Who’s Afraid of the Big, Bad ORF?

A recent paper in the journal GM Crops and Food has generated an outsized splash in the press, particularly in biotechnology-averse Europe. I won’t reward a muckraking tabloid with a link, but here’s a screenshot that shows the basic theme:

Daily Mail hype.

Oh No, Toxic Genes!

Apparently the genetically modified food crops that hundreds of millions of people around the world have been eating without incident for more than a decade are in fact horribly toxic. But it turns out that the research that triggered this alarm proves no such thing. How did an arcane scientific finding get turned into a completely incorrect, apocalyptic headline? Let’s dig into it like scientifically educated journalists.

If we start by going to the source, we immediately hit an obstacle: there’s the abstract, but if we want to read the paper itself we’re expected to pony up $29. It would probably help a lot if journals made papers about important public policy issues freely accessible by default, but we don’t live in that world yet. Fortunately, journalists have an easy way to get around this: contact the authors directly. The Daily Mail appears to have failed at this, as all of the quotes in their article are from other sources. Other articles on the new work similarly lack any representation by the folks who actually did it.

It’s rare for scientists to blow off reporters completely, but sometimes they can be hard to reach, out of the office until after the deadline, or just uninterested in helping. Perhaps that was the case here. Let’s see. The first author is Nancy Podevin of the European Food Safety Authority in Parma, Italy. When I sent a note to her identifying myself as a journalist and asking for a reprint, she replied minutes later: “Please find the article attached. Please be aware that the content of the article has been incorrectly reflected in recent press articles.”

Not exactly hard to reach. Or reticent.

Alright, let’s dig into the work. Here’s the basic plan from the introduction:

Bioinformatic tools are increasingly being used in the evaluation of transgenic crops. Guidelines, proposed by WHO/FAO19 and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity and toxicity. With this aim, the EFSA GMO Panel has updated its guidance for the risk assessment of GM plants and proposed to identify all new ORFs due to the transformation event. New ORFs are defined as strings of codons uninterrupted by the presence of a stop codon at the insert genomic DNA junction and within the insert. The putative translation products of these ORFs are then screened for similarities with known toxins and allergens.

This is a study done entirely on computer databases, in which the scientists looked for novel open reading frames (ORFs) in the transgenes of modified crops, then checked to see if any of those ORFs match any known allergens or toxins. The existence of an ORF doesn’t prove that it gets transcribed and translated into a stable protein, so we’re still several steps short of reality here, but it’s a useful exercise to define what might be possible. In this case, the investigators are looking specifically at a sequence called P35S, a gene promoter borrowed from cauliflower mosaic virus (CaMV). P35S promotes constitutive (constant) expression of the gene in front of it, so it’s been a popular choice for driving introduced transgenes in genetically modified crops. 54 of the transgenic crop strains currently approved in the US use this promoter.

In its original context, the P35S sequence overlaps with a CaMV sequence called gene VI. That means that the P35S sequence could potentially encode a piece of gene VI. Podevin and her colleague Patrick du Jardin searched the various P35S sequences used in transgenic crops, and identified a couple of ORFs. Remember, this is all on a computer. The paper contains no wet lab experiments showing that these ORFs are actually producing stable proteins in any cell. But let’s assume they do for now.

Translating those ORFs on the computer and searching against databases of known allergens and toxins, the researchers found … wait for it …

Nothing.

That’s right, these hypothetical proteins that might not even exist don’t match any known allergens or toxins anyway. They did an additional test that sets the bar lower, and found that by this standard, one of the putative proteins might be allergenic. But it’s a stretch:

The vector support machines (SVM) in AlgPred indicated on the basis of the dipeptide composition that the ORF that encoded part of P6 might have some allergenic properties. The sensitivity and specificity of this method is 88.87% and 81.86% respectively and should therefore always be used in combination with other tools.

All the other tools, though, found no allergenicity. Having established that there’s essentially no human risk, the authors speculated that there could still be effects on the plants themselves, such as plant stunting and late flowering. Considering that the entire point of most crop biotechnology is to increase yields, it seems unlikely that this applies to any of the current commercial strains, but product developers should probably keep an eye out for it in future strains. Either that, or they could simply follow the authors’ final advice:

The -343 variant [of P35S], identified by Odell and colleagues, contains all of the necessary elements for full promoter activity and does not appear to result in the presence of an ORF with functional domains, rendering it and its related variants the most appropriate promoter variants for avoiding unintended effects.

To put this all in context, plant viruses commonly infect all sorts of crops. One survey (PDF here) found CaMV and its colleagues widespread in numerous types of produce. We’re already eating huge quantities of plant viral proteins – not hypothetical ones, real ones – all the time. If there is an ORF from CaMV gene VI being expressed as a protein in transgenic crops, it’s likely one you’ve digested before, even if you eat exclusively organic food.

So there you have it. This was a research paper that used bioinformatic methods to ask yet again if GM crops are any more dangerous than non-GM crops. It ended up adding to the large pile of established data showing that they are not. Through what can only be described as laziness and ideologically blinded reporting, it served as a handy news hook for stories claiming exactly the opposite.

Update 2013.1.22 12:49: After writing this post, I saw this discussion thread, in which several smart folks make essentially the same points.

Update 2013.1.23 7:07: After Dr. Podevin graciously sent the paper, I pinged her with a few additional questions about the work because, well, that’s what I do. I received her reply this morning:

I have been overloaded with requests for the paper and as I am no longer working at EFSA it is difficult for me to react.

To answer you[r] questions I am not planning to work on this topic further. It is difficult how headlines on toxic genes in GMOs can be seen to be linked to our paper as we concluded that there are no indications for toxicity of the encoded protein. This virus has been infecting Cauliflower and related plants with no recorded health effect.

It should also be noted that this promoter [has] an ORF overlaps with Gene VI but that no functional gene is present. So in most cases this gene fragment will not lead to the production of a protein.

Update 2013.1.24 15:06: I’ve now received a note from the journal publisher as well:

I am the publishing director at Landes Bioscience – and for GM Crops & Food. Thanks for your excellent piece which was just brought to my attention. Would also quickly like to note that we have now made this paper OA, ie, freely available to anyone who wants to download and read. [link]

12 thoughts on “Who’s Afraid of the Big, Bad ORF?

  1. Mary

    Thanks very much for looking into the real evidence. This is really helpful to combat TEH TOXINZ1!!!1 claims.

  2. Mike

    Alan,

    Thank you for the effort you’ve put in here. I am an analytical type of guy who knows next to nothing of biology (let alone biochemistry or biotech) and this business with GMOs confuses the heck out of me. I tend to believe peer-reviewed science above hype, but my background isn’t such that this science is really intellectually accessible to me in its raw form. On the other hand, the media is so full of opinions by experts and non-experts on this (and other important topics) that I am a bit numb and distrustful of anything that doesn’t clearly and concisely link back to sources I find credible. Your blog post is a step in the right direction, but I think it would benefit from briefly covering some of the bio basics as part of the discussion, in order to allow the educated reader to understand what it is you are drawing out of the undying references. This is a challenge for a journalist, of course, on this subject and many more.

    Respectfully,

    Mike

  3. Pingback: Actually, That New Study Does NOT Prove That Genetically Modified Food Is Horrible For You | The Las Angeles Times

  4. Ryan

    THANK YOU SLASHDOT COMMENTS!

    Great read. Wish I understood more of it but I still feel a little smarter and a lot better informed about those headlines.

    I was a produce guy for years, stocking conventional and organic produce in California markets. In the late 1990s when organic stuff first caught on and the anti-GMO jihad began, I quickly became jaded towards the media in this area. The reason nearly 7 billion people are able to exist on this world today is due to genetically modified foodstuffs. The only way we will be able to continue supporting the 10 billion plus global population that is project to exist in my lifetime is to continue getting efficiency gains. Advocating organic food is like advocating for massive global starvation in poor countries. I’m not a fan.

    Anyways, thanks for the analysis and keep it coming. :)

    -Ryan

  5. Pingback: Regulators Discover a Hidden Viral Gene in Commercial GMO Crops - SLUniverse Forums

  6. Dogctor

    Not a virologist and wont play one on the internet. Are you Mr. Dove?

    I do note in your “take -down” omission of relevant information.

    1. Unlike allergy tests for atopy, there are no in vitro food allergy tests that mean a whole lot in real life. A double-blind placebo-controlled food challenge is still the gold standard of allergy testing, rather than any blood test or a bioinformatics search of homology.

    2. Gene VI Is an Inhibitor of RNA Silencing
    and could lead to aberrant gene expression in GMO crop plants, with unknown consequences

    2) Gene VI Is a Unique Transactivator of Gene Expression
    Multicellular organisms make proteins by a mechanism in which only one protein is produced by each passage of a ribosome along a messenger RNA (mRNA). Once that protein is completed the ribosome dissociates from the mRNA. However, in a CaMV-infected plant cell, or as a transgene, Gene VI intervenes in this process and directs the ribosome to get back on an mRNA (reinitiate) and produce the next protein in line on the mRNA, if there is one. This property of Gene VI enables Cauliflower Mosaic Virus to produce multiple proteins from a single long RNA (the 35S RNA). Importantly, this function of Gene VI (which is called transactivation) is not limited to the 35S RNA. Gene VI seems able to transactivate any cellular mRNA (Futterer and Hohn 1991; Ryabova et al. 2002). There are likely to be thousands of mRNA molecules having a short or long protein coding sequence following the primary one. These secondary coding sequences could be expressed in cells where Gene VI is expressed. The result will presumably be production of numerous random proteins within cells. The biosafety implications of this are difficult to assess. These proteins could be allergens, plant or human toxins, or they could be harmless. Moreover, the answer will differ for each commercial crop species into which Gene VI has been inserted

    The end.

    1. Alan Post author

      Thanks for the drive-by. Pro tip: try Googling someone before drawing conclusions about their qualifications.

      As for your arguments, if Gene VI is so toxic, why aren’t we all dead already? CaMV infection is widespread in cruciferous vegetables, as I pointed out in the post. That includes organic vegetables and heirloom varieties grown in your back yard. If you eat broccoli or any of its kin, you’ve eaten cells expressing this gene – not hypothetically, not traces of a fragment of it, but for real and in large quantities.

      You also seem to have missed (perhaps willfully) the main point of the post. The paper that triggered the latest round of GMO-bashing actually concluded precisely the opposite of what the “news” stories about it claimed. I looked into how that could’ve happened, and the only reasonable conclusion is that the folks writing those stories deliberately misinterpreted the science in order to mislead the public.

    2. Karl Haro von Mogel

      Great post, by the way. It is good to see people coming to the same conclusions independent of one another.

      The original source for the claim is “Independent Science News” at a small NGO called The Bioscience Resource Project, run by Jonathan Latham and Allison Wilson. Here is where it all began:
      http://independentsciencenews.org/commentaries/regulators-discover-a-hidden-viral-gene-in-commercial-gmo-crops/
      And if you check, it is also where the good Dogctor copied and pasted their arguments from. So not only were they missing the point they were also plagiarizing.

      I agree with Alan that it seems that someone deliberately misrepresented the science to make a scare story, and fingers should be pointing at Latham and Wilson for this affair. Their piece made exaggerated claims about toxicity, and purposefully left out the conclusions of the study in question. It’s as if they expected no one to actually read the study. Well, certainly not the Daily Mail! :)

      1. beta barrel

        Thank you for posting the original source that Dogctor was trying to use as his own. Anonymous posted this link last night and I assume he scooped his “argument” after that.

        It should also be noted that Latham, a virologist, has “published papers in diverse fields” and “regularly presents” at conferences.

        Seems legit.

        http://www.bioscienceresource.org/about-us/our-staff/

      2. Mary

        Yeah, people may not be familiar with Latham and Wilson. But they have a pattern of wild and exaggerated claims to support an ideological position that the environment causes all disease, and that genes don’t matter. It’s led to several smackdowns by regulators, genetics folks, science writers, and science bloggers in the past.

  7. Katie

    Hi Alan,

    This was a great read, thanks for putting so much time into it. I’m pursuing my biology (botany! ftw!) undergrad right now, so I don’t have a real nuanced assessment of GMOs. My understanding is that there wasn’t a lot of lab testing prior to them being released into grocery stores, so how do we know that they’re not toxic? Just because we’ve been eating them and everything appears to be fine? I tend not to by into the GMO hype, and that seems reasonable enough, but isn’t very scientific. Would you mind expanding on that for me? Thanks.

    1. Alan Post author

      Thanks, glad you enjoyed it. The whole GMO story would take at least another post or ten to dissect, as the story tangles up a lot of complex issues. At the extreme ends, both opponents and proponents of the technology often take advantage of that complexity to hide information they’d rather avoid talking about. Speaking strictly as a biologist, though, it’s very hard to find evidence that biotech manipulation of crop plants is inherently any more dangerous than the blind genetic modifications humans have been performing on plants and animals for 10,000 years. Nobody ever did a randomized controlled trial to show that heirloom tomatoes are safe, and nobody seems concerned that organic farmers spray Bt toxin proteins all over their vegetables.

      That said, the main company that owns most of the GMO patents has exhibited exactly the kind of behavior one might expect from a huge corporate monopoly with immense power over an entire industry. Meanwhile, modern agriculture in industrialized countries relies on a Byzantine system of government welfare that stifles innovation and distorts the global economy. GMOs certainly didn’t cause that situation, but they’ve become a lightning rod for it.

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