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You searched for subject:(r protein S4). Showing records 1 – 2 of 2 total matches.

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University of Illinois – Urbana-Champaign

1. Chen, Ke. Evolution and assembly of the ribosome.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

The ribosome is a large macromolecular assembly responsible for protein synthesis in all living cells. A typical bacterial ribosome consists of three ribosomal RNA (rRNA) molecules and approximately fifty ribosomal proteins (r-proteins), which are arranged into two subunits of unequal size and distinct function. The large subunit promotes formation of the peptide bond, and the small subunit enforces the recognition between the mRNA codons and the tRNA anticodons. With the availability of the ribosome crystal structure, it becomes clear that the two major functions, peptide bond formation and decoding, are performed within an entire RNA environment devoid of proteins. Combining with the fact that the majority of the ribosomal components are conserved across all three domains of life, it is believed that the ribosome has its origin deep in the RNA world before the last universal common ancestor (LUCA). Further evolutionary studies lead to the hypothesis that the evolution of the ribosome begins with a prototype ribozyme that catalyzes peptidyl-transferase reaction. Structural and sequence analysis suggests that the small ribozyme capable of catalyzing formation of short peptides may still exist in the core of the modern ribosome. Accordingly, a proto-ribosome model is constructed computationally using RNA fragments near the peptidyl-transferase center (PTC), and is proven to be stable throughout the micro-second molecular dynamics (MD) simulations. The model is capable of incorporating freely diffusing substrates spontaneously into its binding site, and holds them in both pockets long enough to reach a transition intermediate favorable for peptide bond formation. This in silico designed proto-ribosome is then subjected to experimental investigations to test its ability to assemble and bind potential substrates in solution. The successful design of the proto-ribosome presents a possible scenario for the initial development of the early translation apparatus. The proto-ribosome coupled with the probable parallel evolution of ancient tRNAs might have driven the emergence of the oldest coded protein shortly afterwards. The universally conserved r-protein S4 is likely an ancient protein due to its role in the initiation of the 30S assembly, control of the translational accuracy, and regulation of the conserved operon. However, the N-terminal domain of S4 is identified as a “molecular signature” that distinguishes between Bacteria and Archaea, and hence might be a newer addition to the protein. The presence of both an old and a new component in the same protein makes it an extremely interesting case to study for the ribosomal evolution. Therefore, we perform phylogenetic analysis of S4 in relation to a broad sharing of zinc/non-zinc binding sequence in the N-terminal domain of the protein, and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution. The complex history presented for “core” protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects… Advisors/Committee Members: Luthey-Schulten, Zaida A. (advisor), Martin Gruebele (Committee Chair), Luthey-Schulten, Zaida A. (committee member), Ha, Taekjip (committee member), Schulten, Klaus J. (committee member).

Subjects/Keywords: the RNA world; last universal common ancestor (LUCA); ribosomal evolution; ribosomal signature; ribosomal assembly; ribosomal RNA (rRNA); r-proteins; r-protein S4; RNA folding; protein binding; ligand binding; fly-casting mechanism; single-molecule Förster resonance energy transfer (smFRET); selective 20-hydroxyl acylation analyzed by primer extension (SHAPE); footprinting; molecular dynamics simulation; structure-based Go potential; micro-second simulation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Chen, K. (2014). Evolution and assembly of the ribosome. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46886

Chicago Manual of Style (16th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed January 25, 2020. http://hdl.handle.net/2142/46886.

MLA Handbook (7th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Web. 25 Jan 2020.

Vancouver:

Chen K. Evolution and assembly of the ribosome. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2020 Jan 25]. Available from: http://hdl.handle.net/2142/46886.

Council of Science Editors:

Chen K. Evolution and assembly of the ribosome. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46886


Queensland University of Technology

2. Tsao, Theresa Tsun-Hui. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.

Degree: 2008, Queensland University of Technology

Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising strategies to control BBTV. Pathogen-derived resistance (PDR) strategies have been applied successfully to generate plants that are resistant to numerous different viruses, primarily against those viruses with RNA genomes. BBTV is a circular, single-stranded (css) DNA virus of the family Nanoviridae, which is closely related to the family Geminiviridae. Although there are some successful examples of PDR against geminiviruses, PDR against the nanoviruses has not been reported. Therefore, the aim of this thesis was to investigate the potential of BBTV genes to interfere with virus replication when used as transgenes for engineering banana plants resistance to BBTV. The replication initiation protein (Rep) of nanoviruses is the only viral protein essential for viral replication and represents an ideal target for PDR. Therefore, this thesis focused on the effect of wild-type or mutated Rep genes from BBTV satellite DNAs or the BBTV integral genome on the replication of BBTV in banana embryogenic cell suspensions. A new Rep-encoding satellite DNA, designated BBTV DNA-S4, was isolated from a Vietnamese BBTV isolate and characterised. When the effect of DNA-S4 on the replication of BBTV was examined, it was found that DNA-S4 enhanced the replication of BBTV. When the replicative capabilities of DNA-S4 and the previously characterised Rep-encoding BBTV satellite, DNA-S1, were compared, it was found that the amount of DNA-S4 accumulated to higher levels than DNA-S1. The interaction between BBTV and DNA-S1 was also examined. It was found that over-expression of the Rep encoded by DNA-S1 using ubi1 maize polyubiquitin promoter enhanced replication of BBTV. However, when the Rep-encoded by DNA-S1 was expressed by the native S1 promoter (in plasmid pBT1.1-S1), it suppressed the replication of BBTV. Based on this result, the use of DNA-S1 as a possible transgene to generate PDR against BBTV was investigated. The roles of the Rep-encoding and U5 genes of BBTV DNA-R, and the effects of over-expression of these two genes on BBTV replication were also investigated. Three mutants of BBTV DNA-R were constructed; plasmid pUbi-RepOnly-nos contained the ubi1 promoter driving Rep expression from DNA-R, plasmid pUbi-IntOnly-nos contained the ubi1 promoter driving expression of the DNA-R internal gene product (U5), while plasmid pUbi-R.ORF-nos contained the ubi1 promoter driving the expression of both Rep and the internal U5 gene product. The replication of BBTV was found to be significantly suppressed by pUbi-RepOnly-nos, weakly suppressed by pUbi-IntOnly-nos, but strongly enhanced by pUbi-R.ORF-nos. The effect of mutations in three conserved residues within the BBTV Rep on BBTV replication was also assessed. These mutations were all made in the regions in the ATPase motifs and resulted in changes from hydrophilic to hydrophobic residues (i.e. K187→M, D224→I and N268→L). None of…

Subjects/Keywords: banana bunchy top virus; nanoviruses; replication initiation protein (Rep); pathogen-derived resistance; BBTV DNA-R; BBTV DNA-S1; BBTV DNA-S3; BBTV DNA-S4; satellite DNA; ATPase; post-transcriptional gene silencing; RNA silencing suppressor

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Tsao, T. T. (2008). Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Thesis, Queensland University of Technology. Accessed January 25, 2020. https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Web. 25 Jan 2020.

Vancouver:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Internet] [Thesis]. Queensland University of Technology; 2008. [cited 2020 Jan 25]. Available from: https://eprints.qut.edu.au/17031/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Thesis]. Queensland University of Technology; 2008. Available from: https://eprints.qut.edu.au/17031/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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