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DNA Polymerases of Low-GC Gram-Positive Eubacteria: Identification of the Replication-Specific Enzyme Encoded by dnaE. Marjorie H. Barnes, 2002.dnaE, the gene encoding one of the two replication-specific DNA polymerases (Pols) of low-GC-content gram-positive bacteria (E . Dervyn et al., Science 294:1716-1719, 2001; R . Inoue et al., Mol . Genet . Genomics 266:564-571, 2001), was cloned from Bacillus subtilis, a model low-GC gram-positive organism . The gene was overexpressed in Escherichia coli . The purified recombinant product displayed inhibitor responses and physical, catalytic, and antigenic properties indistinguishable from those of the low-GC gram-positive-organism-specific enzyme previously named DNA Pol II after the polB-encoded DNA Pol II of E . coli . Whereas a polB-like gene is absent from low-GC gram-positive genomes and whereas the low-GC gram-positive DNA Pol II strongly conserves a dnaE-like, Pol III primary structure, it is proposed that it be renamed DNA polymerase III E (Pol III E) to accurately reflect its replicative function and its origin from dnaE . It is also proposed that DNA Pol III, the other replication-specific Pol of low-GC gram-positive organisms, be renamed DNA polymerase III C (Pol III C) to denote its origin from polC . By this revised nomenclature, the DNA Pols that are expressed constitutively in low-GC gram-positive bacteria would include DNA Pol I, the dispensable repair enzyme encoded by polA, and the two essential, replication-specific enzymes Pol III C and Pol III E, encoded, respectively, by polC and dnaE . Functional Dissection of the Bacillus subtilis pur Operator Site. Aloke Kumar Bera, 2003.Bacillus subtilis PurR represses transcription of several genes involved in purine synthesis, metabolism, and transport and cofactor synthesis . PurR binds specifically to DNAs containing an inverted repeat of a 14-nucleotide "PurBox" located in the upstream control regions of genes in the PurR regulon . Further biochemical investigation of the interaction of PurR with a series of shortened upstream DNA fragments of the pur operon determined the minimum length and specificity elements of the operator . The relative affinities of the two PurBoxes differ significantly, such that upstream PurBox1 (-81 to -68 relative to the transcription start site) is designated "strong" and downstream PurBox2 (-49 to -36) is designated "weak." Two PurBoxes are required for high-affinity PurR binding, and one of these must be strong . The shortest DNA construct with high affinity for PurR is a 74-bp perfect palindrome in which weak PurBox2 and its flanking sequences are replaced by strong PurBox1 and flanking sequences . Two PurR dimers bind to this symmetric construct . Phosphoribosylpyrophosphate (PRPP), the effector molecule that reduces affinity of PurR for DNA, requires one weak PurBox in the DNA construct to inhibit PurR binding . PRPP binds, as expected, to a PRPP-motif in PurR . A tracks outside the central conserved CGAA sequence of the PurBox may facilitate DNA bending, leading to a proposal for strong and weak designations of PurBoxes in the control regions of other genes regulated by PurR . Dynamics of Microbial Communities on Marine Snow Aggregates: Colonization, Growth, Detachment, and Grazing Mortality of Attached Bacteria. Thomas Kiørboe, 2003.We studied the dynamics of microbial communities attached to model aggregates (4-mm-diameter agar spheres) and the component processes of colonization, detachment, growth, and grazing mortality . Agar spheres incubated in raw seawater were rapidly colonized by bacteria, followed by flagellates and ciliates . Colonization can be described as a diffusion process, and encounter volume rates were estimated at about 0.01 and 0.1 cm3 h-1 for bacteria and flagellates, respectively . After initial colonization, the abundances of flagellates and ciliates remained approximately constant at 103 to 104 and  102 cells sphere-1, respectively, whereas bacterial populations increased at a declining rate to >107 cells sphere-1 . Attached microorganisms initially detached at high specific rates of
10-2 min-1, but the bacteria gradually became irreversibly attached to the spheres . Bacterial growth (0 to 2 day-1) was density dependent and declined hyperbolically when cell density exceeded a threshold . Bacterivorous flagellates grazed on the sphere surface at an average saturated rate of 15 bacteria flagellate-1 h-1 . At low bacterial densities, the flagellate surface clearance rate was
5 x 10-7 cm2 min-1, but it declined hyperbolically with increasing bacterial density . Using the experimentally estimated process rates and integrating the component processes in a simple model reproduces the main features of the observed microbial population dynamics . Differences between observed and predicted population dynamics suggest, however, that other factors, e.g., antagonistic interactions between bacteria, are of importance in shaping marine snow microbial communities .
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