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 α-Proteobacteria, Pseudomonas and Cycloclasticus groups (γ-Proteobacteria)

and the genus Alcanivorax.

Metal bioremediation

Studies show that the major groups of bacteria capable of removing

metals from the environment are α-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.

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 dibenzo-

furans and aminonaphthalenesulfonates

But the metabolic “division of labour” in co-

cultures of aerobic microorganims may not

constitute the most effective situation for the

bioremediation in natural environment .

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.

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 antibiotic-resistance 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 transposición. 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 enzyme´s 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.