Unlike us humans, plants don't have the luxury of packing up their things and moving to a new place if they don't like their neighborhood. Plants live a sedentary life (in case you forgot) but that doesn't mean they live a boring one. In order for plants to survive they must be constantly responding to the environment around them. An obvious task (you're probably thinking) but by no means is it an easy one. Plants don't get the 10-day weather channel forecast or the intuitions of a groundhog predicting a longer winter. Plants have to rely on themselves, on their own DNA, the same DNA, in fact, that makes up you and me. So how does it work? Keep reading.
The purpose of my honors thesis was to investigate and elucidate the immensely important yet incredibly complicated interactions between plant genetics and the environment. More precisely, my project looks at the role of duplicated genes (exactly what they sound like, essentially) in regulating plant development in response to the environment. This regulation is important because different stages of a plant's life have different environmental tolerances. Therefore, a plant must time each of its developmental transitions (from seed to seedling, for example, or from bud to flower) so that the next life stage experiences an environment that favors growth and maximizes fitness. For example, if a seedling needs warm, wet conditions (think springtime!) to grow it's going to be "up a creek without a paddle" (as my mom always says) if its seed accidentally germinates in the dead of winter. A seed needs to restrict its timing of germination to occur under favorable conditions, but if it restricts it too much it may never germinate at all. Ultimately, a plant must not only develop under favorable conditions, it must develop under the widest set of permissible conditions suitable for subsequent survival. It's a fine line. So what controls it? Gene duplication. Well, at least in part.
All organisms have duplicated genes. In fact, duplicated genes (specifically oncogenes) are common in many types of cancer in humans. For plants, duplicated genes are important for evolution and adaption. When a gene is duplicated it gets another copy of itself (told you, exactly what it sounds like). This is important because this new copy may evolve a slightly different function. Or it may be completely nonfunctional. Or it may contribute to the same function but be controlled by different factors. A duplicated gene is like having a twin. You share the same genetic makeup but you can evolve into two completely different people. One twin might like the beach while the other twin prefers the mountains. One plant gene may regulate a developmental process in response to heat while the exact same gene can regulate the exact same process but in response to cold.
The first part of my thesis characterizes the temperature dependent roles of two duplicated gene families during seed germination. Germination is of particular importance because it basically determines how that plant's life is going to unfold. Germination for plants is like marriage for humans (except imagine if we couldn't get a divorce and we were never allowed to leave the church ... scary, right?). Once a plant germinates it must either adapt to its environment or perish, making the timing of seed germination, truly, a matter of life and death. In order to germinate at the right time, plants must be able to accurately sense and respond to a complex host of environmental factors -- moisture, light and temperature, just to name a few. Ultimately, duplicated genes are important players in this complicated dance between the plant genome and the environment because the same gene can contribute to the same developmental process, but in response to different environmental triggers.
The two duplicated gene families that my thesis considers are phytochromes and gibberellin3‑oxidases. Both of these families have duplicated gene copies that have divergent sensitivities to temperature during seed germination. Phytochromes are plant photoreceptors (i.e. they regulate a plant's response to light) and are upstream in the germination pathway. Gibberellin 3-oxidases (GA3ox's) convert an essential plant hormone (gibberellin) from its inactive to bioactive form in one of the final downstream steps of the germination pathway. During seed germination different phytochromes and GA3ox's contribute to germination but in response to different temperature conditions. In other words, multiple copies of these genes contribute to the same physiological process (germination) but the contribution of each copy depends on the temperature conditions a seed experiences both during maturation and after dispersal.
Ultimately, my thesis project was twofold. First, I empirically characterized the environmentally sensitive roles of two duplicated gene families regulating germination through a series of germination assays. Second, I theoretically investigated how environmentally sensitive duplicated genes are able to achieve such a precise regulation through a two-step genetic pathway model. Essentially, this model calculates the probability of a physiological process (such as germination) occurring under a range of environmental conditions. The purpose of this model, therefore, was to determine how the duplication and environmental sensitivity of genes influence the distribution of environmental conditions under which a developmental process will proceed.
Again, this is important because in variable environments (any place with seasons, for example) the environmental regulation of development and physiology is key to understanding plant survival and adaptation. However, the genetic mechanisms that control this environmental regulation remain unclear. This thesis project shows how duplicated genes are an important piece of the puzzle. Duplicated genes allow for plants to sense complex combinations of environmental cues and they tightly regulate how developmental processes proceed in response to these cues. In other words, if a plant's genome was like the weather center, duplicated genes would be well compensated meteorologists.
I would like to give a special thanks to the Donohue lab and to Dr. Kathleen Donohue herself, whose immense knowledge and patient guidance made all of this research possible. I joined Dr. Donohue's lab because I've always been interested in how the environment interacts with biological systems, particularly how environmental factors can regulate physiological responses at the genetic level. Eventually, I hope to take my knowledge and interest in gene-environment interactions from the plant realm to the human one as a future physician interested in environmental health issues. Although I am still unsure of my exact career path, as a result of my time in the Donohue lab, I'm particularly interested in how the environment can effect gene expression in the development of human diseases such as cancer. Ultimately this thesis, and all of the hard work that went into it, has cemented my passion for biological research and my desire to continue exploring gene-environment interactions regardless of my future career path. It has had a profound impact on me and I hope some part of it attracts or resonates with you too.
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