Genetics and Biochemistry of Phytoremediation and Ecological Engineering

Plant genomes typically have approximately 25 000110 000 genes. By comparison, the human genome has a little over 32 000 and typical species of bacteria have about 2500 genes. These order of magnitude differences do not necessarily translate into orders of magnitude differences in protein and enzyme synthesis because (1) some genes seem to lack a specific function, (2) several genes are necessary to express or synthesize some proteins, and (3) some genes generate or contribute to several different proteins. Thus, while anchored in place, fewer in number than microorganisms, lacking an immediate flight response to toxins and environmental insults, and while not being able to excrete as many transformation products as do mammals, plants may not be more highly evolved than humans and other mammals.

The overall number of unique genes for all organisms is difficult to estimate, but the effects of genetic diversity are well known in general and need to be applied more in place of predominant monocultures typically used in early phytoremediation applications. Nevertheless, approximately 10 000 plant proteins and 200 000 plant secondary metabolites are known to exist, which must include the full suite ofbiomolecules necessary to govern, control, and otherwise contribute to growth, maintenance, and senescence. Some of the growth, maintenance, and senescence enzymes serve dual functions in plant metabolism and in detoxification and defense from insults. Less than a hundred enzymes have been identified as useful or potentially applicable in phytoremediation. Thus thousands of other proteins could be important but have not yet been fully characterized as to activity and function.

Because of shorter life spans, microorganisms are expected to evolve responses to xenobiotic and anthropogenic stresses faster than plants and animals. Thus the future tracking of microbial enzymatic activity may be more complicated. But with a typical genome of 2500, many fewer proteins seem to be uncharacterized for bior-emediation or plant-assisted bioremediation applications.

Some simple enzymatic activities such as nitroreduc-tases (EC 1.6.6.-; see Figure 2) may be common to all forms of life due to evolution in the earliest forms of

Figure 2 Tunneling electron miscopy of a monoclonal antibody attached to a putative nitroreductase-humic acid complex shown at 200 nm by 200 nm. Courtesy of George Bailey, US EPA (deceased).

bacteria or cyanobacteria. But animals and plants, which seem to have similar genetic diversity from overlapping ranges of genome sizes, seem to have at least an order of magnitude more proteomic diversity than bacteria. This order of magnitude greater plant enzymatic diversity should be investigated not only for waste management applications but also for the development of new fibers, pharmaceuticals, nutraceuticals, and other products.

The fact that some plant genomes exceed the size of human and some other mammal genomes does not necessarily indicate that plant enzymes and proteins are more evolved. Some plant genomes may have greater genetic redundancy and greater numbers of'introns' (polynucleotide sequence in a nucleic acid or gene sequence that does not code information for protein synthesis). But some plant enzymatic activities seem more evolved as evident from what seem to be the great number of medicines derived from plants. By contrast, some mammalian genes seem more evolved than plant genes. At least one human gene 2E1 expresses a more active cytochrome P450 (EC for transformation of chlorinated solvents than that expressed by plant genes. The number of plant metabolites used in pharmaceuticals cannot be compared to the one investigation of the human gene activity in transgenic plants, because the engineering oftransgenic plants with human genes is presently quite rare.

As a result, plants seem to have an order of magnitude more enzymes than bacteria. Plants have more elaborate metabolic synthesis and photosynthesis, whereas bacteria are normally simple heterotrophs that specialize in metabolism of organic compounds for energy to grow and reproduce. Some animal enzymatic activity seems more evolved than plant metabolism and vice versa. Evolutionary history, practical control of organisms to minimize spread of genetically engineered organisms, and genetic and proteomic diversity must be used to determine if plants or animals are better suited for the genetic engineering that may be necessary to sustainably manage some hazardous wastes in the long term.

From a more holistic and appropriate perspective, microbes, plants, and animals symbiotically cycle nutrients and organic material and manage available energy in ecosystems planetwide. Thus contrasts of genome sizes, genetic diversity, and enzymatic activities are not as important as understanding when unique processes can be lightly managed in the ecological engineering of ecosystems to cleanup and manage wastes. Thus the activities of proteins common to microbes, plants, and animals need to be explored to determine which enzymes are more evolved to use in management of hazardous wastes and for other purposes. The predominant uncharacterized enzymatic activities of plants and animals should be investigated in a systematic manner for waste management and other societal purposes. To understand how contaminants can be sustainably managed, the seminal differences in metabolism must be known to select and lightly manage appropriate ecosystems.

Recently, community effects of plants and insects have been shown to further the transformation of some compounds. (The effects of nutrient cycling by microbes in these simple plant-insect ecosystems have not been fully explored.) This is another indication that plant metabolism seems to be more similar to animal metabolism. This genetic similarity of enzymatic activity also bodes well for addressing general concerns about food chain accumulation of organic contaminants and by-products in animals during phytoremediation applications.

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