Microbial gene expression

Supek, F. and Vlahovicek, K. (2005) Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 6, 182. 

Gene Expression Systems. One of the potentials of genetic engineering of microbes is production of large amounts of recombinant proteias (12,13). This is not a trivial task. Each proteia is unique and the stabiUty of the proteia varies depending on the host. Thus it is not feasible to have a single omnipotent microbial host for the production of all recombinant proteias. Rather, several microbial hosts have to be studied. Expression vectors have to be tailored to the microbe of choice. 

It is well known that survival and proliferation of microbial cells in the environment depend on the expression of advantageous phenotypes controlled by the genotype expression. It is becoming clear that such evolutionary pressure has resulted in a network of sensor mechanisms that transduce environmental stimuli into gene expression and hence a phenotype complementary to the prevail-... 

The performance of a biotreatment system ultimately depends on optimization of the activity of microbes and the ability to control the process parameters of the treatment system [157]. In this respect, the ability to monitor gene copy numbers and gene expression is highly useful for real time optimization of the efficiency of a biotreatment system. Advanced molecular techniques as well as low cost methods (e.g., antibody detection of enzymes based on color reaction strips fluorescence i.e., GFP marked organisms with UV light detection) can also be applied to monitor the microbial community structure, persistence of the added bacteria, and their interactions with indigenous populations. 

S. V. Perry. Three Hundred Years of Bacterial Motility, Judith P. Armitage. Talking to Cells-Cell Membrane Receptors and Their Modes of Action, Robin F. Irvine. Mechanisms in Regulation Protein Phosphorylation, Philip J. Randle. Regulation of Expression of Microbial Genes, Patricia H. Clarke. Antibody Specificity and Diversity The Proteins (Part I), Lisa A. Steiner. Author Index. Subject Index. 

Table 1 describes all the microbe-specific databases, and Table 2 lists databases for the microbial community. These databases provide genomic sequence data, gene and protein information, gene expression data, metabolic reactions and pathways, interaction network,... 

MicrobesOnline a phylogenetic approach to the analysis of microbial genes and genomes (5) currently (January 2012) includes 1,750 bacterial, 94 archaean, and 119 eukaryotic genomes as well as data from several thousand gene expression experiments (i.e., microarray data). 

What is fast What is slow What is relevant The relaxation time concept of Harder and Roels [148] (Fig. 28) maps typical time constants of microbial and cellular control on the level of modification of enzymes (activation, inhibition, dis/association of subunits, covalent modification or digestion) to the range of ms to s, on the level of regulation of gene expression (induction, repression or derepression of transcription) to min, on the level of population selection and evolution to days and larger units. The examples discussed below will clear up how bioengineering is facing the individual time constants. 

These questions are amenable to various combinations of imaging, modelling, metabolic and gene expression studies and field observation to analyse the nutrient dynamics of the forest floor microbial decomposer subsystem, and to provide data for predictive models of forest floor responses to environmental change. 

---