Browsing by Subject "mutagenesis"
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Item Functional genomics of the unicellular cyanobacterium Synechococcus elongatus PCC 7942(2009-05-15) Chen, YouUnicellular freshwater cyanobacterium Synechococcus elongatus PCC 7942 is the model organism for studying the circadian clock in cyanobacteria. Despite tremendous work over the last decade in identification of clock-related loci and elucidation of molecular mechanisms of the central oscillator, many details of the basic steps in generating circadian rhythms of biological processes remain unsolved and many components are still missing. A transposon-mediated mutagenesis and sequencing strategy has been adopted to disrupt essentially every locus in the genome so as to identify all of the loci that are involved in clock function. The complete genome sequence has been determined by a combination of shotgun sequences and transposon-mediated sequences. The S. elongatus PCC 7942 genome is 2,695,903 bp in length, and has a 55.5% GC content. Automated annotation identified 2,856 protein-coding genes and 51 RNA coding loci. A system for community refinement of the annotation was established. Organization and characteristic features of the genome are discussed in this dissertation. More than 95% of the PCC 7942 genome has been mutagenized and mutants affected in approximately 30% of loci have been screened for defects in circadian function. Approximately 70 new clock loci that belong to different functional categories have been discovered through a team effort. Additionally, functional analysis of insertion mutants revealed that the Type-IV pilus assembly protein PilN and the RNA chaperon Hfq are involved in transformation competence of S. elongatus cells. Functional analysis of an atypical short period kaiA insertional mutant showed that the short period phenotype is caused mainly by the truncation of KaiA by three amino acid residues. The interaction between KaiC and the truncated KaiA is weakened as shown by fluorescence anisotropy analysis. Deletion analysis of pANL, the large endogenous plasmid, implies that two toxin-antitoxin cassettes were responsible for inability to cure cells of this plasmid. In summary, the results indicate that this functional genomics project is very promising toward fulfilling our goal to assemble a comprehensive view of the cyanobacterial circadian clock. The mutagenesis reagents and dataset generated in this project will also benefit the greater scientific community.Item Molecular characterization of cation-coupled transporters: the H+-coupled Mg2+-citrate transporter, CitM, and the Na+/sulfate cotransporter, hNaSi-1(2003-01-28) Hongyan Li; Ana M. Pajor; Steven C. King; Steven A. Weinman; Luis Reuss; Joel P. GallagherIn this dissertation, two cation-coupled transporters were characterized at the molecular level. The CitM transporter from Bacillus subtilis was functionally expressed and characterized in E.coli cells. The human NaSi-1 transporter (hNaSi-1) and mutants were functionally expressed in Xenopus oocytes. Antibodies against hNaSi-1 were used to investigate tissue distribution and N-glycosylation. The roles of two conserved serine residues in the transport function of hNaSi-1 were investigated using site-directed mutagenesis and radiotracer assay. \r\n\r\n CitM belongs to a distinct gene family of secondary active transporters that includes the homologous citrate transporter CitH. In this dissertation, the Km of CitM for the complex of Mg2+-citrate was about 300 mM in the presence of saturating Mg2+ concentrations. CitM has a high substrate specificity for citrate. Other tested di- and tricarboxylic acids did not significantly inhibit citrate uptakes in the presence of Mg2+. However, CitM accepts complexes of citrate with metal ions other than Mg2+. The transport was inhibited in more alkaline but not in acidic transport buffer and also inhibited by ionophores that affect the transmembrane proton gradient, including FCCP, TCC and nigericin, suggesting a proton-coupled transport. Valinomycin did not affect the uptake by CitM, supporting an electroneutral transport model in which one proton is coupled to the uptake of one complex of (Mg2+-citrate)1-. \r\n\r\nThe low affinity Na+/sulfate cotransporter, hNaSi-1, belongs to a specific gene family of Na+-coupled transporters that includes the high affinity hSUT-1 and the Na+-coupled dicarboxylate (NaDC) transporters. Antibodies directed against a peptide of hNaSi-1 recognized the native protein in renal membranes as well as the recombinant protein expressed in Xenopus oocytes. There is a single N-glycosylation site, Asn-591, located at the extracellular C-terminus in hNaSi-1. Site-directed mutagenesis studies of Ser-260, Ser-288 and the surrounding amino acid residues of hNaSi-1 suggested that these residues are functionally required for hNaSi-1. MTSET inhibition on sulfate uptakes by the four mutants surrounding Ser-260, T257C, T259C, T261C and L263C, was dependent on the cation and substrate used. Since the presence of sodium and sulfate triggers conformational changes during the transport cycle of hNaSi-1, the cation and substrate dependence of MTSET inhibition suggest that these four substituted cysteines move during the transport cycle. Since the four mutated residues are located in TMD-5, this transmembrane domain is also likely to participate in the conformational movement during the transport cycle of hNaSi-1. \r\n