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marshallz10

Synthetic genes in the brave new world of food crops

marshallz10
19 years ago

The commentary below is one of the clearest cautionary statement against the current reliance on "substantial equivalence" in regulating biotech products. I include it in full because it was posted to a prohibited webpage.

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June 20, 2004

Prof. Joe Cummins

"Synthetic genes in the brave new world of food crops"

In North America genetically modified (GM) foods that are unlabeled and

untested are taking over the food supply. The promotion of such foods

maintained that natural genes "substantially equivalent " to the genes

in normal crops were being shifted from bacteria or viruses to improve

food crops. That promotion ignores the reality of genetic technology.

The genes used to create GM crops are synthetic approximations of

natural genes that contain synthetic DNA sequences tuned to maximize

production of toxins killing insects or degrading herbicides, as well as

providing firm patent protection on the food crop. Synthetic genes are

used because the genes active in bacteria or man are not very active in

crop plants. The DNA code must be adjusted for the codon bias typical of

the crop plant species into which genes from bacteria or mammals are

introduced.

The genetic code is made up of 64 three letter codons (code words) for

twenty amino acids (61 codons) plus words for translation start and

stop. The code words for protein amino acid are encoded for between one

(met and tryp) and six (arg,lue,ser) synonymous code words. The first

two positions of the codon are fixed for a particular amino acid while

the third position is said to wobble allowing for alternate code

letters. The degeneracy of the code allows for alternative gene codes

for a single protein, The frequency with which different codons are used

varies between groups of organisms, so for example, genes from bacteria

are poorly read in higher plants (and visa versa), For optimum

expression the code for a transgene frequently needs to be rewritten to

achieve adequate performance. The codon bias within members of a group

of organisms such as plants is believed to be caused by the presence of

typical isoacceptor transfer RNA families in the different groups of

organisms. The number of possible genes that can code one protein

molecule is staggering, it is estimated to be about five times ten to

the 47th power (1). That number is within three orders of magnitude of

the number of atoms making up earth and five times larger than the

number of water molecules on earth (2). In synthesizing the genes used

in GM crops, say in altering a Bacillus thuringiensis (Bt) cry toxin

gene for useful activity in plants, a table of plant preferred codons is

used to substitute the plant preference for the bacterial

preference.(3). Sometimes it is necessary to substitute one or more of

the amino acids so that the final cry toxin can function in the plant

cell environment (3,4). As plant genetic engineering has "advanced" the

crucial active domains of toxins and enzyme are recognized and

"improved" to such an extent that the original source protein from

living organisms is hardly recognizable.

Regulatory sequences (such genes are frequently referred to as cis

elements) such as promoters, introns and transcription termination

signals are normally are normally taken from higher plants or their

viruses. Nevertheless, progress has been made in creating synthetic

promoters loosely based on the cauliflower mosaic virus (CaMV) commonly

used in plant genetic engineering (5).

The use of synthetic genes in food crops has not been taken into account

sufficiently in the regulatory approval of the food crops. The synthetic

genes , based on bacterial genes or human genes, can be propagated in

bacteria using illegitimate recombination and bacterial plasmids but

such genes are not substantially active in those bacteria nor do they

readily participate in homologous recombination. The synthetic genes

lack DNA homology with the bacterial or human genes from which they

originated. The codon usage of humans and of bacteria diverges from the

codon preference of plants yeast and nematodes. The synthetic genes used

in crop plants do not function successfully in bacteria or humans but

should do well in yeast (and likely other fungi) and in nematodes. In

spite of the obvious differences between the synthetic and the natural

genes from which they arose, regulators have allowed the genes and

proteins produced in bacteria to be considered appropriate surrogates in

safety testing for the synthetic genes and the proteins produced in food

crops (6). The use of the bacterial surrogates has been to spare

corporations the cost of isolating the quantities of DNA and protein

from the crop plants needed for safety testing. That is true even though

the cost of fully testing the "real thing" is negligible relative to the

profits from licensing the GM food crops to farmers. The genes and their

proteins produced in bacteria are no real substitute for the real genes

and proteins produced from them in food crops and the assurances that

the safety tests are fully meaningful is a convenient fiction showing

the unhealthy togetherness of corporations and their regulators (7,8).

There seems to be a convenient fiction propagated by corporations

,government bureaucrats and academics who depend on grant money from

corporations and government to promote the myth that genes from bacteria

are used in producing food crops or that genes from humans are used to

produced plant biopharmaceuticals when , in fact, the genes used in the

crop plants are synthetic approximations used to produce products

similar to the real thing. Even the courts seem to have accepted the

convenient fiction as if it were fact. The next generation of GM crops

is evolving towards a minimal assembly of active protein domains

(domains are active area of proteins that serve as signals for activates

such as toxicity or enzyme function or environment sensors for

regulation) that are frequently patched together from a number of

different proteins. Safety testing is based on unreal surrogates and the

products are not labeled in the marketplace so that subtle changes

caused by a few amino acid changes or failure to heed secondary protein

modifications such as glycosylation will be difficult to trace as people

are adversely effected by consuming the synthetic GM crops.

It is imperative that the synthetic genes and their real products be

tested thoroughly, not only for potentially toxic side effects but for

stability and recombination properties as well. These synthetic genes

have not had an evolutionary history and it is a major mistake to assume

that the genes can be expected to behave in all ways like the gene that

they were built to represent. A distinction must be made between natural

genes and transgenes and the synthetic representations of those genes

used to manufacture GM crops. A polluting synthetic transgene should not

be presumed to be equivalent to a polluting natural transgene.

References

  1. Gustafsson,C,Govindarajan,S. and Minshull,J Codon bias and

    heterologous protein expression 2004 Trends in Biotechnology in

    press pp 1-8
  2. About Big Numbers qaearth=atoms in the earth 2004

    http://pages.prodigy.net/jhonig/bignum/qaearth.html
  3. Fischoff,D. and Perlak,F. Synthetic plant genes 1996 United States

    Patent 5,500,365 pp1-59
  4. Payne,J,Cummings,D,Cannon,R,Narva,K. and Stelman,S. Bacillus

    thuringiensis genes encoding lepidopteran-active toxins 1998

    United States Patent 5,723,758 pp 1-32
  5. Bhullar,S, Chakravarthy,S,Advani,S, Datta,S,Pental,D. and Burma,P.

    Strategies for Development of Functionally Equivalent Promoters

    with Minimum Sequence Homology for Transgene Expression in Plants:

    cis-Elements in a Novel DNA Context versus Domain Swapping 2003

    Plant Physiology 132, . 98898
  6. Cummins,J. Regulation by deceit 2004 Science in Society 22,32-3
  7. Ho,M DNA in food and feed 2004 ISIS press release pp1-8

http://www.i-sis.org.uk/

  1. Ho,M. and Cummins,J. GM food and feed not fit for "man or beast"

    2004 pp1-6

http://www.i-sis.org.uk/

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