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That headline catches your eye, doesn’t it?

Antibiotics by AJC1 via Flickr.

We’ve seen such claims made in popular media such as the March 2010 Fury as EU approves GM potato: Critics claim plant could spread antibiotic-resistant diseases to humans in the Independent: “Opponents fear bacteria inside the guts of animals fed the GM potato – which can cause human diseases – may develop resistance to antibiotics.” Groups that actively work against deregulation of genetically engineered crops have been making such claims for years.

We’ve also seen these claims in peer-reviewed journals (although, far less frequently than in non-peer reviewed media and reports). For example, in the February 2009 issue of Critical Reviews in Food Science and Nutrition, the review Health Risks of Genetically Modified Foods: “An area of concern focuses on the possibility that antibiotic resistance genes used as markers in transgenic crops may be horizontally transferred to pathogenic gut bacteria, thereby reducing the effectiveness of antimicrobial therapy.”

Are antibiotic marker genes in genetically engineered crops really a risk to human health? Many people have raised this question and there seems to be a lot of confusion about the issue. It’s time to look into the risks and reasons more deeply.

What are antibiotic resistance genes for?

In order to understand why these genes are used, we have to look a little at the process of genetic engineering. For some plant types, including corn and rice, immature seeds are dissected to expose the developing embryo. Pieces of carrot roots can be transformed, as can the leaves of tobacco. The desired genes are transferred into the plant cells with either a gene gun or Agrobacterium. The plant cells are then grown up into whole plants in petri dishes, with the help of plant hormones. The process is similar to other asexual plant propagation techniques, but much smaller!

Growing plants up from cells.

Not every cell receives the gene of interest, however, so researchers need a way to find the cells that have it. Enter antibiotic resistance genes. If the cells are transformed with the gene of interest and an antibiotic resistance gene, the appropriate antibiotic can be added to the media in the petri dish so that any cells that didn’t get the genes will die. The antibiotic resistance gene is being used as a selectable marker, since it allows the researcher to select only the desired cells.

Of course, just because these genes are useful doesn’t mean that they are safe or that they should be used. What does the research tell us?

 

Risk: Gene transfer from plants to bacteria

Soil bacteria by Michigan State University.

Fear of antibiotic resistance markers is mainly due to fear of gene transfer from genetically modified plants to bacteria in the soil or bacteria in human or animal guts. There are at least two reasons why this fear is unwarranted. First, soil and gut bacteria naturally contain a variety of antibiotic resistance genes without any human intervention. Second, transfer of genes from a plant to a bacterium is extremely unlikely.

Natural antibiotic resistance

Life for a bacterium isn’t easy. They have to compete fiercely for resources, so it’s not surprising that some bacteria have evolved to produce poison that kills their competitors: antibiotics. The producers of these antibiotics also evolved antibiotic resistance mechanisms so they could survive their own weapons. Additionally, bacteria develop resistance to antibacterial compounds in the environment.

Often, antibiotic resistance is conferred by a single gene. Any bacteria that can find that resistance gene and use it have an advantage. Consequently, antibiotic resistance genes are widespread in natural environments. When humans intervene, using antibiotics in ways that encourage development of resistance in bacteria, that resistance is passed around even faster (no GMOs needed). For some information on how humans, check out the CDC’s pages on antibiotic resistance.

Gene swapping

Genetically modified crops: methodology, benefits, regulation and public concerns, a 2000 review in the British Medical Bulletin has a summary of the risks of horizontal gene transfer from genetically modified crops:

…horizontal transfer of a gene from ingested plant material to bacteria has never been demonstrated, and there is no indication that it has ever occurred during evolution. The probability that it could occur is, therefore, considered to be so low that it is not relevant when compared with the natural occurrence of antibiotic resistance genes.

They sound awfully confident, don’t they?

Bacteria (prokaryotes) are fairly promiscuous when it comes to genes. Many types of bacteria (not all) have the ability to take up DNA from the environment and from other bacteria and integrate it into their own genome during parts or all of their life cycle. This process is called horizontal gene transfer, and the bacteria that have this ability are called competent. Since they have this ability, it makes sense to worry about bacteria picking up antibiotic resistance genes (and other genes as well) from other organisms, including genetically modified crops.

Interestingly, eukaryotes (multicellular organisms like plants and people) also have the ability to take up DNA into their genomes. For example, the August 2007 Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes shows transfer of the entire genome from endosymbiotic bacteria into their hosts’ genomes. A more recent example appeared in January 2010 in the New York Times: Hunting Fossil Viruses in Human DNA. An entire virus genome resides in the human genome, and has been passed down from our simian ancestors.

So we know that bacteria can swap DNA and that eukaryotes can take up DNA from bacteria and viruses. Can prokaryotes take up DNA from eukaryotes?

It doesn’t look like it.

The European Food Safety Authority has the following to say about the subject in their excellent 2009 Statement of EFSA on the consolidated presentation of opinions on the use of antibiotic resistance genes as marker genes in genetically modified plants (section 2.1.1.2., edited slightly for clarity):

While many studies support the evolutionary significance of horizontal gene transfer between bacteria, eukaryotic genes in prokaryotic genomes are a rarity. There is no definitive report of DNA transfer from eukaryotes to bacteria.

As of 24 September 2008 the public genome databases included more than 750 completed prokaryotic genomes. In the first annotation of the putative genes there are frequent cases where closest matches are found with eukaryotic genes, but these preliminary results have not manifested into demonstrations of horizontal gene transfer from eukaryotes to prokaryotes, as judged by the scientific publications interpreting the genomic sequencing data. For one functional gene (phosphoglucose isomerase), phylogenetic analyses indicated that the gene might have been transferred from a eukaryote to bacteria. The transfer was estimated to have happened approximately 500 million years ago.

Homologous recombination from Duke University.

Multiple studies have found that bacteria can take up eukaryote DNA, but only in certain conditions, where the researchers used a sort of genetic trick called homologous recombination. In short, homologous recombination can occur when the ends of the donor DNA have sequences similar to part of the acceptor DNA. The homologous sequences can bind together, and in the next round of replication, the donor DNA can be integrated. In studies that aimed to find evidence of transfer of DNA from eukaryotes to prokaryotes without genetic tricks, none was found.

Table 1 of the EFSA Statement lists all studies prior to its publishing that examined horizontal gene transfer in bacteria (25 studies in all). Of the 18 studies that looked for gene transfer with homologous recombination, 15 found gene transfer and 3 did not. Of the 16 studies that looked for gene transfer without homologous recombination, no evidence of gene transfer was found.

In short, there are many DNA sequences that look like eukaryote genes in prokaryote genomes, but so far only one has been found that might be an actual functional gene. All evidence to date shows that gene transfer from eukaryotes to prokaryotes can only occur when homologous DNA sequences are present in donor and acceptor genomes. The lack of evidence for horizontal gene transfer in the wild suggests that there are some sort of barriers to gene transfer from eukaryotes to prokaryotes.

Barriers to gene swapping

Prokaryotic DNA and eukaryotic DNA are sort of like different computer languages. In fact, each species has slightly different ways of “personalizing” its own DNA with things like methylation and other DNA modifications, different codon preference, post translational modification of RNA, and whether or not introns are present. Eukaryotic DNA is so different from prokaryotic DNA that the bacteria just can’t take it up and use it as they would other bacterial DNA. Additionally, even if all of the barriers to gene uptake occur and all the barriers to gene expression are overcome, the likelihood that the gene will confer a positive trait for the bacterium is low. Most eukaryotic genes aren’t going to be helpful for a prokaryote, such that the few useful genes are few and far between. Even if a bacterium was able to uptake and express an antibiotic resistance gene from a genetically engineered plant, there would have to be selective pressure (i.e. an environment that included the antibiotic that the gene conferred resistance to) in order for the gene to be maintained in a bacterial colony. For more information about barriers to gene swapping, check out the EFSA Statement.

Avoiding the unlikely

Despite the fact that horizontal gene transfer from eukaryotes to prokaryotes is so unlikely (the only known example was estimated to have happened 500 million years ago), there are still precautions that can be taken to make it even more unlikely. For example, if antibiotic resistance genes are used as selectable markers in genetically modified organisms, researchers can avoid using sequences with homology to known bacterial genomes, they can be sure to only use antibiotic resistance genes that include features that make the gene unusable in bacteria, and they can avoid using promoters that are active in bacteria, just to name a few.

Alternative markers

Transformed rice cells expressing GFP via Scuola Superiore Sant’Anna.

Another option is to find alternative marker genes and alternative strategies. Herbicide resistance genes are an alternative selectable marker. Visible markers like GFP or GUS are screenable markers. Marker genes can be bred out, meaning that the final plant line will not contain the marker gene. Finally, it is possible to use no marker genes at all, but that does require far more screening of adult plants which can add expense and time to any project.

 

 

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Photo credit: JENS BUTTNER,JENS BUTTNER/AFP/Getty Images)

Every time I read something Vandana Shiva has written, I become more convinced that she is either 1) willfully ignorant on the subject of farming or 2) willfully ignoring a whole swath of problems in order to focus on a pet peeve. She is another sad example of a self-styled celebrity who plays games with people’s lives because she is unwilling to move from her ideology. One would think she would at least adapt her diatribes to fit peer-reviewed research or the numerous surveys of the people she claims to protect. Unfortunately, she’s still using the same old talking points and flat out lies that have accomplished nothing.

Case in point: Shiva writes about the plight of Indian farmers in the Huffington Post article From Seeds of Suicide to Seeds of Hope: Why Are Indian Farmers Committing Suicide and How Can We Stop This Tragedy? in April of 2009. Instead of focusing on real solutions or the real source of the problems, she points a lazy finger at the boogeyman Monsanto. I don’t have any particular love for big M (or for capitalism in agriculture in general), but it’s reckless to ignore all of the other issues, as she does in this article (and many others). Shiva writes:

Farm saved seeds were replaced by corporate seeds, which need fertilizers and pesticides and cannot be saved.
Corporations prevent seed savings through patents and by engineering seeds with non-renewable traits. As a result, poor peasants have to buy new seeds for every planting season and what was traditionally a free resource, available by putting aside a small portion of the crop, becomes a commodity.
The shift from saved seed to corporate monopoly of the seed supply also represents a shift from biodiversity to monoculture in agriculture. The district of Warangal in Andhra Pradesh used to grow diverse legumes, millets, and oilseeds. Now the imposition of cotton monocultures has led to the loss of the wealth of farmer’s breeding and nature’s evolution.

The majority of “corporate seed” is hybrid. If farmers save seed from hybrids, the resulting plants will not have the benefit of hybrid vigor. That’s biology, and has nothing to do with corporate greed, patents, or genetic engineering. Hybrids can be grown without fertilizers and pesticides, but they will then yield less. Local varieties yield less without fertilizer and pesticides as well. In other words, hybrid seed grown in farming methods that de-emphasize chemical inputs will do as well if not better than saved seed, assuming that the hybrid is appropriate for the environment (wet or dry soil, etc). Sadly, no one is researching the use of improved seed in alternative farming systems. This is not physics, it’s crop science – which might be why she doesn’t seem to understand it. Some activists argue that we shouldn’t be using hybrids at all, but removing hybrids of all types from the food supply would spell starvation for a lot of people.

There is no corporate monopoly of the seed supply in India. Ironically, things might be better if seeds there was such a monopoly, but seed is often bought from cut rate dealers selling counterfeit (mislabeled or fake) seed. To solve this problem, India would need to adopt some sort of seed certifying system. It would also be useful to have more government research into crop varieties including genetically engineered traits, then distribute them to farmers at low cost, as China does.

Farmers are welcome to continue using local varieties; there is no legal requirement for them to take out loans they can’t afford to buy fertilizers, pesticides, and seed (or larger houses, extravagant weddings, etc). One of the biggest problems plaguing farmers and small business owners all over the world is credit – absurdly high interest rates are a bigger problem than Bt could ever be.

Shiva never asks why “corporate seeds” were snapped up so quickly by farmers (perhaps she thinks they are stupid). Farmers all over the world are buying Bt seed of various species because it works. Bt decreases pest damage without increasing pesticide use. It isn’t a silver bullet, though. Bt only controls certain pests, and the specific varieties the trait is in may or may not be suited for the local environment. The best way to use traits like Bt are to integrate them carefully into an Integrated Farm Management Plan and to put the trait in locally adapted varieties.

To solve the existing farm problems in India – including eroded soil, misuse of fertilizers and pesticides, monocultures, and misuse of Bt – India needs farm extension and price regulation. The farmers surely remember how to grow millet, legumes, and oilseeds, but why would anyone choose to grow those if they could get a higher price for cotton?

Some of these and many other issues surrounding the problem of farmer suicides and Bt cotton in India can be found in a report by IFPRI (International Food Policy Research Institute) in October of 2008. I wrote about the report in November of 2008 in Bt cotton and suicides in India.

h/t Luigi.

 

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One valid argument against GMOs is that big corporations control the tech and can charge the farmers sky high prices for the seed. For a long time, I’ve been saying that I don’t like the system, but if countries want to protect their farmers then they should pass some legislation. Well, it’s happened!

The Maharashtra government has fixed the price of genetically modified Bt cotton seeds at 750 rupees [about US $17.40] for a 450 gram [about 1 pound] packet, it said on Wednesday.

This is the maximum price that seed companies can charge from farmers in the current sowing season, which will start from [sic.] June.

Other main cotton growing states like Andhra Pradesh in eastern coast and Gujarat in western coast have already imposed similar price restrictions.

Maharashtra, the biggest cultivator of the fibre crop, this year began fixing seed prices ahead of the sowing operations in the upcoming kharif season [autumn harvest], under a new government act.

via CheckBiotech