Evolution’s Usual Suspects: 1. Plagiarizing Wizards

Our Chimaeric Evolutionary Roots: The Primordial Crimes That Birthed Us

In my last post (“Cavemen in Your Genes“), I described the idea that this bizarre creature we call human (and indeed much of life on earth) is a lot like Frankenstein’s monster, a quilt of many disparate parts patched together by chimaeric forces of evolution. We saw evidence in our genes for hanky-panky between modern humans and Neanderthals (which were once thought to have been our ancestors, but are now known to have been a different species altogether).

But our inter-species promiscuity is the least interesting or tortuous aspect of our pedigree. And I’m afraid I have bad news about our heritage: our ancestors were victimized by and involved knee-deep in a primordial crime syndicate billions of years old. The severity of misconduct spanned the gamut from relatively petty purse snatching or grave robbing to forced entry, kidnapping and all-out hijacking. It’s a crime drama billions of years in the making and written in the tome of our genes.

Plagiarizing Wizards and Grave Robbers of Old

It all began in some backwater lagoon or hydrothermal vent in the multibillion-year depths of Archaean time, when a bacterium found it in its capacity to grab what was not its own to take. Since then, bacteria have become the most accomplished plagiarists of all time. They are unscrupulous scoundrels that feel no remorse nor pangs of conscience (nor anything at all, given their lack of a complex nervous system or nerves of any kind at all) at taking other’s writings and incorporating them into their own manuscripts, all without assigning proper credit.

A cross-section image of a bacterium. Note the red knot of material in the center. That is the coiled mass of its DNA, in a region called the nucleoid. (Image: LadyofHats)

I’m talking about horizontal gene transfer of DNA. Back up a bit. The long thread of a creature’s DNA molecule is like a wizard’s scroll of spells (others have used the analogy of a blueprint that contains the instructions for the manufacture and maintenance of an entire organism, including instructions for the proper order of reading of the blueprint — but the magical metaphor is more fun and colorful, and nearly equally applicable, so long as we are careful not to take it too literally, for there’s no real magic here).

So, with disclaimer in place, DNA is a veritable compendium of incantations (genes and operons, which are like powerful words and sentences composed of combinations of a few molecular ‘letters’) that can be invoked to create useful machines (proteins, enzymes) when they are read (by the cell’s RNA polymerase molecules) to accomplish any task necessary for the creature’s survival. For example, there are passages in this book of magic that allow the creature’s cells to disintegrate poisons or to convert useful food molecules into energy or to build outboard motors to propel it away from danger or toward new feeding grounds.

A section of a DNA molecule, 12 links (nucleotides) long. Genes consist of similar (though usually considerably longer) sections of DNA.

The cell accomplishes its wizardry by invoking one of its minions — a little molecular device called RNA polymerase — to read entries from the scroll of DNA, and then the ‘spoken’ words of the spell (in the form of RNA molecules) are translated into useful machines by other minions called ribosomes. Thus are the micromachines called enzymes created from the DNA spell book for use by the cell.

The magic of the translation of RNA (the long diagonal string scrolling to the left) into a protein (the chain that grows slowly upward at the center of the image as amino acids are added to it) at the ribosome (the big irregularly shaped structure composed of green and yellow subunits). The blue objects that zip to the center of the ribosome and then zip away are T-RNA molecules, whose job it is to ferry amino acids to the site of the ribosome and donate their amino acid to add to the growing protein chain. When the protein is completely assembled, it is released from the ribosome and goes off to accomplish whatever task it was constructed to perform. (Image: Bensaccount)

Over millions and billions of years of time, bacterial wizards have written (by the gradual accumulation of mutations that rewrite DNA) huge troves of such magical spells in response to pressures or opportunities presented by their environment (e.g. the need to dismantle toxins in their vicinity, or the opportunity to use a new food supply if only the bacterium had the enzymes needed to liberate useful energy from this food molecule by breaking it down, just like energetic fire is generated by the uncontrolled breakdown of energy-rich molecules in wood).

Often another bacterial species possesses the genes needed to take advantage of such opportunities or to save it from dangers. If bacteria were capable of human emotions, envy would flow thickly among its neighbors. But sometimes the well-endowed bacterium fortuitously dies, spilling its contents (including its DNA) into the environment when its cell wall disintegrates. The fragments of its DNA disperse, adding to the pool of slowly decomposing DNA already around from other deaths. Genes, genes everywhere! At the scale of microbes, the world is like a field blowing with pages (fragments of DNA) torn from thousands of books (genomes), in various stages of decay. And some of these pages still contain intelligible spells (genes or groups of genes).

The long winding string of a DNA molecule floating freely after being released by a bacterial cell, photographed with an electron microscope. (Image: SeanMack)

Here is where things get really amazing. Our own cells are generally only capable of inheriting genetic material from our parents (be they modern humans or, in the deep past, occasionally Neanderthal), and our cells would consider this freely floating discarded DNA as useless. But many bacteria can take these DNA fragments into their cells and incorporate them into their own DNA, like gluing pages into a book!

Remarkably, bacteria can therefore ‘inherit’ genes not only from their ancestors but from their environment, and this DNA need not have belonged to anything remotely related to them. This is called horizontal gene transfer, also known as lateral gene transfer (“horizontal” or “lateral” referring to the passage of DNA between individuals of potentially the same generation, rather than being passed ‘down’ — ‘vertically’ — to the next generation) [1].

Further, because a bacterium is just a single cell, transformation of its DNA by the incorporation of this alien DNA transforms the genetic identity of the entire organism, and it is then inherited by all of the cell’s progeny as well. For this to work in us, the new genes would have to be added to our sperm or egg cells, the only types of our cells that pass their DNA on to the next generation.

A single cell of the bacterium Escherichia coli dividing multiple times to form a bacterial colony. (Image: Stewart et al., 2005)

Evolution Accelerated by Horizontal Gene Transfer

So can you begin to see how much faster evolution may progress using lateral gene transfer than using simple mutation alone? Suddenly the whole world is a laboratory on which a cell can draw to gain access to new genes generated in mutations in tens of thousands of other species. Indeed, a mathematical model by Michael Deem and Jeong-Man Park [2] demonstrates that horizontal gene transfer would increase the speed of evolution by quickly spreading useful mutations across large populations and communities of life forms. Contrary to what creationist proponents claim, beneficial mutations DO occasionally occur (e.g. the evolution of nylon degradation in bacteria [3]); horizontal gene transfer then helps to preserve them against loss by propagating them like gossip on the internet. Beneficial mutations do not need to be common as long as they can catch on and spread as quickly as wildfire.

Even more amazingly, there is evidence that under stressful conditions (e.g. heavy metal-polluted waterways), the rate of horizontal gene transfer between bacteria increases, as if stress induces a more urgent swapping of genetic ideas for a solution. Conditions such as these result in bacteria that acquire genes to detoxify heavy metals. Such a situation would even further accelerate the process of evolution, because useful mutations are spread around more intensely precisely in the environments in which they could make the most difference.

In a more frightening example of horizontal gene transfer, we have increasingly seen the rapid evolution of bacteria that resist being killed by antibiotics [4]. In many cases, one species of pathogenic (disease causing) bacterium acquires the genes that break down antibiotics from another species, allowing the ability to hop from one species into another, and multiplying our problems.

To bacteria then, the world is littered with great ideas ripe for the scavenging. The little grave robbers absorb some of the genetic remains of their dead neighbors and add them to their own genetic blueprint. They have no laws to discourage plagiarism, and there is no copyright on the genes they acquire this way.

Evidence Written in DNA

But how do we know that horizontal gene transfer has really been a part of evolution? Aside from the myriad instances in which microbiologists have actually observed it to happen in bacteria (e.g. the process of bacterial transformation), we can see evidence when a gene sequence that is characteristic of one species suddenly shows up in another species. This is kind of like the finding of Neanderthal genes in our genome, but (1) bacteria do not need to practice sex, for they can have ‘children’ by simply dividing asexually, and (2) bacteria can acquire genes from other species that are vastly more distantly related to them than are Neanderthals from us. And we see evidence for this.

Graphical representation of horizontal gene transfer. The branched tree-like structure represents the evolutionary lineage (geneological tree) of representatives of earth's major types of life forms. Sometimes genes can be transferred (horizontal gene transfer) between otherwise distantly related species. This is illustrated by bridges forming between branches of the tree, where genes 'jump' from one lineage to another. (Image: Barth F. Smets, Ph.D.)

An example exists in the scientific field around which some of my own research in microbiology revolved: the wild world of photosynthetic bacteria. An ancient group of bacteria (called anoxygenic phototrophs, which means “light-eaters that do not generate oxygen”) are capable of using light from the sun to generate energy to power their cells, in a way similar to but not identical to that of plants and algae [5].

An aerial photograph of grand Prismatic Spring, a hydrothermal vent (spewing super-heated water from volcanic fissures) in Yellowstone National Park. Some of the orange color of the rim of the spring pool is due to solar-powered anoxygenic phototrophic bacteria. (Image: Jim Peaco, National Park Service)

In fact, these bacteria were probably the first solar-powered life on earth, and amazingly, they might have originally evolved to use light not from the sun but from the glowingly-hot water spewing from geysers (hydrothermal vents) in the otherwise pitch-black deep sea…but that’s a story for another day. For now, suffice it to say that their DNA contains a long string of code for the construction of all the proteins and colorful light-trapping pigments (making the cells brilliant hues of orange, purple, red, yellow, green and blue, depending on the species) needed for the cell to capture and store light energy. There are several different distantly related groups of these photosynthetic bacteria, and each has evolved a different type of this pigment-protein machinery to capture light, and the DNA code of each can be read and used to identify which lineage of bacteria it comes from, each lineage possessing a vastly different characteristic code. Sometimes, however, you find a bacterium from one major group possessing the genes for the light-capturing machinery of a completely different group, completely as if the genes from the other group had been pasted into the normal DNA of this species [6]. This phenomenon is seen in many species of bacteria. Sometimes, a single cell will even possess the genes of more than one type of photosynthetic machinery, and one might be incomplete [7], as if the bacterium absorbed a set of genes from a DNA fragment that had already begun to decompose in the environment and was missing some parts.

Our Bacterial Identity

So we see extensive evidence for the evolution-accelerating phenomenon of lateral gene transfer in bacteria. But has it influenced our own evolution? Apparently, yes. Molecular biologists (who study DNA and other molecules of life) have found evidence that bacterial genes have been pasted into our own genome as well [8, 11]. This apparently has not happened too often, and it may be because it is much more common in single-celled life forms that are used to consuming material (including DNA) in their environment [9] instead of relying on the nicely predictable supply of food that a cell experiences in return for its participation in a multicellular (many-celled) life form. Nevertheless, a few of our genes appear to have had bacterial roots.

How might this happen? We’re not completely sure yet, but there is a precedent in nature. The bacterium called Agrobacterium tumefaciens has cellular machinery that gives it the amazing ability to take some of its own DNA and transplant it into the DNA of a plant. This action has a parasitic purpose in nature, leading to the production of a specialized tumor in the plant that helps the bacterium survive as a kind of parasite in its host. The result though, is that the plant’s genome becomes been infected (‘transfected’ is the actual word used) by the genetic material of a bacterium, and its DNA now also harbours bacterial DNA. It is easy to imagine how a similar process may have occurred in which parasitic bacteria produced changes in animal hosts to their advantage, but which resulted in a genetically modified host animal. This bacterial “transfection” is the basis on which much of the genetically modified food industry has been built.

So there we have it: plagiarism and grave robbing by bacteria has helped to build up our own genome. Not a large part, true, but bits of bacteria are nevertheless a part of our genetic identity (and later on, we’ll see how, in a completely different way, bacteria are a hugely greater part of us than most of us realize). In the next post, I’ll focus on a much more invasive crime — genetic hijacking by viruses — that our ancestors suffered (and continue to suffer), but which has contributed much more extensively to our genes.

References

1. Syvanen M (January 1985). Cross-species gene transfer; implications for a new theory of evolutionJ. Theor. Biol. 112 (2): 333–343. doi:10.1016/S0022-5193(85)80291-5

2. Park, J.M., Deem, M.W. 2007. Phase diagrams of quasispecies theory with recombination and horizontal gene transfer. Physical Review Letters. 98. doi: 10.1103/PhysRevLett.98.058101

3. Ohno, S. 1984. Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequenceProceedings of the National Academy of Sciences of the United States of America. 81:2421-2425.

4. Akiba T, Koyama K, Ishiki Y, Kimura S, Fukushima T 1960. On the mechanism of the development of multiple-drug-resistant clones of ShigellaJpn. J. Microbiol. 4: 219–27.

5. Yurkov, V.; Csotonyi, J.T. 2009. New light on aerobic anoxygenic phototrophs. In Hunter, N.; Daldal, F.; Thurnauer, M.C.; Beatty, J.T. (eds.) The Purple Phototrophic Bacteria, pp. 31-55. New York, NY: Springer Science + Business Media B. V.

6. Igarashi, N., harada, J., Nagashima S., Matsuura, K., Shimada, K., Nagashima, V.P. 2001. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. Journal of Molecular Evolution. 52: 333-341. doi: 10.1007/s002390010163

7. Qiang Zheng, Rui Zhang, and Nianzhi Jiao. 2011. Genome sequence of Citromicrobium strain JLT1363, isolated from the South China Sea. The Journal of Bacteriology. 193: 2074-2075

8. Ponting, C.P. 2001. Plagiarized bacterial genes in the human book of life. Trends in Genetics. 17:235-237.

9. Andersson, J.O. 2005. Lateral gene transfer in eukaryotes. Cellular and Molecular Life Sciences. 62: 1182-1197. doi: 10.1007/s00018-005-4539-z

10. Stewart EJ, Madden R, Paul G, Taddei F (2005). Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 3 (2): e45.

11. Francisca C. Almeida, Magdalena Leszczyniecka, Paul B. Fisher and Rob DeSalle. 2008. Examining Ancient Inter-domain Horizontal Gene Transfer. Evolutionary Bioinformatics. 4: 109-119.

Advertisements
This entry was posted in Uncategorized and tagged , , , , , , , , , , , , , , . Bookmark the permalink.

3 Responses to Evolution’s Usual Suspects: 1. Plagiarizing Wizards

  1. Pingback: Frankenstein’s Batteries | Evolutionary Routes

  2. Pingback: The Taming of the Chloroplast | Evolutionary Routes

  3. Pingback: Evolution Powered by Lightning? | Evolutionary Routes

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s