How a Dry Seed Can Live a Thousand Years
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
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