Genetic Engineering in our Daily Lives (pt. 2)

In the last installment, we discussed the history of genetic engineering and how we got from the discovery of DNA’s structure to approximately 1980. The focus of this installment will be to get us to the present moment, and in so doing to shed some light on and thereby demystify the process of making genetically engineered organisms somewhat. This isn’t meant to provide you with the technical understanding required to do genetic engineering yourself – that is the focus of some peoples’ whole careers – but to help you to in general terms understand what goes into foods or other items that have been genetically engineered, how they are different from their un-engineered counterparts, and also to provide you with a framework to understand the complexities that are inherent in some of the issues that surround regulating genetically engineered organisms in our foods, medicine, and so on.

Vocabulary of Genetic Engineering

Just like last installment began with a discussion of GE and GMO and why it is important to distinguish between the two, we need to start now with discussing some vocabulary. Unlike last time, I just need to familiarize you with some terms, because I can’t really avoid using them and keep true to my subject matter. This glossary assumes a high school level understanding of Biology; if that’s not where you’re at, feel free to ask for clarification and I will endeavor to provide it.

  • DNA, RNA and Protein: These are the three basic steps in what is called the “Central Dogma” of molecular biology, or the three steps in the normal transition of genetic information into functional information. It normally works that DNA is kind of like a cell’s 4D blueprints, kept behind protective barriers inside the nucleus so that it wont be altered, because in the DNA is stored the final information on all (or much of) of a cell’s inherent programming. That inherent information is then translated into a an RNA-based “working copy,” and then that is translated into a protein. Protein is the actual actor in this process, normally; all of the other steps are just there for quality control, basically. This is all oversimplified, also, but that is the basic overview of the process.
  • cis- and trans-genic: We see these prefixes thrown about in all sorts of settings, these days. They got their start, for the most part, in chemistry. In that context, cis- meant “on the same side of the molecule [as each other]” and trans- meant “on the opposite side of the molecule [from each other]”. In molecular biology, they are used a little differently. They are, rather than descriptions of chemical structure, instead a description of two major types of genetic engineering. Cis-genic engineering is the engineered alteration of an organism by adding DNA from another population with which that organism can normally interbreed – so, adding wheat DNA to wheat, corn DNA to corn, fruitfly DNA to fruitflies, and so on. Trans-genic engineering is the engineered alteration of an organism by adding DNA from some other organism the source cannot normally breed with – so, adding jellyfish DNA to tuna, or fish DNA to tomatoes, or bacterial DNA to plants.
  • Replication, Transcription, Translation: These are three cellular processes that are very important to genetic engineering. Replication is the process that DNA undergoes in order to reproduce accurately and be sorted into daughter cells. Transcription is the process whereby DNA is turned into readable RNA, often with the intent to turn that RNA into protein. Translation is the last step, the use of an RNA template to drive the creation of a protein with a defined sequence and structure. We name these differently because, although they sound quite similar, they are in fact completely distinct processes in the cell that are each incredibly complicated.
  • Promoters, Enhancers, and Inhibitors: These are three major kinds of genetic sequences that govern transcription. The first of the three directs your cell to transcribe the DNA next to it, at a specific time and under a specific condition. This direction can be as general as “all the time, everywhere” to “in between 8 and 14 years of age inside the pituitary gland” or “whenever I eat lots of sugar”. The second of the three, Enhancers, are basically there to amplify transcription at a certain place and time. Promoters establish an on/off level of transcription, called a “basal” level, where Enhancers tweak that by as much as 100- or 1000-fold in a given place, at a given time. Inhibitors do the opposite. They turn off or turn down the transcription of a certain gene at a certain time/place/condition, either back to the basal level or off entirely.
  • mRNA, tRNA, rRNA, and ds/ssRNA: RNA is a funny critter. It plays many different roles in the cell, which means that it basically plays some part in every role in the transition between DNA and protein. mRNA (messenger RNA) is the “working copy” mentioned earlier, it carries the actual genetic information that is then turned into a protein. rRNA  (ribosomal RNA) is part of the scaffolding on the cellular machinery that drives translation, which is also made up of quite a bit of protein. tRNA (transfer RNA) is the carrier and gatekeeper for the building blocks that make up your proteins, and it is tRNA that does the grunt work of making sure that the right amino acids are inserted in the right sequence into the growing chain that is a protein. The last two kinds, “ds” and “ss” are chemical categories, being abbreviations of “double stranded” and “single stranded”. All normal, working RNA in your body is single stranded; if RNA is ever bonded into a double stranded state, your body basically recognizes it as broken and breaks it down to its constituent nucleotides on the spot, to reclaim the spare parts that would otherwise be wasted.

Glossary of Genetic Engineering Schemes

Rather than go through each of the hundreds of kinds of genetically engineered organisms out there, I’m going to focus on giving you a basic understanding of the various schemes and strategies used in genetic engineering and how they each affect the organism, so that you can more faithfully analyze and more completely understand what it is you’re looking at, when you’re reading an article about genetically modified corn or rice or sugar beets, later on.

Classical trans-genic engineering

This is what most people think of, when they think of genetic engineering. Classical trans-genic engineering is the addition to an organism of trans-genic DNA – so, the addition of something like the DNA of a jellyfish into the DNA of a rice plant. This has been used most often to move resistance traits – genes that confer resistance to things like drought, heat, Roundup, or infestation by certain insects – from one plant to another, so that you can easily and (relatively) swiftly make a plant that is both nutritious and resistant to certain herbicides, or that is both fast-growing and resistant to certain diseases like blight or wheat rust. It is done by taking an entire gene (which includes the part that is translated, a part that tells it when and where to turn on, and usually a couple of parts that helped the gene be moved by the scientists in the first place) out of a host organism, putting it into a mechanism of some kind (the mechanism varies with the organism), and using that mechanism to insert it whole-cloth into the target organism. Sometimes this has to be done several times, in order to insert “helper” genes that improve the function of the primary gene, or to transfer additional traits to the target organism.

Once the DNA has been inserted into the target genome and the target has reproduced a few times, the inserted DNA is chemically indistinguishable from the target’s own DNA. That is because, for all intents and purposes, it is the target’s own DNA.

Regulation of transcription

Sometimes, one doesn’t want to add something new to an organism, but just to get rid of something that’s already there or to make it more/less prominent. Usually, this is done by regulating how often and at what time transcription of a given gene occurs. You can do this by replacing a gene’s promoter, by altering how its enhancer interacts with it, or by allowing an inhibitor to either work or not work on it. Only rarely do these alterations involve the addition of transgenic DNA, since the cell wouldn’t recognize that anyway; they usually involve the alteration, substitution, addition or deletion of existing elements, the effect of which is to simply change how the pieces that make up an organism interact with each other.

Regulatory elements are usually fairly specific to the organism and its close genetic relatives, in the same genus or taxonomic family. So, in altering something that occurs in wheat, you almost never need to do anything that could ever affect the transcription of any other genes of any other organisms, anywhere.

Regulation of translation

Another step in the process where engineering can be targeted is translation. In controlling how and when a gene becomes a protein, a gene’s effect can be very precisely controlled, so that in certain places and times its effect is increased while in others it is diminished or negated entirely. This is also often called by another name – RNAi, or RNA interference – because one kind of translational regulation involves inserting a nonsense gene into an organism, which will affect the way a target gene is translated. This works because RNA, if paired with some other strand whose sequence is its mirror image, will bond to it and end up being double stranded much like DNA. Unlike DNA, though, when RNA becomes double stranded it essentially becomes useless. Cells have the ability to identify dsRNA, and thereafter to degrade it without translating it, seeing to it that the original gene never becomes a protein in the first place.

When performing RNAi, nonsense genes are inserted into a target genome. These nonsense genes do not and cannot become genes themselves, as they lack the sequences to kick start the machinery of translation, and so the only thing they are capable of doing is bonding to their complementary not-nonsense target gene, and inhibit its function.

Cis-genic engineering

Finally, more recently a form of genetic engineering that uses genes from other members of the same species has come into prominence. This essentially speeds up the natural processes of cross-breeding, and targets it to a specific purpose, by using the organisms own genes to give it some property or trait that it didn’t have before. This is easier and more directed than selective breeding, because through other molecular biological procedure we can assess whether the transformation was a success and to what extent, without needing to go through several generations of growth to check for the inclusion of dangerous, deleterious recessive genes.

Popular varieties of genetically engineered organisms

Genetically engineered products have a profound place in our daily lives. When we think of “GMOs” (or, as discussed earlier, the more appropriately named “GEOs”) we think of food, but it doesn’t nearly stop there, and it’s not limited to just the varieties covered in popular media or on the internet. This section is devoted to dispelling that misunderstanding, by rounding up examples of the most popular, widespread kinds of GEOs and a few types that, though uncommon are indicative of some important process or principle.

Genetically Engineered Crops

There are myriad varieties of genetically engineered foods, but most are just variations on a few basic themes. A few are unique, in either what they are intended to do or how they do it. The themes are the variations are:

  • Insect-resistant crops (“Bt” or “killer” crops): One of the two most common types of genetically engineered crops, engineering for insect resistance is one of the most effective and widely utilized forms of engineering on the market today. It relies on a natural toxin produced by a bacterium, Bacillus thuringensis, which kills many insects when it is consumed by them and thereby protects the plant into which it has been engineered from persistent colonization by that insect. This same insecticide, in another life, plays a very different role. When simply sprayed over crops and not engineered to be produced within their cells, it is one of the most common organic pesticides in use today. It is engineered into plants by using transgenic methods, as discussed above.
  • Herbicide-resistant crops (RoundupReady, etc): The other most common kind of crop is one that is resistant to herbicides. That on the surface seems rather counter-intuitive, but the reason is quite simple. When one grows grains of pretty much any kind, the most common weed that grows alongside them and thereby impedes their growth is the wild variety of that same grain, which is usually a form of parasitic grass. This is true of corn, wheat, rice, oats, and other crop species. Herbicides like Roundup (a glyphosate-based herbicide) normally kill both the crop and the weed, so they have to be sprayed carefully around the edges of a field or replaced with other herbicides that do the job but are usually much more toxic and much less effective. By making the crop resistant to glyphosate, a farmer can use that herbicide on his crops without fear of damaging them. The gene for glyphosate resistance comes from a soil bacterium called Agrobacterium sp. strain CD4, and is introduced into crop genomes using normal transgenic methods.
  • Disease-, Drought-, Cold- and Heat-Resistant crops: Another few common kinds of crops are those that have been made resistant to some naturally-occurring condition or disease. These are usually made resistant by first identifying the exact protein that the disease or condition affects first, and then finding an alternate form that is resistant. A good example of this is that of a drought-resistant rice, which was developed by splicing a gene called Deep Rooting into a commonly cultivated variety of rice used throughout Asia. Other examples include a blight resistant potato variety, a fungus resistant wheat variety, and variety of corn that is resistant to persistently dry conditions. The gene, which comes from a different, wild variety causes the rice plants roots to grow deep and straight down, as opposed to shallowly outward as they normally do. These are developed by numerous different techniques, some of them cisgenic and others transgenic in nature.
  • Yield Size and Crop Nutrition Improvements: Finally, there are those varieties of crops that are altered in order to simply improve either the quality or the quantity of the crops of edible fruits or grains that are harvested from the crop. These come in a number of specific forms, from Flavr Savr tomatoes that lose flavor more slowly by using RNAi techniques, to rice varieties that improve yield by growing shorter stalks and larger heads of grain, to the much talked about Golden Rice that uses genes from the daffodil and from a soil bacterium in order to produce beta-carotene and thereby helps prevent malnutrition in the third world.
  • Outcrossing and Breeding Control Mechanisms: This final class of biotech merits a mention, but this also comes with a special note. In the 1990s, this kind of crop – called a “terminator” crop – was under development, but due to public outcry it was never finalized or released for public consumption. These varieties are meant to deal with one hypothetical problem identified by environmental advocates – that is, they were worried that transgenes present in engineered crops would be bred into the wild type neighbors of those crops and render them inadvertently transgenic. Even though this concern has been shown to be only hypothetical, multiple companies including Monsanto and Dow developed crop varieties that were unable to produce viable pollen or seeds except in the lab, thereby rendering it incapable of outcrossing. This would have legitimately burdened third world farmers who would not be able to replant any of their cultivated seed from year to year, however, and so development on this variety was stopped before licensing was even sought for its public cultivation.

Genetically Engineered Medicines

One other common reason we employ genetic engineering is to produce medicines. Previously, when a protein or some other gene product is found to be a useful medicine, large varieties of the source organism would then have to be cultivated in order to extract the medicine from them. Eventually, we learned that we could often use bacteria or yeast to do that grunt work more cheaply, more ethically, and more effectively, by programming the aforementioned micro-organisms to produce what we wanted and then cultivating them instead. Some common medicines that we produce in this manner include insulin (previously extracted from horses), follistim (a fertility drug), albumin (used as a safe filler in a number of medications), antibodies, and vaccines. Instead of breeding whole, infectious viruses and then attenuating them with heat or chemicals, which is a faulty process that sometimes results in inadvertent infection, we can use genetic engineering to create a vaccine that contains only a small, non-infectious part of the virus and none of its infectious DNA/RNA, so that it provokes an immune response and thereby confers immunity but has absolutely no risk of infection.

Genetically Engineered Animals

Another growing area of research has been in the creation of genetically engineered varieties of animal. Leaving aside the countless varieties of engineered organism that are created for research purposes (such as fruit flies that are modified in a particular way, or mice that are modified in a particular way), there are a few varieties that have been created as an end product, meant for final use in their modified state. None of those varieties have been subjected to the process for being approved for human consumption, so there is no such thing as genetically engineered meat or milk or fish in our food supply right now, but they have been developed for other purposes. A variety of mosquito has been developed that can only successfully breed under peculiar laboratory conditions, and will soon be used to fight Malaria (and other insect-borne diseases). A variety of fish has been developed that uses the presence or absence of a visible glow to advertise whether water is clean, so that it is easier for environmental scientists to rapidly detect toxins in the water supply. More varieties of genetically engineered animal are under development, or are being researched with a mind for further development in coming years. Mostly, this is for the same reasons we develop any other GEO – because someone or everyone finds it useful. A tsetse fly that kills other tsetse flies and stops the spread of Sleeping Sickness, a mosquito that fights Malaria, a fish that fights water pollution, all are attractive prospects because they all benefit the public good, in addition to any varieties which might be developed for profit-making or other commercial purposes.

All of this leads us to part 3, The Controversy, which will be released soon. But in order to truly understand that, you needed to have all of this background material. I hope you’ve understood everything up to this point, but if at any point I’ve been unclear please ask for additional information or clarification and I;ll do my best to help. Thanks!

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