Environment

Why Genetic Engineering is Stranger Than You Think it is

There are not too many words in the scientific vocabulary that have made it to the wordbook of the general public. This month’s column comprises two such phrases from the world of the life sciences which have captured the public imagination. Even if the phrases themselves may not always be familiar, their definitions have made a mark in popular depictions of genetics and the life sciences. These phrases are “genetic engineering” and “horizontal gene transfer”, which are being bandied about routinely in popular literature in medical and environmental contexts.

Often, these phrases have been used with delight by scare-mongers, with limited appreciation of subtleties essential to their understanding and application. They in fact merit a discussion on their meaning, and I’ll use examples where these terms imply processes and phenomena of public interest. It’s not a bad time to raise this issue: it’s been 100 years since a chap called Frederick Twort reported the discovery of a virus that infects and at times “engineers” (rather tinkers with) the genetic material of the infected bacterium.

Genetic engineering

First, the term “genetic engineering” typically refers to a precise, artificially introduced modification of the genetic content of an organism. Usually, the outcome of a genetic engineering experiment – in terms of which piece of genetic material is introduced and where – is predictable thanks to decades of fundamental research into cellular processes involved in genetic modification. At least more predictable than genetic modifications introduced by complex breeding crosses or random generation of mutants, followed by the selection of progeny with desired traits. Even more predictable than the variation in genetic material between the parents and progeny of sexually reproducing organisms such as humans.

In a genetic engineering experiment, an artificially constructed piece of DNA, the chemical entity that forms the genetic material of most known organisms with the exception of certain viruses, of a definite composition is introduced into a recipient cell. In many instances, this piece of DNA is not entirely artificial but is part of the natural genetic material of some organism or the other, but does not quite serve the engineer’s purpose in its natural home. In some applications, this piece of DNA exists as an autonomous unit, out of ‘contact’ with the rest of the host’s genetic material, which is composed of what’s called the chromosomal DNA or simply the chromosome. Here, the introduced DNA is referred to as a plasmid. In some situations, the host cell can lose the plasmid. This typically happens when the replication of the plasmid, which is independent of that of the essential host chromosome, is imprecise: certain progeny may not receive the plasmid, and if this subpopulation of cells are able to grow and divide faster than their siblings carrying the plasmid, it’s only a matter of time before the population of cells is dominated by the subset without the plasmid and we’re back to square one.

Such spontaneous loss of the introduced DNA is considerably less likely if it doesn’t exist as a plasmid but is in fact integrated into the host chromosome, something we can do routinely in many contexts today. It’s plausible that many concerns related to the subsequent transfer of an engineered piece of DNA into unanticipated hosts would also significantly diminish when it is introduced into the host chromosome. Genetic engineering does not refer exclusively to the addition of a new piece of DNA into a cell but also to deletions and other modifications of the endogenous DNA of the host cell. But this is beyond the scope of this article.

We’ve already said many things about chromosomes, plasmids and genetic engineering, but there’s an important question that needs answering here. How much of new DNA gets added to the host in a typical genetic engineering attempt? The chromosome – or the endogenous genetic material – of ‘famous’ bacteria such as Escherichia coli or Mycobacterium tuberculosis comprises about 4-5 million alphabets; that of the brewing yeast about thrice as much; and that of you and me about 1,000 times as much. The 4-5 million alphabets comprising the genetic material of the E. coli and M. tuberculosis bacteria can be divided into 4,000-5,000 functional units known as the genes. This relation of 1 gene per 1,000 alphabets does not quite hold for more complex organisms like us, but that’s for another day.

Anyway, a plasmid that is introduced into an E. coli cell, a famous tool for genetic engineering, is about 0.1% or 1 in a 1,000th of the size of its chromosome. Thus, most genetic engineering attempts involve a relatively modest modification of the host genome.

Horizontal gene transfer

Horizontal gene transfer is a form of genetic engineering that usually refers to a phenomenon that happens routinely in nature. Many organisms, chiefly bacteria, can ‘eat’ DNA from their environments. In most situations, they don’t like the DNA they eat and manage to get rid of them. In fact, many organisms have powerful defence mechanisms that prevent themselves from being invaded by foreign DNA while others are more inviting of these tourists. In other situations, a bacterial population that carries this DNA scores over its contemporaries, and so natural selection favours the maintenance of this DNA. As in the case of a genetic engineering experiment, these pieces of DNA can either stay as plasmids or get integrated into the host chromosome. The extent of genetic engineering that a horizontal gene transfer event can cause can vary from a few genes to several tens of genes that make up the complete genetic material of certain viruses.

What can get horizontally transferred, and who can transfer to whom, is also an important question. A naturally occurring plasmid that’s floating around in the environment can be transferred into a single-celled organism if the prospective host is capable of importing it. It’s a lot harder for segments of chromosomal DNA to be transferred this way, except by direct contact between the donor and the recipient cells or by intermediates such as certain viruses. All of these present powerful constraints to gene transfer. A single-celled organism can, by direct contact, transfer pieces of genetic material to another, if it has the right molecular machinery to do so.

Next month, we’ll see how viruses enable horizontal gene transfer and how this contributed to the development of molecular biology and biotechnology!

Relevance to genetically modified food

Both genetic engineering and horizontal gene transfer are subjects of public debate. Various microorganisms can be genetically engineered to produce molecules, including drugs, of our interest by introducing the necessary genes into them. This is done in industrial practice under carefully controlled and contained environments. Horizontal gene transfer is a major mode of spread of antibiotic resistance in bacterial populations. For the moment, it suffices to know this fact and we’ll discuss this phenomenon in greater detail in a later installment of this series. It’s also a mechanism by which certain bacteria acquire traits that make them virulent. In fact, horizontal gene transfer may be a major mechanism by which bacteria evolve. However, the extent to which this influences a multicellular organism like a human is debatable but certainly much less than in single-celled bacteria.

A contentious area of social relevance that involves both genetic engineering and horizontal gene transfer is GM crops. While it’s probably correct – especially in the face of incomplete knowledge – that the release of a genetically engineered organism including plants into the environment should be carefully regulated and subject to extensive testing, certain arguments against the use of such plants need to be critically evaluated. One argument is the unpredictability of a genetic modification. Another is the possibility of horizontal transfer of the introduced gene to humans.

As we’ve already seen, the outcome of a precise genetic modification is more predictable than exercises in crossing and breeding, a cornerstone of our agricultural practice over hundreds of years. Next, what are the chances of a novel gene present in our (cooked) food entering into our genetic material and causing disease, or be transmitted to our children? This can’t be a lot more than such events happening from the 1,000 trillion non-human, microbial inhabitants of each adult human body! To put things in perspective, living among a zoo of microbes, many of which are in persistent and intimate contact with our cells and with the potential of throwing out DNA, primates have incorporated probably a few tens of foreign genes over the million years of their evolution, and hardly any in recent millennia!

It’s also important to realise that the mere acquisition of a piece of foreign DNA – which is somehow depicted as being “unnatural” – does not necessarily result in an adverse effect on the recipient. And it is a fact that many (if not all) ‘non-GM’ crops have had their chromosomes genetically modified without human intervention by horizontal transfer of genes from infecting viruses! We do not stop eating in any case.

A brief history

Before we conclude this instalment of this series of articles, let’s trace the origins of the discovery of horizontal gene transfer as a mechanism of trait innovation. This can be safely credited to a quiet epidemiologist of the early 20th century called Frederick Griffith. He believed that effective control measures against infectious diseases could be taken only when armed with an understanding of the types of pathogenic bacteria that could be isolated from epidemics. Toward that goal, he was working on variants of the bacterial pathogen Streptococcus, which causes pneumonia (also referred to as Pneumococcus). Some variants of this bacterium cause disease and others do not.

Griffith reported in 1928 that when a heat-killed disease-causing variant of this bacterium was mixed with live but benign versions of the same bacterium, the benign acquired disease-causing traits. This resulted in the conclusion that certain material from the dead bacterium was transferred to the live variants, resulting in a new trait. In retrospect, we’ve come to appreciate the contribution of luck in major scientific discoveries. Not all bacterial types do a good job of taking in and utilising naked DNA from their environment, and today we know that Streptococcus happens to belong to the subset of bacteria which can. Had Griffith’s work been on bacteria of other types, he might have never made this discovery. Later experiments by Avery, Macleod and McCarty showed in 1943 that the material that was transferred was likely to be DNA.

Thus, the discovery by Griffiths was epoch-defining, not merely within the scope of describing a phenomenon or informing control measures against epidemics but also in its future impact in enabling us to learn that DNA is indeed our genetic material, and subsequently establishing the molecular basis of heredity and the continuity of life.

Aswin Sai Narain Seshasayee runs a laboratory researching bacterial biology at the National Centre for Biological Sciences, Bengaluru. Beyond science, his interests are in classical art music and history.