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Author Topic: viral genes scary?!
Rachael-
Ludwick
Elite Hybrid
Posts: 125
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Post viral genes scary?!
on: January 22, 2013, 06:29
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So I came across this fairly hyped and breathless story: http://independentsciencenews.org/commentaries/regulators-discover-a-hidden-viral-gene-in-commercial-gmo-crops/

The Daily Fail is of course spreading this news as a hidden "toxic" gene in GMOS (!) (no link because ugh).

The referenced research is this: http://www.es.landesbioscience.com/journals/gmcrops/article/21406/?nocache=1759778285

It seems a fair bit more measured. But honestly I don't really understand what it's getting at from the abstract. Any thoughts?

Karl Haro-
von Mogel
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Posts: 241
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Post Re: viral genes scary?!
on: January 22, 2013, 07:29
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Ah yes, Jonathan Latham, from whom we get fabulous efforts at DNA Denialism: http://blog.openhelix.eu/?p=6369
It appears that Latham and Wilson's anti-biotech blogging project, the Bioscience Resource Project (which would be a fabulous idea if it was in fact a project for generating resources as described) has morphed into "Independent Science News", which has brought us fabulous news-like entities like open letters supporting Seralini: http://independentsciencenews.org/health/seralini-and-science-nk603-rat-study-roundup/

And as usual, they misrepresent the paper that just came out. In the beginning of their 'news' piece they claim that the gene is dangerous, but only people who have access to the paper can check the actual details.

The basic idea of the paper is they compared the different versions of the Cauliflower Mosaic Virus Promoter (CaMV) that many different GE crops use to drive expression of transgenes, and compared their sequence to a viral gene known as P6 (or gene VI). They found that there was sequence similarity between the two, and for longer versions of the CaMV promoter used by genetic engineers, there may be a piece of an open reading frame (ORF) that remains. So they looked into whether there were any potential toxic or allergenic proteins that could be produced from this open reading frame. From the discussion:

“As no scientific literature has been reported on any allergenic properties of CaMV and no similarities have been shown to know allergens, it can be concluded that the P6 protein is most likely not an allergen. In addition, a toxin database was constructed, and no significant sequence similarity with the P35S variants was detected. These data suggest that the P35S variants do not contain ORFs that encode for proteins that have allergenic or toxic properties.”

“In conclusion, different P35S variants are in use to express proteins in transgenic plants. Here, we detailed the overlap of P35S with the coding sequence of gene VI. Our bioinformatic analyses indicated that no ORFs are present in the P35S that are similar to known toxic and allergenic proteins.”

So right off the bat, the claims of Latham and Wilson are off-base. The authors next look at whether there is any potential that the open reading frame could be expressed in plant cells and lead to unintended consequences. They presented a flowchart to summarize their findings, which I have copied here. In summation, they found that the risk was low, and only under very specific conditions would it possibly be expressed. One of those conditions is that the plant would show symptoms of P6 expression, which includes leaf chlorosis (yellowing), vain clearing, plant stunting, late flowering and reduced fertility. These are traits that would immediately be recognized by a plant biologist working with GE plants.

In contrast, Latham and Wilson declare that the only sane reaction to this study is the following:
"The only course of action consistent with protecting the public and respecting the science is for EFSA, and other jurisdictions, to order a total recall. This recall should also include GMOs containing the FMV promoter and its own overlapping Gene VI."
To this I say, since Latham knows that 'environment must be the entire cause of ill health,' I think they should more closely examine what factors in their environment lead them to mistake foolishness for wisdom. Maybe it was something they ate, or some variant of a powdered fruity drink that they may have imbibed.
Image

Rachael-
Ludwick
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Posts: 125
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Post Re: viral genes scary?!
on: January 22, 2013, 07:39
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Sense About Science is also answering questions about this paper (and the news stories on it).

So what does P6 do ordinarily?

MaryM
Elite Hybrid
Posts: 436
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Post Re: viral genes scary?!
on: January 22, 2013, 07:52
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I don't have access to the paper, but my first thought was that ORF ≠ protein. There are plenty of stretches of nucleotides that could be technically an open reading frame, but there's no chance of them becoming actual proteins. Functional ribosome binding site on the transcript (is there a transcript?), translation start site, starting methionine, etc.

If there was CaMV infection you could get this protein expressed. But that would be because of this virus infection. Are they calling for world-wide testing for CaMV presence in anything and banning those foods?

EDIT to add comments from others:

RT @jonathandgjones: http://t.co/3hWwJ6ay cauliflower mosaic virus gene VI homology in 35S promoter- so what, if protein not expressed?

RT @alandove: .@r343l @CarbonCounter_ Organic crops are also loaded with viral sequences. As are we. @JoannaBlythman

Karl Haro-
von Mogel
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Post Re: viral genes scary?!
on: January 22, 2013, 08:20
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From what I understand, P6 is a multi-functional protein that is involved in virulence and expression of closely-packed viral genes. Normally, the ribosome will disassociate from an mRNA when protein translation is terminated, however, gene VI appears to make the ribosome start translating the next gene on the messenger RNA, which can be immediately after the end of the previous gene. Some viruses try to produce proteins so fast that they put many protein-encoding ORFs on the same mRNA to try to make an end run around the normal cellular limitations of their hosts.

Latham and Wilson's description of the basic function of the gene appears to be correct, however I would have to check up on their references to be sure that they are not exaggerating other abilities of the gene that they report. For instance, they opine about possible human health consequences, when this is a plant virus - not a human virus - and even if it had some abilities in human cells it would first have to get in the cells intact. In other words, forget the human digestive tract, stomach acid, and protein-digesting enzymes.

There is another practical way of thinking about this issue. Cruciferous vegetables such as Cauliflower, Broccoli, Brussel Sprouts, etc, get infected by the complete, intact Cauliflower Mosaic Virus, and about 10% of these vegetables that we buy in the store are infected with this virus. If, as Latham and Wilson suggest, the mere possibility that a fragment of a gene similar to viral gene VI is cause for a total and complete recall of every GMO containing it until more research is done, then therefore all cruciferous vegetables must be recalled and a moratorium on their growth and sale put in place to prevent any possible unintended consequence from the expression of the functional, intact viral genes that CaMV is producing in these cells. If their description of the risk of harm is correct (and I argue based on the paper that started this whole affair above that it is not), then they must therefore agree that broccoli et al. should be banned until further notice. Consistency demands this, and if they disagree and say that crops containing entirely functional and complete CaMV viral genes are ok to eat, then they should abandon their latest foray into sensationalist claims.

Rachael-
Ludwick
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Posts: 125
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Post Re: viral genes scary?!
on: January 22, 2013, 08:30
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Well, that's certainly true. A similar concern gets thrown about for Rainbow papaya.

But (to put on the devil's advocate hat) the possibility mentioned in the abstract seems to also include an unexpected protein, seemingly different from either the base plant or the CaMV (since they were specifically looking for allergens). Or am I misreading?

(Note: I don't really think this is a real concern, but trying to find all the possible objections or concerns and what they really mean).

Karl Haro-
von Mogel
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Post Re: viral genes scary?!
on: January 22, 2013, 08:43
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Are you talking about the "variants" mentioned in the abstract? If so, they are talking about pieces of the CaMV promoter that are different lengths. Essentially, different transgenic constructs using the CaMV promoter do not use the exact same-sized piece of it. The paper did not say that there were any new proteins produced, or that any of the open reading frames were expressed. They were just talking about open reading frames, which are sections of DNA between start and stop codons, basically places where if an mRNA was produced it could be translated into a sequence of amino acids by the ribosome. It is a decent paper that outlines a set of nested "IF" logic statements, and all but one path leads to no consequence for the plant. However Latham and Wilson turn that into something completely different.

Rachael-
Ludwick
Elite Hybrid
Posts: 125
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Post Re: viral genes scary?!
on: January 22, 2013, 08:53
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I don't disagree the news stories are turning it into far more than it is. Just trying to figure out *how* they turned it into that.

Mentioned in the abstract: "No relevant similarity was identified between the putative peptides and known allergens and toxins, using different databases."

That's where I was getting the idea of allergies from. Presumably if CaMV isn't thought to be allergenic (and as you note it's in lots of plants we eat all the time), you wouldn't expect parts of it in a plant to express something allergenic, assuming it's expressing something similar to what CaMR already does (I hope that makes sense). On the other hand, if you're someone who worries that GE is "messy" and that novel and undetected proteins must be created by the process, this reads like "we don't know that it isn't allergenic" fears.

(Sorry to be obtuse, but I'm trying to get a handle on how a seemingly dry and not terribly surprising paper -- i.e. there's no unexpected effects -- gets turned into "sky is falling" news stories.)

Bernie-
Mooney
Wild Accession
Posts: 2
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Post Re: viral genes scary?!
on: January 22, 2013, 10:24
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Thanks Rachel and Karl. This came in over my digital transom the other day and I was going to post a question about it.

MaryM
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Posts: 436
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Post Re: viral genes scary?!
on: January 22, 2013, 10:42
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Is there any evidence anywhere of a plant virus impacting human health?

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