Bioremediation is a technology that utilizes the metabolic potential of microorganisms to clean up contaminated environments.

It constitutes an attractive alternative to physicochemical methods of remediation, may be less expensive, less harmful to the environment, etc.

Here are some examples:

Marine petroleum hydrocarbon degradation:
Spilled-oil bioremediation experiments show that the bacteria involved in degradation are some gropus of -Proteobacteria, Pseudomonas and Cycloclasticus groups (-Proteobacteria) and the genus Alcanivorax.

Metal bioremediation
Studies show that the major groups of bacteria capable of removing metals from the environment are -Proteobacteria ,Actinobacteria and some some species of the genus Ralstonia, like Ralstonia metallidurans o Ralstonia eutropha.

However, although a large number of microorganisms have been isolated in recent years that are able to degrade compounds previously considered to be non-degradable, there are a number of factors, some non-biological, that contribute to the persistence of some pollutants in the environment, one of which is the fact that current pathways for the metabolism of xenobiotics are not optimal.

This is particularly true for highly toxic pollutants such as dioxins, dibenzofurans and PCBs, for which effective pathways have not yet been described. Moreover, most microbial activities that can serve as the basis of biotechnological applications do not function optimally under process conditions and can almost always be improved. Thus, biotechnology allows the design of improved biocatalysts involves different aspects of optimization.

A variety of strategies for designing new or imprived catalysts for bioremediation have been developed over recent years: The simplest strategy is improving the biodegradative performance of a consortium (a mixed bacterial culture) through the addition of a specialist organism; in this case, a consortium is designed Consortia that exhibit novel catabolic activitie.
In some cases, a simple two- or three member consortium is obtained, one member of which may carry out the initial catabolic reaction , and another of wich may complete the sequence. Such consortia have been developed for the mineralization of bicyclic aromatics such as chlorinated biphenyls (PCBs), chlorinated dibenzofurans and aminonaphthalenesulfonates But the metabolic division of labour in cocultures of aerobic microorganims may not constitute the most effective situation for the bioremediation in natural environment .

The most effective strategy is the transfer of catabolic genes from its original host to an appropriate recipient , that result in the combination of a central pathway with a pathway sequence that enable a new substrate to be channelled into the central pathway.

Gene cloning generally circumvents barrier to natural gene transfer and, of course, involves precisely predertermined genes and expression signals.

Plasmid cloning vector may, however, suffer from the same instability as natural plasmids and, moreover, have antibiotic-resistance selection makers, which are undesirable from enviromental applications.

For these reasons , minitransposon cloning vector have been developed to insert heterologous genes stably into the chromosomes of host bacteria without the use of antibioticresistance makers or, more recently, with makers that can be selectively eliminated after gene transfer.

As the transposase gene is not cotransferred, the transposon vector do not cause sequence instability or rearrangements at the site of transposition, not do they mediate inmunyty to transposicin. They can therefore be used for multiple, sequential cloning evets in the same host organism.

The University of Minnesota Biocatalysis/Biodegradation Database should soon offer a systematic display of theoretical routes from one substrate to a specific intermediate or central metabolite.
http://umbbd.msi.umn.edu/index.html

Some bioremediation processes require an increase in the rate of pollutant removal. Achieving this goal involves identifying the enzymatic or regulatory step fo the pathway that is rate limiting, followed by experimental elevation of the activity of the rate-limiting protein through an increase in the transcription or translation of its gene, or in its stability or kinetic properties.

Transcription of the genetic determinants of metabolic pathways, which are usually organized in operons, is generally controled by positively-acting regulatory proteins that are activated by pathway substrates or metabolites. Mutants of regulatory proteins have been produced that either mediate higher levels of transcription than the wild-tipe regulator or respod to new effectors. The use of artificial regulatory systems allows the expression of catabolic genes to be uncoupled from the signals that ordinarily control their expression and offers considerable flexibility for process control.

Thus, the use of starvation-induced promoters can uncouple gene expression from growth and augment catabolic activity in nutrient-limited environments or when target pollutants fall below certain thresholds.

Protein engineering can be exploited to improve an enzymes stability specifity and kinetic properties. However, the number of degradative enzimes whose structure has been elucidated still small and this constitutes a major limitation for rational protein design. An alternative to improve enzyme activity is combining the best attributes of related enzymes is to extange subunits or subunit sequences. A more recently developed and powerful alternative method for obtaining proteins with new activities involves shuffling their gene sequences.

It is sometimes assumed that a major problem in the use of designed inoculants is their poor competitiveness in natural environments.

Nevertheless, improving inoculant survival is an important goal in the further development of bacterial inocula for biotechnological applications in the environment, where the microorganisms are exposed to a variety of stresses such as toxic metals, solvents and extremes of temperature and pH.

The combination of resistance to environmental stresses and catabolic phenotypes in appropriate bacterial strains is expected to yield microbial catalysts with significantly improved survival characteristics in hostile habitats. For example, solvent-resistant bacteria able to mineralize hydrophobic pollutants have recently been engineered.

However, the most striking case is the use of Deinococcus radiodurans for the metal remediation in radioactive mixed waste environments. The high cost of remediating radioactive waste sites from nuclear weapons production has stimulated the development of bioremediation strategies using this bacteria, the most radiation resistant organism known.

Using genetic engineering, deinococos have been used in bioremediation to consume and digest solvents and heavy metals, even in highly radioactive areas.

The mercuric reducing bacterial gene of Escherichia coli (merA) was cloned in the deinococo to detoxify ionic mercury commonly found in radioactive wastes from the manufacture of nuclear weapons. The same engineers developed a kind of deinococo able to detoxify mercury and toluene in mixed radioactive wastes.

Deinococcus radiodurans

Synthetic biology is the engineering of biology: the synthesis of complex, biologically based (or inspired) systems which display functions that do not exist in nature.

This engineering perspective may be applied at all levels of the hierarchy of biological structures from individual molecules to whole cells, tissues and organisms. In essence, synthetic biology will enable the design of biological systems in a rational and systematic way.

In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the first synthetic organism. This took about two years of painstaking work. In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks. In 2007 it was reported that several companies were offering the synthesis of genetic sequences up to 2000 bp long, for a price of about $1 per base pair and a turnaround time of less than two weeks. As of the present date, September 2009, the price has dropped to less than $0.50 per base pair with some improvement in turn around time. Not only is the price judged lower than the cost of conventional cDNA cloning, the economics make it practical for researchers to design and purchase multiple variants of the same sequence to identify genes or proteins with optimized performance.

Recently, a group of scientists headed by Craig Venter have created a cell controlled entirely by man-made genetic instructions -- the latest step toward creating life from scratch. The achievement is a landmark in the emerging field of "synthetic biology," which aims to control the behavior of

organisms by manipulating their genes.