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Phosphorylation/dephosphorylation is likely the most crucial chemical reaction taking place in all living organisms. It is the basis for the regulatory control of many diverse biological events triggered by extracellular effectors. Moreover, it is a ubiquitous element of intracellular signal transduction pathways that regulates a wide range of processes. While protein phosphorylation has been extensively characterized in eukaryotes, far less is known about its emerging counterparts in prokaryotes. This study involved determination of the crystal structures and functional characterization of two protein kinases, YihE and AceK (also a protein phosphatase), and two nucleotide pyrophosphatases, YjjX and YhdE. X-ray crystallographic structure determination combined with bioinformatics analyses, mutageneses and biochemical experiments, both in vitro and in vivo, were utilized for the functional characterization of each protein. YihE was found to be a previously unknown kinase component of a new type of bacterial phospho-relay mechanism, thus adding kinase activity as another response to the Cpx sensing system that functions to maintain cellular homeostasis. AceK, which possesses both kinase and phosphatase activities, modifies isocitrate dehydrogenase (ICDH) to regulate the flux of isocitrate into the glyoxylate cycle. The structures of Acek alone and in complex with its substrate, ICDH, provided us with information to explain the mechanisms underlying its bifunctionality and its molecular switch. Through structural comparison and, particularly, functional characterization, we revealed that YjjX is a novel ITPase/XTPase responsible for the removal of non-canonical nucleotides from the cell during oxidative stress in Escherichia coli. YhdE, identified as a novel dTTPase, was observed to retard cell growth and form a filamentous phenotype when overexpressed in the cell, suggesting that YhdE is involved in the control of cell growth and division by regulating the cell nucleotide pool for DNA synthesis. In summary, this research has made a substantial ii contribution to the investigation of bacterial phosphorylation and dephophorylation systems that respond to various environmental conditions. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2009-05-29 11:41:41.832

Transcription initiation is an important step in the process of gene regulation in prokaryotes. Promoters are stretches of DNA sequence that are present in the upstream region of transcription start sites (TSSs), where RNA polymerase and other transcription factors bind to initiate transcription. Recent advancement in sequencing technologies has resulted in huge amount of raw data in the form of whole genome sequences. This sequence data has to be annotated, in order to identify coding, non-coding and regulatory regions. Computational tools are useful for a quick and fairly reliable annotation of many genome sequences. Promoter prediction is an important step in genome annotation process which is needed, not only for the validation of predicted genes, but also for the identification of novel genes, especially those coding for non-coding RNA, which are missed by gene prediction programs. DNA sequence dependent structural properties such as DNA duplex stability, bendability and intrinsic curvature have been found to be associated with promoter regions in all domains of life. The work presented in this thesis focuses on the analysis of these structural features in the promoter regions of published prokaryotic transcriptome data. Furthermore, promoters were predicted using these structural features and their role in gene expression were studied. The organization of thesis is as follows. An overview of transcription machinery of prokaryotes, promoter architecture, available promoter prediction programs and sequence dependent structural features is presented in chapter 1. Chapter 2 describes the datasets and methods used in entire study. Structural features of promoters associated with primary and operon TSSs of H.pylori26695 genes and their orthologs (chapter 3) Promoter regions in genomic sequences from all domains of life show similar trends in their structural properties such as stability, bendability, curvature. This chapter dis-cuss the DNA duplex stability and bendability of various classes of promoter regions (based on the identification of different classes of transcription start sites, viz. primary, secondary, internal, operon TSSs etc, in transcriptome study) of Helicobacter pylori 26695 strain. It is found that the primary TSS and operon associated TSS promoters show significantly strong structural features in their promoter regions. DNA free energy based promoter prediction tool PromPredict has been used to annotate promoters of different classes and very high recall values (80%) are obtained for primary TSS. Orthologous genes from 10 different strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision values. DNA duplex stability of promoter region is conserved in the orthologous genes in 10 different strains of Helicobacter pylori genome. Sequence dependent structural features of promoters in prokaryotic transcriptome (chapter 4) Next-generation sequencing studies have revealed that a wide range of transcripts such as primary, internal, antisense and non-coding RNA, are present in the prokaryotic transcriptome and a large fraction of them are functionally involved in various regulatory activities. Identification of promoters associated with different transcripts is important for characterization of transcriptome. The current chapter discusses DNA sequence dependent structural properties like stability, bendability and curvature in the promoter region of six different prokaryotic transcriptomes (Helicobacter pylori, Anabaena, Synechocystis, Escherichia coli, Salmonella and Klebsiella). Using these structural features, promoters associated with different category of transcripts were predicted, which constitute an integral part of the transcriptome. Promoter annotation using structural features is fairly accurate and reliable as compared to motif-based approach since different category of transcripts show poor sequence conservation in the promoter region. Most importantly, it is universal in nature unlike sequence-based approach that is generally organism specific. Role of sequence dependent structural properties in gene expression in prokaryotes (chapter 5) DNA duplex stability, bendability and intrinsic curvature play crucial roles in the process of transcription initiation. Hence, in order to understand the relationship be-tween these structural features and gene expression, the relative differences in stability, bendability and curvature in the promoter regions of high and low expressed genes were studied. It is found that these features are relatively accentuated in the promoter regions associated with high gene expression as compared to low gene expression. Promoter regions associated with high gene expression are annotated more reliably using DNA structural features, compared to those for low gene expression. Sequence dependent structural properties in the promoter region of essential and non-essential genes of the prokaryotes (chapter 6) Essential genes are the minimal possible set of genes required for the survival of organism. These sets of genes can be identified by experiments such as single gene deletion and transposon mediated inactivation. Here, the analysis of DNA duplex stability and bendability in the promoter regions of essential and nonessential genes of prokaryotes is reported. It is found that the average free energy and bendability pro-files are distinct in the promoters regions of essential and nonessential genes. Whole genome promoter predictions using in-house program, PromPredict, for essential and nonessential genes has also been carried out. Chapter 7 present the summary and conclusion of the entire thesis work followed by future perspectives in the field. Optimization of PromPredict algorithm and updating PromBase with newly sequenced genomes (Appendix A) PromPredict is an in-house program, which is based on the relative stability of the DNA in flanking regions. It was found to perform well in predicting promoters across all organisms. In previous studies, it was observed that for organisms having low genomic GC content (<35%), promoter prediction resulted in low precision values, which indicates higher false positive rate. Threshold values of PromPredict algorithm were re-vised in order to optimize the algorithm with low false positive rate. PromBase is a comparative genomics database of microbial genomes. It stores different genomic and structural properties of the microbial genomes. It also displays the predictions obtained from PromPredict in a graphical as well as tabular format. Newly sequenced genomes were downloaded from NCBI and processed using in-house programs and added to the mysql database (back end of the PromBase). Stability profiles for predictions were also added for the RNA coding genes, earlier only profiles for protein coding genes were displayed. Comparative genomics of asymmetric gene orientation in prokaryotes (Appendix B) Transcription proceeds in 5’ to 3’ direction on the template strand, hence it provides directionality. Prokaryotic genomes show asymmetry in gene orientation on leading and lagging strands. The different phyla of prokaryotes were analyzed in terms of asymmetry in gene orientation. It is found that organisms belonging to a particular phyla known as “Firmicutes”, show high asymmetry in gene orientation, which are known to have different DNA polymerase systems for replication.

Reporter gene technology has facilitated greatly the analysis of gene expression and the study of individual promoters and their regulation. Although various reporter gene systems are available, none of them are universally applicable and consequently, studies aimed at screening of new reporters are continuing. Toward this end, an acid phosphatase, designated SapS, was identified and characterized from the culture supernatant of a Staphylococcus aureus strain isolated from vegetables. Biochemical characterization of the 30-kDa monomeric enzyme indicated that it displayed optimum activity at 40°C and pH 5, using p-nitrophenyl phosphate (pNPP) as substrate. The enzymatic activity was enhanced by Mg2+, but was inhibited by EDTA and molybdate. Based on its properties and amino acid sequence analyses, SapS was classified as a new member of the bacterial class C family of non-specific acid phosphatases. The S. aureus SapS enzyme was subsequently evaluated as a reporter for host strain evaluation and cell surface display. Bacillus halodurans of which the major cell wall protease gene (wprA) was inactivated was used as expression host, and the cell wall-binding domain of the cwlC gene from B. halodurans was used as an anchoring motif for cell surface display. The results from in vitro enzyme activity assays indicated that extracellular production of the SapS reporter enzyme was improved 3.5-fold in the mutant compared to wild-type B. halodurans strain. Zymographic detection of SapS activity showed that the SapS-CwlC fusion protein was localized in the B. halodurans cell wall fraction, thus demonstrating the potential of SapS as a reporter for cell surface display of heterologous proteins. The versatility of the SapS enzyme as a reporter for gene expression and protein secretion in both Gram-positive and Gram-negative bacteria was also investigated. Transcriptional and translational fusions of the sapS gene with selected heterologous promoters and signal sequences were constructed, and expressed in Escherichia coli, B. subtilis and B. halodurans. The strongest promoter for heterologous protein production in each of the host strains was identified, i.e. the E. coli lacZ promoter in E. coli, the B. halodurans alkaline protease promoter in B. subtilis, and the B. halodurans σD promoter in B. halodurans. / Thesis (PhD)--University of Pretoria, 2010. / Microbiology and Plant Pathology / unrestricted

In eukaryotic cells, some mRNAs localize to distinct areas of the cell where RNA is translated and the encoded protein is specifically localized. Recent studies have suggested that even though prokaryotic cells lack internal compartmentalization, different RNAs can localize to distinct regions of the bacterial cell. Our lab is developing methods for labeling and detecting RNA with the goal of determining localization of endogenous RNAs within single cells. We currently employ an eIF4a protein-specific aptamer for RNA labeling using one of two methods. (1) Target RNA is tagged with the aptamer sequence at the 3' end and the aptamer triggers protein complementation of two fusion proteins, each containing split EGFP and split eIF4A proteins. (2) Two RNA probes, each containing a half of a split eIF4a-specific aptamer and an antisense sequence complementary to the target RNA, bind the unmodified transcript through complementary interactions. This binding brings the two fragments of the split aptamer in close proximity and allows proper folding of a split aptamer. A fluorescent signal is generated by the aptamer-driven reassociation of the fusion proteins. In this work, we investigate the sensitivity of the first method for detecting transcripts expressed from their natural chromosomal loci, and describe attempts to increase the sensitivity of the method by using multiple aptamer tagging. We also present results suggesting that the second method, combining protein complementation and split aptamer approach, provides high sensitivity enabling detection of endogenous bacterial RNAs expressed at low level.

The process of decoding is the most crucial determinant of the quality of protein synthesis. Ribosomal protein L9 was first implicated in decoding fidelity when a mutant version of L9 was found to increase the translation of a T4 phage gene. Later studies confirmed that the absence of L9 leads to increased translational bypassing, frameshifting, and stop codon readthrough. L9 is part of the large subunit of the prokaryotic ribosome and is located more than 90 Å from the site of decoding, making it difficult to envision how it might affect decoding and reading frame maintenance. Twenty years after the identification of L9's putative function, there is no mechanism for how a remotely located L9 improves translation fidelity. This mystery makes our picture of translation incomplete. Despite the high conservation of L9 in eubacteria, E.coli lacking L9 does not exhibit any obvious growth defects. Thus, the evolutionary advantage conferred by L9 in bacteria is masked under laboratory conditions. In order to uncover unique L9-dependent conditions, a library of E. coli mutants was screened to isolate those that rely on L9 for fitness. Interestingly, factors found to be synergistic with L9 had no known role in fidelity. Six independent mutants were isolated, each exhibiting a severe growth defect that is partially suppressed in the presence of L9. One class of L9-dependent mutations was present in an essential ribosome biogenesis factor, Der. Der's established function is in the maturation of the large ribosomal subunit. The identified mutations severely impaired the GTPase activity of Der. Interestingly, L9 did not directly compensate for the defective GTPase activity of mutant Der. The second class of L9-dependent mutations was present in EpmA and EpmB, factors required to post-translationally modify elongation factor, EF-P. EF-P's established function is in the translation of poly-proline containing proteins. EF-P deficient cells were nearly inviable in the absence of L9; however, L9 did not directly influence poly-proline translation. Therefore, in each case, L9 improved cell health without altering the activity of either Der or EF-P. Remarkably, the der mutants required only the N domain of L9, whereas the absence of active EF-P required full-length, wild-type L9 for growth complementation. Thus, each mutant class needed a different aspect of L9's unique architecture. In cells lacking either active EF-P or Der, there was a severe deficiency of 70S ribosomes and the indication of small subunit maturation defects, both of which worsened upon L9 depletion. These results strongly suggest that L9 plays a role in improving ribosome quality and abundance under certain conditions. Overall, the genetic screen lead to the discovery that bacteria need L9 when either of two important translation factors (Der or EF-P) is inactivated. This work has characterized the physiological requirement for L9 in each case and offers a new insight into L9's assigned role in translation fidelity.