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Experimental and Theoretical Bases of Specific Affinity, a Cytoarchitecture-Based Formulation of Nutrient Collection Proposed To Supercede the Michaelis-Menten Paradigm of Microbial Kinetics. D. K. Button, 2004.A theory for solute uptake by whole cells was derived with a focus on the ability of oligobacteria to sequester nutrients . It provided a general relationship that was used to obtain the kinetic constants for in situ marine populations in the presence of naturally occurring substrates . In situ affinities of 0.9 to 400 liters g of cells–1 h–1 found were up to 103 times smaller than those from a "Marinobacter arcticus " isolate, but springtime values were greatly increased by warming . Affinities of the isolate for usual polar substrates but not for hydrocarbons were diminished by ionophores . A kinetic curve or Monod plot was constructed from the best available data for cytoarchitectural components of the isolate by using the theory together with concepts and calculations from first principles . The order of effect of these components on specific affinity was membrane potential > cytoplasmic enzyme concentration > cytoplasmic enzyme affinity > permease concentration > area of the permease site > translation coefficient > porin concentration . Component balance was influential as well; a small increase in cytoplasmic enzyme concentration gave a large increase in the effect of permease concentration . The effect of permease concentration on specific affinity was large, while the effect on Km was small . These results are in contrast to the Michaelis-Menten theory as applied by Monod that has uptake kinetics dependent on the quality of the permease molecules, with Km as an independent measure of affinity . Calculations demonstrated that most oligobacteria in the environment must use multiple substrates simultaneously to attain sufficient energy and material for growth, a requirement consistent with communities largely comprising few species . R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements. Dietmar Böltner, 2002.The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements . Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair . While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139 . Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements . A total of 96 open reading frames were identified; of these, 30 could not be assigned a function . Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27 . A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified . Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously . Novel Group I Intron in the tRNALeu(UAA) Gene of a  -Proteobacterium Isolated from a Deep Subsurface Environment.Alexey A. Vepritskiy, 2002.A group I intron has been found to interrupt the anticodon loop of the tRNALeu(UAA) gene in a bacterium belonging to the -subdivision of Proteobacteria and isolated from a deep subsurface environment . The subsurface isolate SMCC D0715 was identified as belonging to the genus Pseudomonas . The group I intron from this isolate is the first to be reported for
-proteobacteria, and the first instance of a tRNALeu(UAA) group I intron to be found in a group of bacteria other than cyanobacteria . The 231-nucleotide (nt) intron's sequence has group I conserved elements and folds into a bona fide group I secondary structure with canonical base-paired segments P1 to P9 and a paired region, P10 . The D0715 intron possesses the 11-nt motif CCUACG .. . UAUGG in its P8 region, a feature not common in bacterial introns . To date, phylogenetic analysis has shown that bacterial introns form two distinct families, and their complex distribution suggests that both lateral transfer and common ancestry have taken part in the evolutionary history of these elements .
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