Applications of whole-cell bacterial sensors in biotechnology and environmental science

Biosensors have major advantages over chemical or physical analyses with regard to specificity, sensitivity, and portability. Recently, many types of whole-cell bacterial biosensors have been developed using recombinant DNA technology. The bacteria are genetically engineered to respond to the presence of chemicals or physiological stresses by synthesizing a reporter protein, such as luciferase, β-galactosidase, or green fluorescent protein. In addition to an overview of conventional biosensors, this minireview discusses a novel type of biosensor using a photosynthetic bacterium as the sensor strain and the crtA gene, which is responsible for carotenoid synthesis, as the reporter. Since bacteria possess a wide variety of stress-response mechanisms, including antioxidation, heat-shock responses, nutrient-starvation, and membrane-damage responses, DNA response elements for several stress-response proteins can be fused with various reporter genes to construct a versatile set of bacterial biosensors for a variety of analytes. Portable biosensors for on-site monitoring have been developed using a freeze-dried biosensing strain, and cell array biosensors have been designed for high-throughput analysis. Moreover, in the future, the use of single-cell biosensors will permit detailed analyses of samples. Signals from such sensors could be detected with digital imaging, epifluorescence microscopy, and/or flow cytometry.     

Applications of the Saccharomyces cerevisiae Flp-FRT system in bacterial genetics

The Flp-FRT site-specific recombination system from Saccharomyces cerevisiae is a powerful and efficient tool for high-throughput genetic analysis of bacteria in the postgenomic era. This review highlights the features of the Flp-FRT system, describes current bacterial genetic methods incorporating this technology and, finally, suggests potential future uses of this system. In combination with improved allele replacement methods, recyclable FRT mutagenesis cassettes, whose antibiotic resistance markers can be excised from the chromosome in vivo, are useful for the rapid construction of multiple, unmarked mutations in the same chromosome, and thus aid in the generation of live vaccine strains or food-safe bacteria. The high-specificity of the Flp-FRT system makes it also applicable for manipulation of whole genomes, including in vivo cloning of large genomic segments. Integration-proficient vectors, from which antibiotic resistance markers and replication functions can be evicted after integration of the desired sequences into the chromosome, are useful for the construction of strains destined for environmental release, e.g. strains used as biosensors or for bioremediation. Although the Flp-FRT system is extremely efficient and easy to use, its true potential in bacterial genetics has not yet been fully exploited. On the contrary, in many instances this technology is probably greatly underutilized, especially in gram-positive bacteria.     

Applications of oxidoreductases.

Oxidoreductases comprise the large class of enzymes that catalyze biological oxidation/reduction reactions. Because many chemical and biochemical transformations involve oxidation/reduction processes, developing practical biocatalytic applications of oxidoreductases has long been an important goal in biotechnology. During the past year, significant progress has been made in the development of oxidoreductase-based diagnostic tests and improved biosensors, in the design of innovative systems for regeneration of essential coenzymes, in the construction bioreactors for biodegradation of pollutants and for biomass processing, and in the development of oxidoreductase-based approaches for synthesis of polymers and oxyfunctionalized organic substrates.     

Quantum computing with molecular magnets

We discuss the potential of molecular magnets as the building blocks of a quantum computer. The simplification in the control procedure for the quantum gates in many-spin systems coming from the high symmetry is shown to lead to a relatively simple way to address the spin degrees of freedom in molecular magnets. The advantage of an anisotropic effective spin interaction in memory applications is demonstrated on the example of the Grover quantum search algorithm in a generic easy-axis molecular magnet. Electric control of the coupling between the spins is shown to enable two-qubit quantum gates in polyoxometalates.     

Analysis of bacterial biotin-proteins.

The biotin-protein populations in several bacterial strains were analyzed by solubilization of [3H]biotin-labeled cells with sodium dodecylsulfate followed by electrophoresis on polyacrylamide gels containing the detergent. A variety of patterns of biotin-labeled polypeptide chains was seen, ranging from a single biotin-protein in Escherichia coli, corresponding to the biotin carboxyl carrier protein component of acetyl-CoA carboxylase, to multiple species in Enterobacter aerogenes, Pseudomonas citronellolis, Bacillus cereus, Propionibacterium shermanii, Lactobacillus plantarum, and Mycobacterium phlei, which probably represent subunits of multiple biotin-dependent enzymes present in these organisms. In the case of Pseudomonas citronellolis two major biotin-containing polypeptides with approximate molecular weights of 65 000 and 25 000 were shown to correspond to the biotin carboxyl carrier components of pyruvate carboxylase and acetyl-CoA carboxylase, respectively. Thus in the case of Pseudomonas citronellolis two different biotin-dependent enzymes in the same cell do not share common biotin carboxyl carrier subunits.     

The bacterial cytoskeleton.

In recent years it has been shown that bacteria contain a number of cytoskeletal structures. The bacterial cytoplasmic elements include homologs of the three major types of eukaryotic cytoskeletal proteins (actin, tubulin, and intermediate filament proteins) and a fourth group, the MinD-ParA group, that appears to be unique to bacteria. The cytoskeletal structures play important roles in cell division, cell polarity, cell shape regulation, plasmid partition, and other functions. The proteins self-assemble into filamentous structures in vitro and form intracellular ordered structures in vivo. In addition, there are a number of filamentous bacterial elements that may turn out to be cytoskeletal in nature. This review attempts to summarize and integrate the in vivo and in vitro aspects of these systems and to evaluate the probable future directions of this active research field.     

Conformational studies of bacterial polysaccharides. II. Optical activity of some bacterial capsular polysaccharides

The optical activity of the Klebsiella capsular polysaccharides of serotypes K1, K5, K6, K8, K11, K56, and K57 has been studied in aqueous solution. Measurements of ORD in the range 185–450 nm reveal anomalous ORD with Cotton effects near λ₀ = 195nm. The results are evaluated quantitatively according to hte Moffitt-Yang and the Drude equations. Straight lines are obtained in the Moffitt-Yang plots, while the corresponding Drude plots yield bent curves. The b₀ values, calculated from the slope of the stright lines in the Moffitt-Yang plot, range from 90 to 270 and suggest a helical superstructure for the capsular polysaccyharides. Positive b₀ values have been found for K1, K5, and K6 and negative b₀ values for K8, k11, K56, ad K57. Circular dichrosim has been mesured, but the CD curves are found to be truncated at the lower-wavelength end due to the 185-nm limit of the spectrometer used. Measurements of the temperature dependence of the specific optical rotation [α] reveal in all cases cooperative order–disorder transitions at temperatures, T_m, fro m298 to 323°K. The van′t Hoff enthalpies derived from the width of the transition curves are found to be similar in value to those of polypeptieds in aqueous solution. The K8 polysaccharide shows a two-step transition. The results are discussed in relation to the known primary structure and x-ray data from oriented and partially crystalline films. A model is suggested for the two-step transition in the K8 polysaccharide.     

Organization of the bacterial chromosome.

Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction between a large plasmid and a second chromosome is discussed. Recent information on repeated sequences and chromosomal rearrangements is presented. The growing understanding of limitations on the rearrangements that can be tolerated by bacteria and those that cannot is summarized, and the sensitive region flanking the terminator loci is described. Sources and types of genetic variation in bacteria are listed, from simple single nucleotide mutations to intragenic and intergenic recombinations. A model depicting the dynamics of the evolution and genetic activity of the bacterial chromosome is described which entails acquisition by recombination of clonal segments within the chromosome. The model is consistent with the existence of only a few genetic types of E. coli worldwide. Finally, there is a summary of recent reports on lateral genetic exchange across great taxonomic distances, yet another source of genetic variation and innovation.     

Mechanics of bacterial macrofiber initiation.

The twisting and writhing during growth of single-cell filaments of Bacillus subtilis which lead to macrofiber formation was studied in both left- and right-handed forms of strains FJ7 and RHX. Filament bending, touching, and loop formation (folding), followed by winding up into a double-strand fiber, were documented. Subsequent folds that produced multistrandedness were also examined. The rate of loop rotation during winding up was measured for 26 loops from 16 clones. In most cases, the first loop formed turned at a lower rate than those produced by the following cycles of folding. The sequence of folding topologies differed in FJ7 and RHX strains and in left- versus right-handed structures. Right-handed FJ7 routinely gave rise to four-stranded helices at the second fold, whereas left-handed FJ7 and both left-handed and right-handed forms of RHX made structures with predominantly two double-stranded helical regions. Left-handed RHX structures frequently produced second folds within the initial loop itself, resulting in T- or Y-shaped fibers. Sixteen cases in which the initial touch of a filament to itself produced a loop that snapped open before it could wind up into a double-strand fiber were found. The snap motions were used to obtain estimates of the forces generated by helical growth of single filaments and to investigate theoretical models involving the material properties of cell filaments. In general, the mechanical behavior of growing single-cell filaments and fibers consisting of two-, three-, or four-strand helices was similar to that described for larger, mature, multifilament macrofibers. The behavior of multicellular macrofibers can be understood, therefore, in terms of individual cell growth.