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Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs. Xiang-Qin Liu, 2004.The ThyX class of thymidylate synthases was previously characterized by a common ThyX motif, RHRX7S . We report bacterial ThyX sequences having distinctive ThyX motifs, suggesting a more general ThyX motif, R/THRX7-8S . One ThyX sequence has an intein in its ThyX motif that was shown to do protein splicing and a group II intron in its gene, suggesting a hot spot for these self-splicing mobile elements. P2 Growth Restriction on an rpoC Mutant Is Suppressed by Alleles of the Rz1 Homolog lysC. Dmitry Markov, 2004.Escherichia coli strain 397c carries a temperature-sensitive mutation, rpoC397, that removes the last 50 amino acids of the RNA polymerase ß' subunit and is nonpermissive for plating of bacteriophage P2 . P2 gor mutants productively infect 397c and define a new gene, lysC, encoded by a reading frame that extensively overlaps the P2 lysis accessory gene, lysB . The unusual location of lysC with respect to lysB is reminiscent of the Rz/Rz1 lysis gene pair of phage  .
Indeed, coexpression of lysB and lysC complemented the
growth defect of
Rz/Rz1 null mutants, indicating that the LysB/C pair is
similar to Rz/Rz1 in both gene arrangement and function . Cells
carrying the rpoC397 mutation exhibited an early onset of
P2-induced lysis, which was suppressed by the gor mutation in
lysC . We propose that changes in host gene expression
resulting from the rpoC397 mutation result in changes in the
composition of the bacterial cell wall, making the cell more
susceptible to P2-mediated lysis and preventing accumulation of
progeny phage sufficient for plaque formation .
Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms. Yutaka Uyeno, 2004.A rapid and simple approach to the small-subunit (SSU) rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems has been developed . The method employs sequence-specific cleavage of rRNA molecules with oligonucleotides and RNase H . Defined mixtures of SSU rRNAs were mixed with an oligonucleotide (referred to as a "scissor probe") that was specifically designed to hybridize with a particular site of targeted rRNA and were subsequently digested with RNase H to proceed to sequence-dependent rRNA scission at the hybridization site . Under appropriate reaction conditions, the targeted rRNAs were correctly cut into two fragments, whereas nontargeted rRNAs remained intact under the same conditions . The specificity of the cleavage could be properly adjusted by controlling the hybridization stringency between the rRNA and the oligonucleotides, i.e., by controlling either the temperature of the reaction or the formamide concentration in the hybridization-digestion buffer used for the reaction . This enabled the reliable discrimination of completely matched rRNA sequences from single-base mismatched sequences . For the detection of targeted rRNAs, the resulting RNA fragment patterns were analyzed by gel electrophoresis with nucleotide-staining fluorescent dyes in order to separate cleaved and intact rRNA molecules . The relative abundance of the targeted SSU rRNA fragments in the total SSU rRNA could easily be calculated without the use of an external standard by determining the signal intensity of individual SSU rRNA bands in the electropherogram . This approach provides a fast and easy means of identification, detection, and quantification of a particular group of microbes in clinical and environmental specimens based on rRNA . ZipA Is Required for Recruitment of FtsK, FtsQ, FtsL, and FtsN to the Septal Ring in Escherichia coli. Cynthia A. Hale, 2002.
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