The bacterial ribosome is essential to cell growth yet little is known about how its proteins attain their mature structures. Recent studies indicate that certain Staphlyococcus aureus bacteriophage protein sequences contain specific sites that may be cleaved by a non-bacteriophage enzyme (Poliakov et al. 2008). The phage cleavage site was found to bear sequence similarity to the N-terminus of S. aureus ribosomal protein L27. Previous studies in E. coli (Wower et al.1998; Maguire et al. 2005) found that L27 is situated adjacent to the ribosomal peptidyl transferase site, where it likely aids in new peptide formation. The predicted S. aureus L27 protein contains an additional N-terminal sequence not observed within the N-terminus of the otherwise similar E. coli L27; this sequence appears to be cleaved, indicating yet-unobserved ribosomal protein post-translational processing and use of host processes by phage. Phylogenetic analysis shows that L27 processing has the potential to be highly conserved. Further study of this phenomenon may aid antibiotic development.

Cheng, Tat Cheung. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 181-188). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Leung Tak Yuen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 57-63). / Abstracts in English and Chinese. / Acknowledgments --- p.i / Abstract --- p.ii / Abbreviations --- p.iii / Abbreviations of amino acids --- p.iv / Abbreviations of nucleotides --- p.iv / Naming system for TRP mutants --- p.v / Chapter Chapter 1 --- I ntroduction / Chapter 1.1 --- Hyperthermophile and hyperthermophilic proteins --- p.1 / Chapter 1.2 --- Hyperthermophilic proteina are highly similar to their mesophilic homologues --- p.2 / Chapter 1.3 --- Hyperthermophilic proteins and free energy of stabilization --- p.3 / Chapter 1.4 --- Mechanisms of protein stabilization --- p.4 / Chapter 1.5 --- The difference in protein stability between mesophilic protein and hyperthermophilic protein --- p.4 / Chapter 1.6 --- Ribosomal protein L30e from T. celer can be used as a model system to study thermostability --- p.9 / Chapter 1.7 --- Protein engineering of TRP --- p.10 / Chapter 1.8 --- Purpose of the present study --- p.12 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- Bacterial strains --- p.13 / Chapter 2.2 --- Plasmids --- p.13 / Chapter 2.3 --- Bacterial culture media and solutions --- p.13 / Chapter 2.4 --- Antibiotic solutions --- p.13 / Chapter 2.5 --- Restriction endonucleases and other enzymes --- p.14 / Chapter 2.6 --- M9ZB medium --- p.14 / Chapter 2.7 --- SDS-PAGE --- p.14 / Chapter 2.8 --- Alkaline phosphatase buffer --- p.15 / Chapter 2.9 --- DNA agarose gel --- p.15 / Chapter 2.10 --- "Gel loading buffer, DNA" --- p.16 / Chapter 2.11 --- "Ethidium bromide (EtBr), lOmg/ml" --- p.16 / Chapter 2.12 --- Constructing mutant TRP genes --- p.16 / Chapter 2.12.1 --- Polymerase Chain Reaction (PCR) --- p.17 / Chapter 2.12.2 --- Gel electrophoresis --- p.19 / Chapter 2.12.3 --- DNA purification from agarose gel --- p.19 / Chapter 2.12.4 --- "Construction of R39A, R39M, K46A, K46M, E47A, E50A, R54A, R54M" --- p.19 / Chapter 2.12.5 --- "Construction of double mutant R39A/E62A, R39M/E62A" --- p.20 / Chapter 2.13 --- Sub-cloning --- p.21 / Chapter 2.13.1 --- Restriction digestion --- p.22 / Chapter 2.13.2 --- Ligation vector with mutant TRP gene insert --- p.22 / Chapter 2.13.3 --- Amplifying vector carrying mutant TRP gene insert --- p.22 / Chapter 2.13.4 --- Mini-preparation of DNA --- p.22 / Chapter 2.13.5 --- Preparations of competent cells --- p.23 / Chapter 2.13.6 --- Transformation of Escherichia coli --- p.24 / Chapter 2.13.7 --- Screening tests --- p.25 / Chapter 2.14 --- Over expression of mutant TRP --- p.26 / Chapter 2.14.1 --- Transformation --- p.26 / Chapter 2.14.2 --- Expression --- p.26 / Chapter 2.14.3 --- Cell harvesting --- p.27 / Chapter 2.14.4 --- Expression checking --- p.27 / Chapter 2.14.5 --- SDS-PAGE --- p.27 / Chapter 2.14.6 --- Staining the acrylamide gel --- p.28 / Chapter 2.15 --- Purification of mutant TRP protein --- p.28 / Chapter 2.15.1 --- Cells lysis --- p.28 / Chapter 2.15.2 --- Chromatography --- p.29 / Chapter 2.15.3 --- Concentrating TRP as protein stock --- p.31 / Chapter 2.16 --- Protein stability --- p.32 / Chapter 2.16.1 --- Chemical stability --- p.33 / Chapter 2.16.2 --- Thermal stability --- p.34 / Chapter Chapter 3 --- Results / Chapter 3.1 --- Construction of mutant TRP genes --- p.36 / Chapter 3.1.1 --- PCR mutagenesis --- p.36 / Chapter 3.1.2 --- Sub-cloning of mutant TRP gene to express vector pET8c --- p.37 / Chapter 3.2 --- Expression and purification of mutant TRP --- p.38 / Chapter 3.3 --- Protein stability --- p.39 / Chapter 3.3.1 --- Free energy of unfolding --- p.39 / Chapter 3.3.2 --- Thermal stability --- p.43 / Chapter Chapter 4 --- Discussion / Chapter 4.1 --- "Effect of R39, K46, E62, E64" --- p.47 / Chapter 4.2 --- Double mutation at R39 and E62 --- p.50 / Chapter 4.3 --- Effect of R54 --- p.51 / Chapter 4.4 --- Effect of E47 and E50 --- p.53 / Chapter 4.5 --- Conclusion --- p.54 / References --- p.57 / Appendix --- p.64

by Patrick, Tik-wan Law. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 144-155). / Acknowledgements --- p.i / Contents --- p.ii / Abstract --- p.vi / Abbreviations --- p.viii / List of figures --- p.ix / List of tables --- p.xiv / Chapter Chapter One: --- Introduction --- p.1-17 / Chapter 1.1 --- General introduction --- p.1 / Chapter 1.2 --- The Human genome project --- p.2 / Chapter 1.3 --- The EST approach --- p.3 / Chapter 1.4 --- Significance of the EST approach --- p.3 / Chapter 1.5 --- Human heart cDNA sequencing --- p.5 / Chapter 1.6 --- Significance of the human adult heart EST project --- p.7 / Chapter 1.7 --- Ribosomal proteins --- p.8 / Chapter 1.7.1 --- The ribosomal constituents --- p.8 / Chapter 1.7.2 --- Eukaiyotic ribosomal proteins --- p.10 / Chapter 1.8 --- Mammalian ribosomal proteins --- p.11 / Chapter 1.8.1 --- Evolution of mammalian ribosomal proteins --- p.11 / Chapter 1.8.2 --- Significance of mammalian ribosomal proteins --- p.12 / Chapter 1.9 --- Possible functional roles of ribosomal protein --- p.14 / Chapter 1.10 --- Nomenclature of ribosomal proteins --- p.16 / Chapter 1.11 --- The theme of the thesis --- p.17 / Chapter Chapter Two: --- Materials and Methods --- p.18-49 / Chapter 2.1 --- Cycle sequencing --- p.18 / Chapter 2.1.1 --- Plating out the cDNA library --- p.18 / Chapter 2.1.2 --- Amplification of the cDNA clones by PCR --- p.19 / Chapter 2.1.3 --- Purification and quantitation of the PCR product --- p.20 / Chapter 2.1.4 --- Cycle DNA sequencing --- p.20 / Chapter 2.2 --- Cloning of hrpL29 in pUC 18 cloning vector --- p.21 / Chapter 2.2.1 --- Amplification of the phage by plate lysate --- p.21 / Chapter 2.2.2 --- Amplification of the insert by PCR --- p.22 / Chapter 2.3 --- Screening for hrpL29 transformant --- p.22 / Chapter 2.3.1 --- Mini-preparation of plasmid DNA (Sambrook et al，1989) --- p.22 / Chapter 2.3.2 --- Large scale preparation of plasmid DNA --- p.24 / Chapter 2.4 --- Primer design for cloning of an intron of hrpL29 --- p.26 / Chapter 2.5 --- Isolation of the intron of hrpL29 by PCR --- p.26 / Chapter 2.6 --- Restricted endonuclease digestion --- p.27 / Chapter 2.7 --- Purification of DNA from the agarose gel --- p.27 / Chapter 2.8 --- Dephosphorylation of linearized plasmid DNA --- p.29 / Chapter 2.9 --- DNA ligation --- p.29 / Chapter 2.10 --- "Preparation of competent bacterial cells for transformation (Hanahan,1985)" --- p.30 / Chapter 2.11 --- Plasmid DNA Transformation --- p.31 / Chapter 2.12 --- Unicycle DNA sequencing by T7 polymerase (Pharmacia) --- p.32 / Chapter 2.13 --- Synthesis of radiolabelled DNA probe --- p.33 / Chapter 2.14 --- "Oligonucleotide synthesis, deprotection and purification" --- p.34 / Chapter 2.14.1 --- Oligonucleotide synthesis --- p.34 / Chapter 2.14.2 --- Deprotection and purification of oligonucleotides --- p.35 / Chapter 2.15 --- Southern analysis --- p.36 / Chapter 2.15.1 --- "Isolation of genomic DNA from leukocytes (Ciulla et al,1988)" --- p.36 / Chapter 2.15.2 --- Restricted digestion and fractionation of genomic DNA --- p.37 / Chapter 2.15.3 --- Southern transfer of DNA onto a membrane support --- p.37 / Chapter 2.15.4 --- Prehybridization of the Southern blot --- p.40 / Chapter 2.15.5 --- Hybridization of the Southern blot --- p.40 / Chapter 2.16 --- Northern analysis --- p.41 / Chapter 2.16.1 --- "Isolation of total RNA by using the AGPC-RNA method (Chomczynski and Sacchi,1987, modified)" --- p.41 / Chapter 2.16.2 --- Separation of total RNA by electrophoresis and transfer onto a membrane support --- p.43 / Chapter 2.16.3 --- Prehybridization of the Northern blot --- p.46 / Chapter 2.16.4 --- Hybridization of the Northern blot --- p.47 / Chapter 2.17 --- First strand cDNA synthesis (Pharmacia) --- p.48 / Chapter 2.18 --- PCR of the first strand cDNA --- p.48 / Chapter Chapter Three: --- Results --- p.50-113 / Chapter 3.1 --- Partial sequencing of adult human heart cDNA clones --- p.50 / Chapter 3.2 --- DNA homology searching by using the program BLASTN --- p.52 / Chapter 3.2.1 --- Catalogue of the 502 ESTs of the cardiovascular system --- p.54 / Chapter 3.2.2 --- Classification and frequency of the human adult heart cDNA clones --- p.63 / Chapter 3.3 --- Submission of the cDNA sequences to NCBI --- p.64 / Chapter 3.4 --- Pattern of gene expression in the human adult cardiovascular system --- p.66 / Chapter 3.5 --- "Sequence determination of hrpL29 (Law et. al., 1996)" --- p.72 / Chapter 3.5.1 --- Cycle Taq sequencing of hrpL29 --- p.72 / Chapter 3.5.2 --- Subcloning of the hrpL29 cDNA insert into the pUC18 DNA cloning vector --- p.75 / Chapter 3.5.3 --- Unicycle T7 sequencing of hrpL29 --- p.77 / Chapter 3.6 --- Sequence alignment and comparison of hrpL29 with other known sequences in the databases --- p.79 / Chapter 3.7 --- The primary structure of hrpL29 --- p.83 / Chapter 3.8 --- Results of RT-PCR and PCR --- p.88 / Chapter 3.9 --- Genomic analysis of hrpL29 --- p.92 / Chapter 3.9.1 --- Isolation of the first intron of hrpL29 --- p.92 / Chapter 3.9.2 --- Southern analysis of hrpL29 --- p.97 / Chapter 3.10 --- Northern analysis of hrpL29 --- p.103 / Chapter 3.10.1 --- Tissue distribution of hrpL29 mRNA in rat tissues --- p.103 / Chapter 3.10.2 --- Time course of hRPL29 expression in mouse heart --- p.106 / Chapter 3.10.3 --- Time course of hRPL29 expression in mouse brain --- p.110 / Chapter Chapter Four: --- Discussion --- p.114-139 / Chapter 4.1 --- Characterization of the ESTs --- p.114 / Chapter 4.2 --- Significance of the heart EST project --- p.116 / Chapter 4.3 --- Redundancy of the EST sequencing --- p.118 / Chapter 4.4 --- The importance of frequent database searching --- p.119 / Chapter 4.5 --- The importance of an efficient comparison algorithm --- p.120 / Chapter 4.6 --- Human ribosomal protein L29 (hRPL29) --- p.122 / Chapter 4.7 --- Internal duplication in hRPL29 --- p.124 / Chapter 4.8 --- Primary structure analysis of hRPL29 --- p.126 / Chapter 4.9 --- RT-PCR and PCR of the first strand cDNA with primers using the C095-ATG and dT primer --- p.128 / Chapter 4.10 --- Southern analysis of hrpL29 --- p.128 / Chapter 4.11 --- Northern analysis of hrpL29 --- p.133 / Chapter 4.11.1 --- Tissue distribution of the mRNA species of hrpL29 --- p.133 / Chapter 4.11.2 --- Time course of hRPL29 expression in mouse heart and brain --- p.134 / Chapter 4.12 --- Possible functional role of hRPL29 --- p.135 / Chapter 4.13 --- Further aspects --- p.137 / Appendix --- p.140-143 / References --- p.144-155

Ribosomal proteins (RPs), synthesized in the cytoplasm, need to be transported from the cytoplasm to the nucleolus (a nuclear compartment), where a single molecule of each RP assembles with rRNAs to form the large and small ribosomal subunits. The objectives of this research were to identify nuclear/nucleolar localization signals (NLSs/NoLSs; generally basic motifs) that mediate the transport of Arabidopsis RPL23aA, RPL15A and RPS8A into the nucleus and nucleolus, and to study transcriptional regulation and subcellular localization of RPs. While all previous research has shown that nucleolar localization of proteins is mediated by specific basic motifs, in this study, I showed that a specific number of basic motifs mediated nucleolar localization of RPL23aA, rather than any specific motifs. In this protein, single mutations of any of its eight putative NLSs (pNLSs) had no effect on nucleolar localization, however, the simultaneous mutation of all eight completely disrupted nucleolar localization, but had no effect on nuclear localization. Furthermore, mutation of any four of these pNLSs had no effect on localization, while mutation of more than four increasingly disrupted nucleolar localization, suggesting that any combination of four of the eight pNLSs is able to mediate nucleolar localization. These results support a charge-based system for the nucleolar localization of RPL23aA. While none of the eight pNLSs of RPL23aA were required for nuclear localization, in RPS8A and RPL15A, of the 10 pNLSs in each, the N-terminal two and three NLSs, respectively, were absolutely required for nuclear/nucleolar localization. Considering the presence of only a single molecule of each RP in any given ribosome, which obligates the presence of each RP in the nucleolus in equal quantities, I studied transcriptional regulation of Arabidopsis RP genes and the subcellular localization of five RP families to determine the extent of coordinated regulation of these processes. Variation of up to 300-fold was observed in the expression levels of RP genes. However, this variation was drastically reduced when the expression level was considered at the RP gene family level, indicating that coordinate regulation of expression of RP genes, coding for individual RP isoforms, is more stringent at the family level. Subcellular localization also showed differential targeting of RPs to the cytoplasm, nucleus and nucleolus, together with a significant difference in the nucleolar import rates of RPS8A and RPL15A. Although one could expect coordinated regulation of the processes preceding ribosomal subunit assembly in the nucleolus, my results suggest differential regulation of these processes.

Ribosomes which conduct protein synthesis in all living organisms are comprised of two subunits. The large 60S ribosomal subunit catalyzes peptidyl transferase reactions and includes the polypeptide exit tunnel, while the small (40S) ribosomal subunit recruits incoming messenger RNAs (mRNAs) and performs proofreading. The plant 80S cytoplasmic ribosome is composed of 4 ribosomal RNAs (rRNAs: 25-28S, 5.8S and 5S in the large subunit and 18S in the small subunit) and 81 ribosomal proteins (r-proteins: 48 in the large subunit, 33 in the small subunit). RPS15a, a putative small subunit primary binder, is encoded by a six member gene family (RPS15aA-F), where RPS15aB and RPS15aE are evolutionarily distinct and thought to be incorporated into mitochondrial ribosomes. In vitro synthesized cytoplasmic 18S rRNA, 18S rRNA loop fragments, and RPS15a mRNA molecules were combined in electrophoretic shift assays (EMSAs) to determine the RNA binding characteristics of RPS15aA/-D/-E/-F. RPS15aA/F, -D and -E bind to cytoplasmic 18S rRNA in the absence of cellular components. However, RPS15aE r-protein tested that binds mitochondrial 18S rRNA. In addition, RPS15aA/F only binds one of three 18S rRNA loop fragments of helix 23 whereas RPS15aD/-E bind all three 18S rRNA helix 23 loop fragments. Additionally, RPS15aD and RPS15aE did not bind their respective mRNA transcripts, likely indicating that this form of negative feedback is not a post-transcriptional control mechanism for this r-protein gene family. Furthermore, the addition of RPS15a transcripts to the EMSAs did not affect the binding of RPS15aA/F, -D and -E to 18S rRNA helix 23 loop 4-6, indicating that rRNA binding is specific. Supershift EMSAs further confirmed the specificity of RPS15aA/F and RPS15aE binding to loop fragment (4-6) of 18S rRNA. Taken together, these data support a role for RPS15a in early ribosome small subunit assembly.

Ribosomes which conduct protein synthesis in all living organisms are comprised of two subunits. The large 60S ribosomal subunit catalyzes peptidyl transferase reactions and includes the polypeptide exit tunnel, while the small (40S) ribosomal subunit recruits incoming messenger RNAs (mRNAs) and performs proofreading. The plant 80S cytoplasmic ribosome is composed of 4 ribosomal RNAs (rRNAs: 25-28S, 5.8S and 5S in the large subunit and 18S in the small subunit) and 81 ribosomal proteins (r-proteins: 48 in the large subunit, 33 in the small subunit). RPS15a, a putative small subunit primary binder, is encoded by a six member gene family (RPS15aA-F), where RPS15aB and RPS15aE are evolutionarily distinct and thought to be incorporated into mitochondrial ribosomes. In vitro synthesized cytoplasmic 18S rRNA, 18S rRNA loop fragments, and RPS15a mRNA molecules were combined in electrophoretic shift assays (EMSAs) to determine the RNA binding characteristics of RPS15aA/-D/-E/-F. RPS15aA/F, -D and -E bind to cytoplasmic 18S rRNA in the absence of cellular components. However, RPS15aE r-protein tested that binds mitochondrial 18S rRNA. In addition, RPS15aA/F only binds one of three 18S rRNA loop fragments of helix 23 whereas RPS15aD/-E bind all three 18S rRNA helix 23 loop fragments. Additionally, RPS15aD and RPS15aE did not bind their respective mRNA transcripts, likely indicating that this form of negative feedback is not a post-transcriptional control mechanism for this r-protein gene family. Furthermore, the addition of RPS15a transcripts to the EMSAs did not affect the binding of RPS15aA/F, -D and -E to 18S rRNA helix 23 loop 4-6, indicating that rRNA binding is specific. Supershift EMSAs further confirmed the specificity of RPS15aA/F and RPS15aE binding to loop fragment (4-6) of 18S rRNA. Taken together, these data support a role for RPS15a in early ribosome small subunit assembly.

Ribosomal proteins (RPs), synthesized in the cytoplasm, need to be transported from the cytoplasm to the nucleolus (a nuclear compartment), where a single molecule of each RP assembles with rRNAs to form the large and small ribosomal subunits. The objectives of this research were to identify nuclear/nucleolar localization signals (NLSs/NoLSs; generally basic motifs) that mediate the transport of Arabidopsis RPL23aA, RPL15A and RPS8A into the nucleus and nucleolus, and to study transcriptional regulation and subcellular localization of RPs. While all previous research has shown that nucleolar localization of proteins is mediated by specific basic motifs, in this study, I showed that a specific number of basic motifs mediated nucleolar localization of RPL23aA, rather than any specific motifs. In this protein, single mutations of any of its eight putative NLSs (pNLSs) had no effect on nucleolar localization, however, the simultaneous mutation of all eight completely disrupted nucleolar localization, but had no effect on nuclear localization. Furthermore, mutation of any four of these pNLSs had no effect on localization, while mutation of more than four increasingly disrupted nucleolar localization, suggesting that any combination of four of the eight pNLSs is able to mediate nucleolar localization. These results support a charge-based system for the nucleolar localization of RPL23aA. While none of the eight pNLSs of RPL23aA were required for nuclear localization, in RPS8A and RPL15A, of the 10 pNLSs in each, the N-terminal two and three NLSs, respectively, were absolutely required for nuclear/nucleolar localization. Considering the presence of only a single molecule of each RP in any given ribosome, which obligates the presence of each RP in the nucleolus in equal quantities, I studied transcriptional regulation of Arabidopsis RP genes and the subcellular localization of five RP families to determine the extent of coordinated regulation of these processes. Variation of up to 300-fold was observed in the expression levels of RP genes. However, this variation was drastically reduced when the expression level was considered at the RP gene family level, indicating that coordinate regulation of expression of RP genes, coding for individual RP isoforms, is more stringent at the family level. Subcellular localization also showed differential targeting of RPs to the cytoplasm, nucleus and nucleolus, together with a significant difference in the nucleolar import rates of RPS8A and RPL15A. Although one could expect coordinated regulation of the processes preceding ribosomal subunit assembly in the nucleolus, my results suggest differential regulation of these processes.

No description available.

Ribosomes, large enzymatic complexes containing an RNA catalytic core, drive protein synthesis in all living organisms. 80S cytoplasmic eukaryotic ribosomes are comprised of four rRNAs and approximately 80 ribosomal proteins (r-proteins). R-proteins are encoded by gene families with large families (average of twelve members) predominating in mammals and smaller families (two to seven members) in plants. Increased ribosome heterogeneity is possible in plant ribosomes due to multiple transcriptionally active members in each family, whereas, in mammalian r-protein gene families, only one member is typically active. Multiple functional paralogs provide for greater plasticity in response to environmental/developmental cues, as well as, increasing the possibility of individual paralogs procuring or retaining extraribosomal functions. This research investigated the effects of r-protein mutations on plant growth and development. Through RNA interference (RNAi) mediated knockdown (KD) of type I (cytoplasmic: RPS15aA/D and F) and type II (non-cytosolic: RPS15aB and E) RPS15a family members I was able to confirm the delineation between the two types. Subcellular localization of the type I isoforms was nuclear/nucleolar while localization of type II isoforms was non-mitochondrial and probably cytosolic. Illumina sequencing of two r-protein mutant transcriptomes, pfl1 (rps18a) and pfl2 (rps13a), identified a novel set of up and down regulated genes, previously unknown or linked to r-protein mutants. The 20 genes identified were classified into four groups (1) plant defense, (2) transposable elements, (3) nitrogen metabolism and (4) genes with unknown function. Illumina miRNOME analysis revealed no changes in the miRNA profile of pfl1 and pfl2 plants. These data do not support the previously proposed theory that a disruption in ribosome biogenesis (by decreased r-protein synthesis) disrupts miRNA-mediated degradation of a range of auxin response genes. Finally, a novel double r-protein mutant, rps18a:HF/RPL18B, presented a late flowering/thickened bolt phenotype not seen in a rps13a:HF/RPL18B mutant, suggesting that RPS18A has an extraribosomal role in plant growth and development in Arabidopsis.