“Jumping Genes”: Our Genetic Sequences Aren't Set in Stone

Our genetic material is complex—so complex that 
even now we’re still discovering new things about it.

When we learned about DNA and genetics in class, we learned that our genomes contain alleles which code for genotypes that determine our phenotypes (our traits). DNA replication is a very delicate process and, although it occurs at rapid rates, there are very few mistakes. Enzymes exist which would correct any mistakes made, as even a simple base substitution mutation—that is, the changing of one nucleotide for another (for example, the change of adenine to thymine, guanine, or cytosine) could result in a disorder that can plague a person their whole life. An example of this is sickle cell anemia. In individuals with sickle cell anemia, the base adenine in the codon GAG which codes for glutamic acid in hemoglobin is exchanged for thymine, so that the codon becomes GTG and codes for valine instead. Hemoglobin is the protein found in red blood cells which is responsible for binding oxygen. Due to the change in amino acid, hemoglobin’s structure is distorted and so is the shape of the red blood cell—changing from the flattened disk shape to a curved, sickle-like shape.  This leads to weakness, fatigue, and shortness of breath because the abnormal hemoglobin doesn’t carry oxygen as efficiently as normal hemoglobin does, and can crystallize in blood vessels. Given that even the change of one base in our DNA can have profound consequences, we would assume that our genomes are, in general, quite fixed throughout our lives, unless we develop a disorder. Recent studies show that that is not the case.

Within our genome, there are DNA molecules that can jump from one locus to another, and might influence brain function and behavior. “Retrotransposons” are one such type of mobile DNA which copy-paste themselves into various areas of the genome, and have been found to compose over 40% of the human genome. In order to investigate this phenomenon, the Roslin Institute in Edinburgh, Scotland, undertook the task of mapping the retrotransposon insertion sites in human brain cells. These brain cells were extracted from the tissue of healthy individuals who showed no sign of disease or abnormality after they passed away.

What they found was that, even when looking at only the hippocampus (which is responsible for memory) and the caudate nucleus, there was a dizzyingly large number of retrotransposon insertion sites—specifically, 25,000 different sites! These genes were found to integrate themselves in “genes that were expressed in the brain.”  This is due to the fact that, normally, our chromosomes are coiled in such a way that they aren’t always accessible for transcription and, in this case, retrotransposon insertion. Examples of such genes include neurotransmitter receptors in neurons, membrane transporters that remove remaining neurotransmitters from the synaptic gap after the signal has been transmitted to the post-synaptic neuron, genes which suppress tumor growth (which are deleted in brain cancer patients) and those which have been linked to psychiatric disorders such as schizophrenia.

As would be expected, retrotransposon activity is normally suppressed in order to prevent mutation that could negatively affect developing gametes, but during brain development, when stem cells are dividing to produce new neurons, they are mobilized and insert themselves into accessible areas of the chromosome during DNA replication when the two strands of the double helix are separated. Since the hippocampus is responsible for learning and memory, and therefore produces new cells throughout the human life span, retrotransposon activity in this area of the brain was found to be higher than in the caudate nucleus.

 Diagram showing retrotransposition

These jumping genes insert themselves into random areas in the genome quite often, occurring several hundred times in most brain cells, and resulting in genetic variability within these cells. When inserted, they can cause mutations which express themselves negatively, but it is also possible that retrotransposon activity could influence our behavior and neural activity in ways that aren’t always bad. As Faulkner says, “it is entirely possible that retrotransposition is generally a good thing but sometimes contributes to disease.”

I find these jumping genes quite interesting and believe that we could better understand brain disorder and behavioral changes from analyzing how and under what conditions will retrotransposition cause harm to brain cells.  It is well understood that human cells are able to replicate masses of DNA within short periods of time with a mechanism to prevent or minimize errors. Understanding how and under what conditions adverse mutation can occur might allow us to help our body deal with retrotransposition so that, when such DNA sequences are copy-pasted into random regions of the genome, they don’t cause harm, and simply give genetic variability in our cell populations.

Genetic variety helps living organisms survive through sometimes drastically changing conditions and environments. Plants cross pollinate in order to create genetic diversity so that disasters like epidemics don’t wipe out the whole species. Humans achieve genetic variety through crossing over and random orientation of homologous chromosomes during meiosis I. Perhaps retrotransposition is another means by which humans have been attempting to achieve genetic variety, so that in survival of the fittest, we are able to deal with harmful external factors and better our chances of not going extinct.

Images:

http://upload.wikimedia.org/wikipedia/commons/thumb/5/50/L1_Retrotransposon.jpg/400px-L1_Retrotransposon.jpg

http://sahavicha.kalasin3.go.th/UserFiles/Image/DNA.jpg

Phototropism, Geotropism….. Scentropism?

Tropisms are directional growth responses to external stimuli. Common tropisms include phototropism and geotropism—both of which we discussed in biology class. Phototropism is positive for plant stems and negative for roots—that is, the stem will lean towards sunlight as the plant grows while the roots will grow away from the light. The opposite is true for geotropism—growth in response to gravity—as the stems grow counter to the force of gravity, and the roots grow in the direction gravity is acting, which is down. These tropisms seem reasonable enough. Plants use sunlight for photosynthesis so it makes sense that they would grow towards it in order to maximize the amount of sunlight they are exposed to. But what of parasitic plants without the ability to photosynthesize?

Cuscuta pentagona—an orange vine with small white flowers—lacks chlorophyll and therefore is unable to convert light energy into chemical energy and make its own food. It would not benefit from phototropism, which leads plants to the light energy source they need to produce sustenance. Sure, the Cuscuta grows its roots into the dirt and its vines upward, like other plants. However, it attains the nutrients it needs by attaching itself to a host plant and sending “microprojections” into the tomato’s phloem - through which the plant transports sugars (mostly sucrose, but also glucose), amino acids, plant hormones, and mRNA—to siphon off the host plant’s photosynthesized sugar supplies. Without a host to live off of, a young Cuscuta plant will inevitably die. To prevent this from happening, the Cuscuta has a plant-detecting mechanism by which it locates the target host plant it will attack through smell.

Cuscuta pentagona commonly latches onto tomato plants. As a Cuscuta pentagona seedling grows, it probes its surroundings, growing and rotating its shoot tip until it finds a tomato (or other) plant in its vicinity, then wraps around this new host’s stem in order to have access to the plant’s phloem. Consuelo De Moraes hypothesized that the Cuscuta or dodder plant detected its host through “chemical signaling.” She noticed that, despite variable conditions—light or shade, in the presence of other plants (specifically, wheat), empty pots, or  pots with fake plants—dodder vines always grew towards the tomato plants! To test her hypothesis, she synthesized a tomato perfume, or “eau de tomato”, with extracts from the stem of a tomato plant. She then soaked cotton swabs with this perfume and placed them on sticks in a pot next to the dodder. As she hypothesized, the dodder indeed grew towards the cotton that gave off the scent of a tomato plant. Dodders grow towards tomato plants because tomato plants contain beta-myrcene, in addition to two other chemicals. All three of these chemicals are easily turned into gases and give off odors which attract dodders.

This is not the only case in which non-tactile plant communication occurs. University of Washington scientists David Rhoades and Gordon Orians, observed that willow trees neighboring those that were plagued by caterpillars were less likely to be attacked by caterpillars. Upon investigation, Rhoades found that the leaves of trees  found next to, but not touching, the infested willows contained phenolic and tannin—chemicals that repel the insects which feed on them. These chemicals were absent in healthy willows which were not surrounded by caterpillar-plagued willows. Since neither the roots nor branches of the damaged and healthy trees had contact with each other, Rhoades proposed that, via pheromones, the infested trees sent a warning message to healthy trees so that they could defend themselves against the impending insect attack.

Plants aren’t as altruistic as they seem, however, as Martin Heil, a Mexican scientist, found. Heil posited that the infected plants didn’t intend on warning their neighbors at all—the pheromones released by damaged leaves were directed at the remaining healthy leaves of the infested plant. Neighboring plants simply detected these pheromones and reacted to protect themselves. To test his hypothesis, Heil isolated damaged leaves in a sealed plastic bag to determine whether this disrupts pheromone communication. As he had suspected, the damaged leaves were unable to transmit their warning message to healthy leaves on the same plant, and these healthy leaves remained the same. Heil concluded that the chemicals released by damaged leaves are necessary for the rest of the plant to defend itself from further attacks.

Of course, plants don’t smell in the same way that we do—with nerves that send signals to our brain and tell us of what scents are around us—but they are most definitely capable of detecting and responding to chemicals in the air around them. This makes a lot of sense. We all know that plants, flowers especially, give off odors and aromas which attract pollinators and vectors, like nocturnal animals, for seed transport. But, just as humans speak and can hear, plants give off odors and can detect scents.

I found this really eye-opening and intriguing. It shows that we can still discover new things about even seemingly simple organisms with which we are familiar. Although we don’t have enough information to conclude definitively the nature of pheromone communication, Heil’s experiment doesn’t rule out the existence of a warning system. The chemicals released by damaged leaves may be necessary for the survival of the healthy leaves, but this fact alone doesn’t preclude the intention of the infected plant to warn neighboring plants of its plight. It would be interesting to explore the details of pheromone communication, how it varies, if at all, among different plant species. Pheromones could be the key to giving us a better understanding of plant communication. Another thing I found ironic is that humans, although thought to be one of the most complex organisms with conscious thought, aren’t capable of understanding the pheromones we release, whereas plants can. Maybe we aren’t as superior to other organisms as some might think.

Image:

http://fnpsblog.blogspot.com/2012/04/cuscuta-pentagona-dodder-that-wont.html