP2. We propose a model in which Rett syndrome is caused by two types of mutations: either disrupting the interaction with DNA or affecting the interaction with the identified complex, which has an effect on the global state of chromatin. The presented findings can help to develop new therapies for Rett syndrome in the future.
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Humphrey, Tania Vivienne. "Characterisation of a putative G-protein coupled receptor and its protein interacting partner in Arabidopsis /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16260.pdf.
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Cheung, Ngai. "Structural and functional characterization of EEN/EndophilinA2, a fusion partner in acute leukemia /." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B31540284.
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Cheung, Ngai, and 張毅. "Structural and functional characterization of EEN/EndophilinA2, a fusion partner in acute leukemia." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B45014760.
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O'Kane, Neil D. "TREK-1 investigation of a physiological role and identification of novel binding partner proteins /." abstract and full text PDF (UNR users only), 2009. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1472969.
Full textBooks on the topic "Partner proteins"
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Isserlin, Benjamin Alkan. Syntrophin expression and interacting protein partners in the central nervous system. Ottawa: National Library of Canada, 2000.
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Ten tea parties: Patriotic protests that history forgot. Philadelphia: Quirk Books, 2012.
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Srinanda, Dasgupta, ed. Indian politics: Protests and movements. New Delhi: Anmol Publications, 2003.
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Schimmang, Jochen. Der schöne Vogel Phönix. Hamburg, Germany: Edition Nautilus, 2013.
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Janssen, Hilde. Ciz As a Fusion Partner for Tet-proteins in Leukemia: Models for Leukemogenesis & Interaction Partners (Acta Biomedica Lovaniensia). Leuven Univ Pr, 2006.
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Mabuto, Yolanda. Identification of Protein Interaction Partners of Chromodomain Helicase DNA Binding Protein 6. Independently Published, 2018.
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PIas1: A protein partner of the homeodomain transcription factor CHX10. Ottawa: National Library of Canada, 2002.
Find full textBook chapters on the topic "Partner proteins"
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Chroboczek, J., E. Gout, A. L. Favier, and R. Galinier. "Novel Partner Proteins of Adenovirus Penton." In Current Topics in Microbiology and Immunology, 37–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05597-7_2.
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Oke, Muse, Manal S. Zaher, and Samir M. Hamdan. "PCNA Structure and Interactions with Partner Proteins." In Molecular Life Sciences, 1–8. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4614-6436-5_138-1.
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Oke, Muse, Manal S. Zaher, and Samir M. Hamdan. "PCNA Structure and Interactions with Partner Proteins." In Molecular Life Sciences, 866–72. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4614-1531-2_138.
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Austin, Brian P., Sreedevi Nallamsetty, and David S. Waugh. "Hexahistidine-Tagged Maltose-Binding Protein as a Fusion Partner for the Production of Soluble Recombinant Proteins in Escherichia coli." In Methods in Molecular Biology, 157–72. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-196-3_11.
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Sun, Ping, Joseph E. Tropea, and David S. Waugh. "Enhancing the Solubility of Recombinant Proteins in Escherichia coli by Using Hexahistidine-Tagged Maltose-Binding Protein as a Fusion Partner." In Methods in Molecular Biology, 259–74. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-61737-967-3_16.
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Hofmann, Kay. "Bioinformatics of Ubiquitin Domains and Their Binding Partners." In Protein Degradation, 318–47. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/352760586x.ch12.
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Hussain, Mahboob Ul. "Interaction Partners of Connexin Proteins." In SpringerBriefs in Biochemistry and Molecular Biology, 33–37. New Delhi: Springer India, 2014. http://dx.doi.org/10.1007/978-81-322-1919-4_9.
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Guilbert, Solenn M., Alice-Anaïs Varlet, Margit Fuchs, Herman Lambert, Jacques Landry, and Josée N. Lavoie. "Regulation of Actin-Based Structure Dynamics by HspB Proteins and Partners." In Heat Shock Proteins, 435–56. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16077-1_18.
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Groschner, Klaus, Niroj Shrestha, and Nicola Fameli. "Non-Orai Partners of STIM Proteins." In Calcium Entry Channels in Non-Excitable Cells, 177–96. Boca Raton : Taylor & Francis, 2017. | Series: Methods in signal transduction series: CRC Press, 2017. http://dx.doi.org/10.1201/9781315152592-10.
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Sharma, Sahil, and Cynthia M. Sharma. "Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq." In Methods in Molecular Biology, 111–33. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1851-6_6.
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AbstractCRISPR-Cas systems consist of a complex ribonucleoprotein (RNP) machinery encoded in prokaryotic genomes to confer adaptive immunity against foreign mobile genetic elements. Of these, especially the class 2, Type II CRISPR-Cas9 RNA-guided systems with single protein effector modules have recently received much attention for their application as programmable DNA scissors that can be used for genome editing in eukaryotes. While many studies have concentrated their efforts on improving RNA-mediated DNA targeting with these Type II systems, little is known about the factors that modulate processing or binding of the CRISPR RNA (crRNA) guides and the trans-activating tracrRNA to the nuclease protein Cas9, and whether Cas9 can also potentially interact with other endogenous RNAs encoded within the host genome. Here, we describe RIP-seq as a method to globally identify the direct RNA binding partners of CRISPR-Cas RNPs using the Cas9 nuclease as an example. RIP-seq combines co-immunoprecipitation (coIP) of an epitope-tagged Cas9 followed by isolation and deep sequencing analysis of its co-purified bound RNAs. This method can not only be used to study interactions of Cas9 with its known interaction partners, crRNAs and tracrRNA in native systems, but also to reveal potential additional RNA substrates of Cas9. For example, in RIP-seq analysis of Cas9 from the foodborne pathogen Campylobacter jejuni (CjeCas9), we recently identified several endogenous RNAs bound to CjeCas9 RNP in a crRNA-dependent manner, leading to the discovery of PAM-independent RNA cleavage activity of CjeCas9 as well as non-canonical crRNAs. RIP-seq can be easily adapted to any other effector RNP of choice from other CRISPR-Cas systems, allowing for the identification of target RNAs. Deciphering novel RNA-protein interactions for CRISPR-Cas proteins within host bacterial genomes will lead to a better understanding of the molecular mechanisms and functions of these systems and enable us to use the in vivo identified interaction rules as design principles for nucleic acid-targeting applications, fitted to each nuclease of interest.
Conference papers on the topic "Partner proteins"
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Ringuette, Maurice, Rong Xhu, Baoqian Zhu, Jaro Sodek, and Theodore J. Brown. "IDENTIFICATION OF A NOVEL ATP/GTP-BINDING PROTEIN PARTNER FOR OSTEOPONTIN." In 3rd International Conference on Osteopontin and SIBLING (Small Integrin-Binding Ligand, N-linked Glycoprotein) Proteins, 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.278.
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Amorim, Guilherme Vieira, BRUNA TOBIAS DOS SANTOS, DALYLA MARGARIDA PEREIRA, VITOR HUGO DE SOUZA GREGOLIN, and RENATO MASSAHARU HASSUNUMA. "SIMULAÇÃO COMPUTACIONAL DA ESTRUTURA BIOQUÍMICA DA AQUAPORINA-1." In III Congresso Brasileiro de Ciências Biologicas. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/iii-conbracib/6772.
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Introdução: As aquaporinas são proteínas canais que realizam o transporte de água através da membrana plasmática em eritrócitos, células endoteliais, células do revestimento gastrointestinal, de glândulas sudoríparas e pulmões. Estruturalmente, são homotetrâmeras, ou seja, são formadas por quatro subunidades proteicas idênticas. Assim, a água é transportada por cada um destes quatro canais de cada subunidade, sendo que na entrada de cada canal existem aminoácidos que impedem a entrada de solutos e íons como o hidrônio ou hidroxila pelos canais. Objetivo: O objetivo principal da atual pesquisa foi desenvolver scripts para o software RasMol para criação de imagens que ilustram a estrutura bioquímica da aquaporina-1. Metodologia: A partir do levantamento de arquivos PDB sobre aquaporina-1, obtidos no site Protein Data Bank, foram scripts para o software RasMol no intuito de observar a estrutura secundária da proteína. Resultados: A partir do arquivo 1FQY.pdb foi desenvolvido um script para o software RasMol, em que é possível observar a estrutura bioquímica de uma das subunidades da aquaporina-1. Cada subunidade é formada por oito alfa-hélices, representadas por espirais que na figura desenvolvida estão representadas nas cores amarelo matiz, laranja, vermelho, azul matiz, verde matiz, ciano, púrpura e rosa. Estas oito alfa-hélices formam uma estrutura que possui o formato de um canal, por onde as moléculas de água são transportadas. Conclusão: Na análise da estrutura bioquímica da aquaporina-1 foi possível observar que cada subunidade dela é formada por uma proteína do tipo toda alfa, apresentando um total de oito alfa-hélices, as quais formam um canal por onde as moléculas de água são transportadas.
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Xue, Li C., Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, and Vasant Honavar. "Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces." In the 2nd ACM Conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2147805.2147866.
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Dias, André, Mateus Boiani, and Rafael Parpinelli. "Aplicação de Evolução Diferencial em GPU Para o Problema de Predição de Estrutura de Proteínas com Modelo 3D AB Off-Lattice." In XXI Simpósio em Sistemas Computacionais de Alto Desempenho. Sociedade Brasileira de Computação, 2020. http://dx.doi.org/10.5753/wscad.2020.14080.
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A função que uma proteína exerce está diretamente relacionada com a sua estrutura tridimensional. Porém, para a maior parte das proteínas atualmente sequenciadas ainda não se conhece sua forma estrutural nativa. Este artigo propõe a utilização do algoritmo de Evolução Diferencial (DE) desenvolvido na plataforma NVIDIA CUDA aplicado ao modelo 3D AB Off-Lattice para Predição de Estrutura de Proteínas. Uma estratégia de nichos e crowding foi implementada no algoritmo DE combinada com técnicas de autoajuste de parâmetros, rotinas para reinicialização da população, dois níveis de otimização e busca local. Quatro proteínas reais foram utilizadas para experimentação e os resultados obtidos se mostram competitivos com o estado-da-arte. A utilização de paralelismo massivo através da GPU ressalta a aplicabilidade desses recursos a esta classe de problemas atingindo acelerações de 708.78x para a maior cadeia proteica.
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Aversa, Felipe Pires de Campos, RENATO MASSAHARU HASSUNUMA, and PATRÍCIA CARVALHO GARCIA. "USANDO A BIOINFORMÁTICA PARA COMPREENDER A INIBIÇÃO DA PROTEÍNA SNAP-25 PELA TOXINA BOTULÍNICA DO SOROTIPO A." In III Congresso Brasileiro de Ciências Biologicas. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/iii-conbracib/6533.
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Introdução: A neurotoxina botulínica do sorotipo A (BoNT/A) é a mais utilizada atualmente em produtos para uso estético e terapêutico. A ação da BoNT/A decorre da sua ligação de seu domínio de ligação com o receptor (DLR) com proteínas como a proteína associada ao sinaptossoma de 25 kDa (SNAP-25). Desta forma, a paralisia promovida pela BoNT/A ocorre a partir da ligação com a SNAP-25, a qual é essencial para a fusão de vesículas sinápticas. Objetivo: Desenvolver scripts para o software RasMol para produção de imagens que demonstrem a ligação entre a SNAP-25 e o DLR da BoNT/A. Metodologia: O levantamento de arquivos PDB que apresentam a SNAP-25 e o DLR da BoNT/A foi realizado no site Protein Data Bank. A partir do arquivo selecionado foram desenvolvidos scripts para o programa computacional RasMol. Resultados: A partir dos scripts desenvolvidos para o arquivo 1XTG.pdb, foi observado que a extremidade amino-terminal da proteína SNAP-25 interage com o exosítio alfa do DLR. O exosítio alfa é formado por quatro alfa-hélices, formadas pelos resíduos 102-113 (alfa-hélice 1), 310-321 (alfa-hélice 2), 335-348 (alfa-hélice 3) e 351-358 (alfa-hélice 4). A extremidade carboxi-terminal da proteína SNAP-25 apresenta uma fita beta formada pelas 201-203. Esta extremidade se liga ao exosítio beta do DLR, formada por duas fitas betas constituída pelos resíduos 255-259 e 242-246. Assim, a extremidade carboxi-terminal e o exosítio beta formam uma folha beta compostas por três fitas beta. Conclusão: Os scripts produzidos demonstraram que a ligação entre a SNAP-25 e o DLR da BoNT/A decorrem principalmente a partir das extremidades da proteína SNAP-25 com os exosítios alfa e beta do DLR.
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Garcia, Luan Ednelson Soares, Fábio Aparecido Da Silva, Renato Massaharu Hassunuma, and Patrícia Carvalho Garcia. "TELOMERASE: UMA SOLUÇÃO BIOQUÍMICA PARA O ENVELHECIMENTO?" In II Congresso Brasileiro de Bioquímica Humana On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/conbraqui/19.
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Introdução: O processo de envelhecimento está intimamente ligado com o encurtamento dos telômeros, que correspondem à extremidade dos cromossomos. O DNA telomérico apresenta cerca de mil repetições da sequência TTAGGG e é protegido por várias proteínas, chamadas coletivamente de “shelterin” (do inglês shelter, que significa proteger). A telomerase é uma transcriptase reversa composta por ribonucleoproteínas, capaz de adicionar DNA telomérico às extremidades de cromossomos de células eucariontes, prevenindo o envelhecimento precoce. Estudos indicam que a baixa atividade da telomerase está associada ao aumento de risco de desenvolvimento de neoplasias. Objetivos: o objetivo principal da presente pesquisa foi o desenvolvimento de scripts para o software RasMol 2.7.4.2, no intuito de produzir imagens que apresentem a estrutura da telomerase. Material e métodos: Foi realizado o levantamento e a seleção de arquivos PDB sobre a telomerase obtidos no site Protein Data Bank. A partir da análise dos arquivos PDB selecionados e da análise de artigos publicados sobre a estrutura bioquímica da telomerase, foram desenvolvidos vários scripts para o programa computacional RasMol, com o objetivo de demonstrar a estrutura molecular da telomerase. Resultados: Nos scripts desenvolvidos para o arquivo 6D6V.pdb foi observado que a telomerase corresponde a complexo formado por RNA-proteína, sendo que a sequência de RNA da telomerase (TER) é utilizada como molde para a síntese de DNA dos telômeros; enquanto que a proteína é uma transcriptase reversa especializada (TERT). A função enzimática da telomerase depende da interação de várias proteínas associadas à telomerase (TAPs). O script desenvolvido apresenta um segmento de DNA, a TER, a TERT e as TAPs: proteínas 50, 82 e p65 associadas à telomerase (TAP50, TAP82 e P65, respectivamente) e proteínas 2 e 3 de ligação a repetições teloméricas (TEB2 e TEB3). As TAPs participam da fixação do complexo junto ao telômero e da movimentação da telomerase durante a síntese de DNA. Conclusão: Os scripts desenvolvidos mostraram a disposição espacial da TER, TERT, TAPs e DNA. Futuras pesquisas sobre este assunto poderão ser importantes na busca de tratamento e prevenção das doenças relacionadas ao processo de envelhecimento.
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"Regulation of PARP1 activity by its protein partners." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-593.
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Araújo, Maysa Mirelly De Lima, Izaqueu Rodrigues Da Silva, Tonny Cley Campos Leite, Amanda Reges De Sena, and Jaciana Dos Santos Aguiar. "AVALIAÇÃO IN VITRO DA ATIVIDADE ANTIBACTERIANA DE HIDROLISADOS PROTEICOS OBTIDOS DA PROTEÓLISE DA CLARA DO OVO DE GALINHA CAIPIRA." In II Congresso Brasileiro de Biotecnologia On-line. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/conbiotec/52.
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Introdução: Enzimas são biocatalisadores de origem microbiana, vegetal e animal possuindo diversas propriedades que permitem seu uso em diferentes áreas industriais, como alimentícia e farmacêutica. Essas biomoléculas são substâncias favoráveis aos diversos processos, pois possuem propriedades de inocuidade, eficiência e adequação as matérias-primas utilizadas. Entre as diversas classes de biocatalisadores, as hidrolases possuem uma maior aplicação em escala industrial. A hidrólise enzimática controlada para a obtenção de produtos com diferentes graus de hidrólise tem recebido muita atenção por parte da área da saúde e diversos estudos também têm reportado a produção de hidrolisados proteicos e seus peptídeos originados de proteínas do ovo, com maior frequência da clara. Os hidrolisados proteicos são fragmentos específicos de proteínas que apresentam impacto positivo sobre funções fisiológicas. Objetivo: A partir do exposto, o objetivo do presente trabalho foi avaliar a atividade antibacteriana de hidrolisados proteicos obtidos da clara de ovo de galinha caipira. Metodologia: Os hidrolisados foram previamente obtidos por ação de bromelina, parcialmente purificada, extraída de folhas da macambira (Bromelia laciniosa). A atividade antibacteriana, frente às bactérias Gram-negativas (Escherichia coli UFPEDA 234 e Pseudomonas aeruginosa UFPEDA 216), foi realizada segundo a metodologia da microdiluição em caldo segundo o Clinical & Laboratory Standards Institute. Resultado: Todos os hidrolisados apresentaram atividade antimicrobiana contra as bactérias testadas. A concentração Mínima Inibitória contra a P. aeruginosa variou entre 5 a 4000 µg/mL e entre 100 e 4000 µg/mL para E. coli. No entanto, somente o hidrolisado 13 apresentou atividade frente aos dois micro-organismos avaliados, 5 µg/mL contra a P. aeruginosa e 100 µg/mL contra E. coli. Conclusão: A partir do exposto pode-se concluir que os hidrolisados obtidos a partir da clara de ovo de galinha caipira têm potencial antibacteriano, podendo ser indicados para o uso em conservação de alimentos ou produtos farmacêuticos. Ademais, o hidrolisado 13 destacou-se em relação aos demais tanto na CMI quanto na CMB para as duas bactérias avaliadas. Contudo, novos testes são necessários para comprovar a bioatividade dos compostos obtidos bem como realizar ensaios com outros micro-organismos.
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Sônego, Thiago, BRUNA MESQUITA THIAGO, RENATO MASSAHARU HASSUNUMA, and PATRÍCIA CARVALHO GARCIA. "ESTUDO BIOQUÍMICO ESTRUTURAL DA HEMOGLOBINA E HUMANA UTILIZANDO O SOFTWARE RASMOL." In III Congresso Brasileiro de Ciências Biologicas. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/iii-conbracib/8463.
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Introdução: A hemoglobina E foi descoberta em 1954 por Itano, Bergren e Sturgeon. Neste tipo de hemoglobina ocorre uma única mutação, onde a sequência GAG é substituída por AAG nas cadeias beta da molécula, sendo o resíduo de ácido glutâmico da 26ª posição substituído pela lisina. Em relação à prevalência, depois das hemoglobinas A e S, hemoglobina E é a terceira mais frequente no mundo, ocorrendo principalmente na população do sudeste asiático. Em pacientes homozigotos, ocorre anemia microcítica leve com células-alvo evidentes e em heterozigotos é assintomática, com microcitose sem anemia e células-alvo em esfregaço de sangue periférico. Objetivo: A atual pesquisa teve como objetivo principal desenvolver um script para o programa computacional RasMol no intuito de estudar a estrutura bioquímica da hemoglobina E humana, principalmente no que se refere à visualização da região de mutação da proteína. Metodologia: A partir do levantamento de arquivos PDB sobre a hemoglobina E humana, obtidos no site Protein Data Bank, foram desenvolvidos scripts para o software RasMol no intuito de observar a estrutura quaternária da proteína, bem como localizar a região onde ocorre a mutação na molécula. Resultados: A partir do desenvolvimento de um script a partir do arquivo 1NQP.pdb para o programa computacional RasMol, foi gerada uma imagem que mostra a estrutura de uma molécula de hemoglobina E humana, sendo possível observar que a hemoglobina E é formada por duas cadeias alfa e duas cadeias beta. Cada uma das cadeias possui um grupamento heme. Na figura pode ser visualizada a mutação pontual que ocorre nas cadeias beta, onde um resíduo de ácido glutâmico na posição 26 é substituído pela lisina. Conclusão: A partir da análise estrutural da hemoglobina E humana, foi possível desenvolver um script para o programa computacional RasMol que mostra a mutação puntiforme que ocorre nesta proteína.
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Araújo, Maysa Mirelly De Lima, Higor Weverton Dos Santos Silva, Tonny Cley Campos Leite, Amanda Reges De Sena, and Jaciana Dos Santos Aguiar. "AVALIAÇÃO IN VITRO DA ATIVIDADE ANTIOXIDANTE DE HIDROLISADOS PROTEICOS OBTIDOS DA PROTEÓLISE DA CLARA DO OVO DE GALINHA CAIPIRA." In II Congresso Brasileiro de Biotecnologia On-line. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/conbiotec/53.
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Introdução: Proteases são enzimas que catalisam a hidrólise das ligações peptídicas presentes nas proteínas e peptídeos, entre as quais se encontra a Bromelina. A bromelina é uma enzima proteolítica da classe das hidrolases. Vários substratos podem ser utilizados para a obtenção de hidrolisados proteicos, os quais são fragmentos de proteínas, apresentando diferentes atividades biológicas. Objetivo: A partir do exposto, o presente trabalho teve como objetivo avaliar in vitro a atividade antioxidante de hidrolisados proteicos obtidos da clara do ovo de galinha caipira. Metodologia: Os hidrolisados foram previamente obtidos por ação da bromelina extraída de folhas da macambira (Bromelia laciniosa). Após a hidrólise enzimática foi realizado o estudo da atividade antioxidante, a qual foi determinada pela eliminação dos radicais ABTS•+ e DPPH•. Todos os hidrolisados obtidos demonstraram atividade antioxidante nos dois métodos avaliados. Verificou-se que houve uma variação nos valores obtidos demonstrando a importância da otimização de processos. Os hidrolisados proteicos apresentaram atividade antioxidante entre 57,86 e 95,34% para o radical ABTS•+ e entre 13,31 e 23,78% para o radical DPPH•. Verificou-se que a hidrólise enzimática foi eficaz em melhorar as propriedades funcionais dos 17 hidrolisados obtidos da clara do ovo de galinha caipira. Resultados: Obtém-se no presente trabalho sugerem que os hidrolisados proteicos podem ser usados como ingredientes funcionais no desenvolvimento de alimentos saudáveis, em alimentos objetivando diminuir a oxidação lipídica, em produtos nutracêuticos e indústria química. Ademais, Conclusão: conclui-se que a aplicação da bromelina extraída da macambira na obtenção de hidrolisados proteicos pode aumentar o valor agregado e usos deste vegetal encontrado na caatinga, contribuindo desta forma para a melhoria da qualidade de vida do pequeno agricultor.
Reports on the topic "Partner proteins"
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Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.
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Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.
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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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Gafni, Yedidya, and Vitaly Citovsky. Molecular interactions of TYLCV capsid protein during assembly of viral particles. United States Department of Agriculture, April 2007. http://dx.doi.org/10.32747/2007.7587233.bard.
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Tomato yellow leaf curl geminivirus (TYLCV) is a major pathogen of cultivated tomato, causing up to 100% crop loss in many parts of the world. The present proposal, a continuation of a BARD-funded project, expanded our understanding of the molecular mechanisms by which CP molecules, as well as its pre-coat partner V2, interact with each other (CP), with the viral genome, and with cellular proteins during assembly and movement of the infectious virions. Specifically, two major objectives were proposed: I. To study in detail the molecular interactions between CP molecules and between CP and ssDNA leading to assembly of infectious TYLCV virions. II. To study the roles of host cell factors in TYLCV assembly. Our research toward these goals has produced the following major achievements: • Characterization of the CP nuclear shuttling interactor, karyopherin alpha 1, its pattern of expression and the putative involvement of auxin in regulation of its expression. (#1 in our list of publication, Mizrachy, Dabush et al. 2004). • Identify a single amino acid in the capsid protein’s sequence that is critical for normal virus life-cycle. (#2 in our list of publications, Yaakov, Levy et al. in preparation). • Development of monoclonal antibodies with high specificity to the capsid protein of TYLCV. (#3 in our list of publications, Solmensky, Zrachya et al. in press). • Generation of Tomato plants resistant to TYLCV by expressing transgene coding for siRNA targeted at the TYLCV CP. (#4 in our list of publications, Zrachya, Kumar et al. in press). •These research findings provided significant insights into (i) the molecular interactions of TYLCV capsid protein with the host cell nuclear shuttling receptor, and (ii) the mechanism by which TYLCV V2 is involved in the silencing of PTGS and contributes to the virus pathogenicity effect. Furthermore, the obtained knowledge helped us to develop specific strategies to attenuate TYLCV infection, for example, by blocking viral entry into and/or exit out of the host cell nucleus via siRNA as we showed in our publication recently (# 4 in our list of publications). Finally, in addition to the study of TYLCV nuclear import and export, our research contributed to our understanding of general mechanisms for nucleocytoplasmic shuttling of proteins and nucleic acids in plant cells. Also integration for stable transformation of ssDNA mediated by our model pathogen Agrobacterium tumefaciens led to identification of plant specific proteins involved.
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Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7695852.bard.
Full textAbstract:
Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and many more remain to be discovered. The abundance of such proteins is critical and is likely to be determined to a significant extent by their stability, which in turn, is influenced by chloroplast protease activities. The primary goal of this project was to link specific proteases to specific substrates, and in particular, to specific regulatory and assembly proteins. We proposed a two-pronged approach, involving genetic analysis of the consequences of the mutational loss of chloroplast proteases, and biochemical analysis of the degradation pathways of specific proteins that have been shown to control chloroplast gene expression. Our initial bioinformatic analysis of chloroplast proteases allowed us to identify the set of pro teases that is targeted to the chloroplast. We used that information to recover three Arabidopsis mutants with T - DNA insertions in specific chloroplast protease genes. We carried out the first analysis of the stability of a regulator of chloroplast gene expression (CRS2), and found that the protein is much less stable than are typical components of the photosynthetic apparatus. Genetic reagents and analytical methods were developed that have set the stage for a rapid advancement of our understanding of chloroplast proteolysis. The results obtained may be useful for manipulating the expression of transgenes in the chloroplast and for engineering plants whose photosynthetic activity is optimized under harsh environmental conditions.
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Chamovitz, Daniel, and Albrecht Von Arnim. Translational regulation and light signal transduction in plants: the link between eIF3 and the COP9 signalosome. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7696515.bard.
Full textAbstract:
The COP9 signalosome (CSN) is an eight-subunit protein complex that is highly conserved among eukaryotes. Genetic analysis of the signalosome in the plant model species Arabidopsis thaliana has shown that the signalosome is a repressor of light dependent seedling development as mutant Arabidopsis seedlings that lack this complex develop in complete darkness as if exposed to light. These mutant plants die following the seedling stage, even when exposed to light, indicating that the COP9 signalosome also has a central role in the regulation of normal photomorphogenic development. The biochemical mode of action of the signalosome and its position in eukaryotic cell signaling pathways is a matter of controversy and ongoing investigation, and recent results place the CSN at the juncture of kinase signaling pathways and ubiquitin-mediated protein degradation. We have shown that one of the many CSN functions may relate to the regulation of translation through the interaction of the CSN with its related complex, eukaryotic initiation factor (eIF3). While we have established a physical connection between eIF3 subunits and CSN subunits, the physiological and developmental significance of this interaction is still unknown. In an effort to understand the biochemical activity of the signalosome, and its role in regulating translation, we originally proposed to dissect the contribution of "h" subunit of eIF3 (eIF3h) along the following specific aims: (i) Isolation and phenotypic characterization of an Arabidopsis loss-of-function allele for eIF3h from insertional mutagenesis libraries; (ii) Creation of designed gain and loss of function alleles for eIF3h on the basis of its nucleocytoplasmic distribution and its yeast-two-hybrid interactions with other eIF3 and signalosome partner proteins; (iii) Determining the contribution of eIF3h and its interaction with the signalosome by expressing specific mutants of eIF3h in the eIF3h- loss-of function background. During the course of the research, these goals were modified to include examining the genetic interaction between csn and eif3h mutations. More importantly, we extended our effort toward the genetic analysis of mutations in the eIF3e subunit, which also interacts with the CSN. Through the course of this research program we have made several critical scientific discoveries, all concerned with the apparent diametrically opposed roles of eIF3h and eIF3e. We showed that: 1) While eIF3e is essential for growth and development, eIF3h is not essential for growth or basal translation; 2) While eIF3e has a negative role in translational regulation, eIF3h is positively required for efficient translation of transcripts with complex 5' UTR sequences; 3) Over-accumulation of eIF3e and loss-of-function of eIF3h both lead to cop phenotypes in dark-grown seedlings. These results were published in one publication (Kim et al., Plant Cell 2004) and in a second manuscript currently in revision for Embo J. Are results have led to a paradigm shift in translation research – eIF3 is now viewed in all systems as a dynamic entity that contains regulatory subuits that affect translational efficiency. In the long-term agronomic outlook, the proposed research has implications that may be far reaching. Many important plant processes, including developmental and physiological responses to light, abiotic stress, photosynthate, and hormones operate in part by modulating protein translation [23, 24, 40, 75]. Translational regulation is slowly coming of age as a mechanism for regulating foreign gene expression in plants, beginning with translational enhancers [84, 85] and more recently, coordinating the expression of multiple transgenes using internal ribosome entry sites. Our contribution to understanding the molecular mode of action of a protein complex as fundamental as eIF3 is likely to lead to advances that will be applicable in the foreseeable future.
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Sengupta-Gopalan, Champa, Shmuel Galili, and Rachel Amir. Improving Methionine Content in Transgenic Forage Legumes. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7580671.bard.
Full textAbstract:
Leguminous forage crops are high in proteins but deficient in S- amino acids. It has been shown that both wool quality and milk production can be limited by the post-ruminal supply of sulfur-containing amino acids. Efforts to use conventional plant breeding and cell selection techniques to increase the S-amino acid content of alfalfa have met with little success. With the objective to increase the S-amino acid content of forage legumes, the goal of this project was to co- express the methionine rich zein genes from corn along with a gene for a key enzyme in methionine biosynthesis, aspartate kinase(AK). The zeins are seed storage proteins from corn and are groupec into four distinct classes based on their amino acid sequence homologies. The b-zein (15kd) and the 6zein (10kD and 18kD) have proportionately high levels of methionine (10%, 22% and 28%, respectively). Initial studies from our lab had shown that while the 15kD zein accumulated to high levels in vegetative tissues of transgenic tobacco the l0kD zein did not. However, co-expression of the 10kD zein with the 15kD zein genes in tobacco showed stabilization of the 10kD zein and the co-localization of the 10kD and 15kD zein proteins in unique ER derived protein bodies. AK is the key enzyme for producing carbon skeletons for all amino acids of the aspartate family including methionine. It is, however, regulated by end-product feedback inhibition. The specific objectives of this proposal were: i. to co-express the 15kD zein with the 10/18kD zein genes in alfalfa in order to enhance the level of accumulation of the 10/18kD zein; ii. to increase methionine pools by expressing a feedback insensitive AK gene in transformants co-expressing the 15kD and 10/18kD zein genes. The Israeli partners were successful in expressing the AK gene in alfalfa which resulted in an increase in free and bound threonine but not in methionine (Galili et al., 2000). Since our target was to increase methionine pools, we changed our second objective to replace the AK gene with the gene for cystathionine gamma synthase (CGS) in the co-expression studies. The first methionine specific reaction is catalyzed by CGS. An additional objective was to develop a transformation system for Berseem clover, and to introduce the appropriate gene constructs into it with the goal of improving their methionine content. Genes for the 15kD zein along with the genes for either the 10kD or 18kD zein have been introduced into the same alfalfa plant both by sexual crosses and by re-transformation. Analysis of these zein co-expressors have shown that both the IOkD and 18kD zein levels go up 5 to 10 fold when co-expressed with the 15kD zein (Bagga et al., MS in preparation). Incubation of the leaves of transgenic alfalfa co-expressing the 15kD and 10kD zein genes, in the rumen of cows have shown that the zein proteins are stable in the rumen. To increase the level of zein accumulation in transgenic alfalfa different promoters have been used to drive the zein genes in alfalfa and we have concluded that the CaMV 35S promoter is superior to the other strong leaf -specific promoters. By feeding callus tissue of alfalfa plants co-expressing the 15kD and 10kD zein genes with methionine and its precursors, we have shown that the zein levels could be significantly enhanced by increasing the methionine pools. We have now introduced the CGS gene (from Arabidopsis; kindly provided to us by Dr. Leustek), into the 15kD zein transformants and experiments are in progress to check if the expression of the CGS gene indeed increases the level of zein accumulation in alfalfa. We were not successful in developing a transformation protocol for Berseem clover.
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Morrison, Mark, Joshuah Miron, Edward A. Bayer, and Raphael Lamed. Molecular Analysis of Cellulosome Organization in Ruminococcus Albus and Fibrobacter Intestinalis for Optimization of Fiber Digestibility in Ruminants. United States Department of Agriculture, March 2004. http://dx.doi.org/10.32747/2004.7586475.bard.
Full textAbstract:
Improving plant cell wall (fiber) degradation remains one of the highest priority research goals for all ruminant enterprises dependent on forages, hay, silage, or other fibrous byproducts as energy sources, because it governs the provision of energy-yielding nutrients to the host animal. Although the predominant species of microbes responsible for ruminal fiber degradation are culturable, the enzymology and genetics underpinning the process are poorly defined. In that context, there were two broad objectives for this proposal. The first objective was to identify the key cellulosomal components in Ruminococcus albus and to characterize their structural features as well as regulation of their expression, in response to polysaccharides and (or) P AA/PPA. The second objective was to evaluate the similarities in the structure and architecture of cellulosomal components between R. albus and other ruminal and non-ruminal cellulolytic bacteria. The cooperation among the investigators resulted in the identification of two glycoside hydrolases rate-limiting to cellulose degradation by Ruminococcus albus (Cel48A and CeI9B) and our demonstration that these enzymes possess a novel modular architecture specific to this bacterium (Devillard et al. 2004). We have now shown that the novel X-domains in Cel48A and Cel9B represent a new type of carbohydrate binding module, and the enzymes are not part of a ceiluiosome-like complex (CBM37, Xu et al. 2004). Both Cel48A and Cel9B are conditionally expressed in response to P AA/PPA, explaining why cellulose degradation in this bacterium is affected by the availability of these compounds, but additional studies have shown for the first time that neither PAA nor PPA influence xylan degradation by R. albus (Reveneau et al. 2003). Additionally, the R. albus genome sequencing project, led by the PI. Morrison, has supported our identification of many dockerin containing proteins. However, the identification of gene(s) encoding a scaffoldin has been more elusive, and recombinant proteins encoding candidate cohesin modules are now being used in Israel to verify the existence of dockerin-cohesin interactions and cellulosome production by R. albus. The Israeli partners have also conducted virtually all of the studies specific to the second Objective of the proposal. Comparative blotting studies have been conducted using specific antibodies prepare against purified recombinant cohesins and X-domains, derived from cellulosomal scaffoldins of R. flavefaciens 17, a Clostridium thermocellum mutant-preabsorbed antibody preparation, or against CbpC (fimbrial protein) of R. albus 8. The data also suggest that additional cellulolytic bacteria including Fibrobacter succinogenes S85, F. intestinalis DR7 and Butyrivibrio fibrisolvens Dl may also employ cellulosomal modules similar to those of R. flavefaciens 17. Collectively, our work during the grant period has shown that R. albus and other ruminal bacteria employ several novel mechanisms for their adhesion to plant surfaces, and produce both cellulosomal and non-cellulosomal forms of glycoside hydrolases underpinning plant fiber degradation. These improvements in our mechanistic understanding of bacterial adhesion and enzyme regulation now offers the potential to: i) optimize ruminal and hindgut conditions by dietary additives to maximize fiber degradation (e.g. by the addition of select enzymes or PAA/PPA); ii) identify plant-borne influences on adhesion and fiber-degradation, which might be overcome (or improved) by conventional breeding or transgenic plant technologies and; iii) engineer or select microbes with improved adhesion capabilities, cellulosome assembly and fiber degradation. The potential benefits associated with this research proposal are likely to be realized in the medium term (5-10 years).
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Bar-Joseph, Moshe, William O. Dawson, and Munir Mawassi. Role of Defective RNAs in Citrus Tristeza Virus Diseases. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575279.bard.
Full textAbstract:
This program focused on citrus tristeza virus (CTV), the largest and one of the most complex RNA-plant-viruses. The economic importance of this virus to the US and Israeli citrus industries, its uniqueness among RNA viruses and the possibility to tame the virus and eventually turn it into a useful tool for the protection and genetic improvement of citrus trees justify these continued efforts. Although the overall goal of this project was to study the role(s) of CTV associated defective (d)-RNAs in CTV-induced diseases, considerable research efforts had to be devoted to the engineering of the helper virus which provides the machinery to allow dRNA replication. Considerable progress was made through three main lines of complementary studies. For the first time, the generation of an engineered CTV genetic system that is capable of infecting citrus plants with in vitro modified virus was achieved. Considering that this RNA virus consists of a 20 kb genome, much larger than any other previously developed similar genetic system, completing this goal was an extremely difficult task that was accomplished by the effective collaboration and complementarity of both partners. Other full-length genomic CTV isolates were sequenced and populations examined, resulting in a new level of understanding of population complexities and dynamics in the US and Israel. In addition, this project has now considerably advanced our understanding and ability to manipulate dRNAs, a new class of genetic elements of closteroviruses, which were first found in the Israeli VT isolate and later shown to be omnipresent in CTV populations. We have characterized additional natural dRNAs and have shown that production of subgenomic mRNAs can be involved in the generation of dRNAs. We have molecularly cloned natural dRNAs and directly inoculated citrus plants with 35S-cDNA constructs and have shown that specific dRNAs are correlated with specific disease symptoms. Systems to examine dRNA replication in protoplasts were developed and the requirements for dRNA replication were defined. Several artificial dRNAs that replicate efficiently with a helper virus were created from infectious full-genomic cDNAs. Elements that allow the specific replication of dRNAs by heterologous helper viruses also were defined. The T36-derived dRNAs were replicated efficiently by a range of different wild CTV isolates and hybrid dRNAs with heterologous termini are efficiently replicated with T36 as helper. In addition we found: 1) All CTV genes except of the p6 gene product from the conserved signature block of the Closteroviridae are obligate for assembly, infectivity, and serial protoplast passage; 2) The p20 protein is a major component of the amorphous inclusion bodies of infected cells; and 3) Novel 5'-Co-terminal RNAs in CTV infected cells were characterized. These results have considerably advanced our basic understanding of the molecular biology of CTV and CTV-dRNAs and form the platform for the future manipulation of this complicated virus. As a result of these developments, the way is now open to turn constructs of this viral plant pathogen into new tools for protecting citrus against severe CTV terms and development of virus-based expression vectors for other citrus improvement needs. In conclusion, this research program has accomplished two main interconnected missions, the collection of basic information on the molecular and biological characteristics of the virus and its associated dRNAs toward development of management strategies against severe diseases caused by the virus and building of novel research tools to improve citrus varieties. Reaching these goals will allow us to advance this project to a new phase of turning the virus from a pathogen to an ally.