Are some scientists just taking the cis out of genetic engineering? Pt II

By Guest Work 12/02/2010 3


By Prof. Jack Heinemann*

Part 2: If it looks like a duck and it quacks like a duck, it probably is a duck.

Scientists and non-scientists alike understand that gene function matters for the safety assessment of GMOs (de Cock Buning et al., 2006). Creating a new function in an organism using parts from that organism is still a new function. Melt dow­­n a plough and reform the metal as a sword and you have a fundamentally new risk. It isn’t the chemistry of the genetic material that interests the risk assessor, but the informational content when it is in the context of an organism that will express that gene.

The genes we are talking about are coded by the particular order of nucleotides (indicated by the letters A, G, C and T). Humans, for example, have 3 billion nucleotides in their DNA genomes. Since there are only four different letters, it isn’t the chemical properties of the nucleotide but their sequence that is translated into functions, just like the English alphabet has 26 letters and all words are made by particular combinations of these (Table). Organisms of different ’species’ can have some very different strings in their genomes and some very similar strings but within their context the strings have different functions.

Insertions, deletions, substitutions and rearrangements of the same letters make different meanings.

common English word

similar word1

sequence similarity of matched words

sequence-independent shared letter similarity

change (relative to hypothetical word)

count ****

80%

80%

insertion
luck ****

75%

75%

substitution
this ****

50%

100%

rearrangement
wore *****

80%

80%

deletion
cis ****

50%

50%

substitution + deletion
1 not shown

Take for instance the average similarity of DNA sequences in genes of humans and monkeys (98%), where in fact about 98% of genes in common are nearly 100% identical (de la Cruz and Davies, 2000), but produce noticeably different developmental outcomes (Figure). Over 50% of genes in common between single celled yeast and humans are between 30-50% identical (Botstein et al., 1997).

The cisgeneticist is confined to no minimum string length for manipulation and thus, from the raw building blocks common to all genomes, can create strings just as ’foreign’ to that same genome as any that came from a different species. Any gene from a human being could be rearranged to become 2%, 50% or 70% different from itself and as different as the average gene from a human was to the average gene from a single-celled soil microorganism. To me, a cis/intragenic construct looks and quacks like a transgenic duck.

Figure: Developmental outcomes of two genomes where about 98% of genes are about 100% identical
Figure: Developmental outcomes of two genomes where about 98% of genes are about 100% identical

The risk spectrum of such manipulation is no different based on where the DNA comes from. Significantly different functions can arise from seemingly small changes in information and surprisingly similar functions can arise from very different strings.  Rearranging the nucleotides taken from a genome and putting them back into the same genome is no guarantee of safety. That is why, just like with any other DNA source for making GMOs, cisgenic products will have to be tested case-by-case and subject to the same rigour of testing as any other product of genetic engineering.

As with all genetic engineering processes, the DNA upon entry into a recipient cell can integrate at more than one place (and usually does), and parts of the introduced DNA fragment into small pieces that land without control into various parts of the genome. Multiple copies of the same piece of DNA can result in very different risks, as in the case where ’toxic potatoes or tomatoes can be engineered by inserting extra copies of species-specific alkaloid genes that raise the concentration of solanines (e.g., for pest resistance)’ (de Cock Buning et al., 2006). Each of these changes caused by insertions or deletions of DNA has to be painstakingly discovered, but because the length of the sequence can be quite short, they are often not found (BAT). Once again, the source of the DNA does not matter for its ability to scramble the informational content in the vicinity of its insertion, just as the text of a book fragmented with letter strings of different lengths at random throughout would lose its informational cohesiveness.

Genetic engineering can change grammar, not just spelling. This is a key point missed by the protagonists of cisgenics. The sequences that are inserted can also include punctuation symbols, and html codes such as <b> that say ‘read me loudly’ or ‘don’t read me at all’. These rule changes can be imposed upon the integrating DNA by the DNA surrounding its insertion site, or the integrating DNA can impose a new rule on its new neighbours (Schubert and Williams, 2006). We simply don’t know all these rules yet, nor the sequences of which they are made. Moreover, one of the grammar rules that can change can start a small chain reaction of other unintended changes, for example by activating natural elements in genomes that ’hop’ into new places (Wu et al., 2009). Just such events are specific to the process of genetic engineering, not the source of the DNA.

Finally, and critically, there is no experimental evidence that cisgenics avoids the hazards of any other kind of genetic engineering. For example, protagonists claim that there are fewer changes in GMOs than in the products of crop breeding. When you look behind such claims you find no or very little evidence of experiments designed to prove that very thing (de Cock Buning et al., 2006). Such assertions are usually backed by non-transparent and personal assumption frameworks that are used in the protagonist’s logic. In a recent review of the literature I could find little evidence to support a general claim that GE had less effect on organisms than breeding or mutagenesis (Heinemann, 2007). The small number of studies that may be relevant to this statement regarding the relative effects of GE, breeding and mutagenesis have such hugely differing methodologies that comparison at this level is at best misleading and is certainly not an example of thorough scientific evaluation. Worse still, the argument assumes that the changes that come from breeding will affect the genome, transcriptome, proteome and metabolome in the same way as GE, for which there is no evidence whatsoever that I could find. There is evidence to the contrary. For example, protein aggregation is more likely for highly expressed transgenes than for the same protein under normal expression levels (Tartaglia et al., 2007).

Cis/intragenics could be seen as a way to evade case-by-case risk assessment. Case-by-case risk assessment was meant to eliminate the possibility that the particular change, or the particular combination of changes that have occurred in the GMO, will cause no unacceptable hazard. The purpose of GE is to create a clear change in the characteristics of the organism. A risk assessment attempts to evaluate the effects of such changes on human food and our environment. But more than this, a good risk assessment is capable of finding all additional unanticipated or unintended ways this product may have been changed so that we can be properly informed before regulators agree or disagree to its use.

That is why all products of genetic engineering regardless of what we choose to call them need to conform to the same levels of rigorous pre-market testing.

In New Zealand, we have created a science and technology industry where the goals of our scientists and their employers often includes developing financial interests in their own products, yet this same community has a responsibility to dispassionately advise both government and the public on the safety and practicality of these technologies or alternatives to them. This mixture of duties cannot be reliably achieved in any sector, as numerous studies have shown (Millstone and van Zwanenberg, 2002, Shorett et al., 2003). The increase in financial and political power flowing to technology developers also puts pressure on professional bodies because they will increasingly have the same scientists on their councils, boards and executives. These appointments also increase the chances of political appointments, such as to the Prime Minister’s Science Advisory Committee. Cis/intragenics may be just another symptom of a troubled public science system that increasingly is packaging public persuasion in the guise of dialogue.

References:

BAT.  Biosafety Assessment Tool, https://bat.genok.org/bat/.  Date of Access: 5 February 2010.

Botstein, D., Chervitz, S. A. and Cherry, J. M. (1997). Yeast as a model organism. Science 277, 1259-1260.

De Cock Buning, T., Lammerts van Bueren, E. T., Haring, M. A., de Vriend, H. C. and Stuik, P. C. (2006). ‘Cisgenic’ as a product designation. Nat. Biotechnol. 24, 1329-1331.

De la Cruz, F. and Davies, J. (2000). Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol. 8, 128-133.

Heinemann, J. A. (2007). Letter to the Editor. Environ. Plan. Law J. 24, 157-160.

Millstone, E. and van Zwanenberg, P. (2002). The evolution of food safety policy-making institutions in the UK, EU and Codex Alimentarius. Soc. Pol. Admin. 36, 593-609.

Schubert, D. and Williams, D. (2006). ‘Cisgenic’ as a product designation. Nat. Biotechnol. 24, 1327-1328.

Shorett, P., Rabinow, P. and Billings, P. R. (2003). The changing norms of the life sciences. Nat. Biotechnol. 21, 123-125.

Tartaglia, G. G., Pechmann, S., Dobson, C. M. and Vendruscolo, M. (2007). Life on the edge: a link between gene expression levels and aggregation rates of human proteins. Trends Biochem. Sci. 32, 204-206.

Wu, R., Guo, W. L., Wang, X. R., Wang, X. L., Zhuang, T. T., Clarke, J. L. and Liu, B. (2009). Unintended consequence of plant transformation: biolistic transformation caused transpositional activation of an endogenous retrotransposon Tos17 in rice ssp. japonica cv. Matsumae. Plant Cell Rep. 28, 1043-1051.

* Professor Jack Heinemann, College of Science (Biological Sciences), University of Canterbury


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