It’s so hot, I’m mutating! The effect of heat on mutation in plants
Introduction
Even before scientists discovered that DNA was the heritable material of life, it was known that heat increased the mutation rate in plants, with studies dating back to the 1930s. For example, in 1936, researchers exposed Datura seeds to heat stress and observed a higher number of mutant germinated offspring [1]. In the modern day, there have been multitudes of research on the effects of heat stress on mutation rates in other eukaryotic organisms such as yeast, Drosophila, and C.elegans. However, despite early studies of heat-induced mutation occurring in plants, this field has only recently come back into major scientific focus.
Plants, which are sessile organisms, are extremely vulnerable to temperatures outside of their normal climatic range. This focus is extremely important, considering that average global temperatures are climbing due to climate change, pushing plants out of their desired temperature range. Plants are also critical to human agriculture and ecosystem stability, as the vast majority of heterotrophic organisms depend on plants either directly or indirectly for energy and for oxygenic respiration. Knowing the effects that rising temperatures will have on them has wide-ranging implications from conservation to breeding, to agricultural practice.
Mutation manifests in an array of different manners, from nucleotide matching errors in DNA replication, to chromosomal abnormalities, to transposable elements. The further study of mutation has only recently become widely accessible and affordable due to technological advances such as long-read DNA sequencing. Mutation is the source of genetic and phenotypic variation for evolution to act upon. Given that heat can increase mutation rates in plants, further studies in this area are essential. This review will discuss past and current studies into this subject matter, primarily in the model organism Arabidopsis thaliana, but also in other commercially grown plants, like the common rose. It will then discuss future paths of research that could be explored in regard to the effect of heat on the mutation rate in plants.
Heat on mutation at a nucleotide scale
In Arabidopsis thaliana, both individuals and populations exposed to different levels of heat stress showed higher rates of mutation compared to their non-stressed counterparts [2]. Certain types of mutations were found to occur more commonly in heat-stressed lines as well. Large-scale mutations (duplications and transpositions ≥1000 bp) were found to be uncommon. In contrast to larger mutations, small-scale mutations became more common under heat stress, including single nucleotide polymorphisms (SNPs), which involve changes to a single DNA base pair, and small insertions or deletions (indels), particularly those 1 or 2 base pairs in length. Most of these small mutations were also found to occur mostly in intergenic, non-protein coding regions and long single nucleotide (homopolymeric) sequences, especially A:T runs [3]. When they did occur in genic regions, they were found to favor genes regarding stimuli response, reproduction and development, and regulation, although this may be due to selection, as these genes may have lesser impact on the plant’s survival ability in a laboratory setting [2].
Mutation occurred highest when DNA was in its loosest state, often during replication, and least often in its tighter nucleosomed state [3]. This could imply that heat stress may have greater mutagenic effects during plant development, gametogenesis, and in meristematic tissue. The source of these mutations appears to be due to an increase of mutagenic reactive oxidative species, which are created at a higher rate under heat stress, and not due to inhibition in the DNA mismatch repair pathway (MMR), although other repair pathways appear to be heat-stress inhibited [2][3].
Heat effect on chromosomal scale mutation
Heat stress has been found to affect cell division and chromosome recombination in multiple eukaryotic branches, including plants. For example, polyploidy occurs when an organism has more than two copies of a chromosome due to an error in chromosomal separation, primarily during the creation of gametes. In roses, exposure to heat stress leads to increased rates of polyploidy. This is because the heat stress interferes with spindle fiber formation in both meiosis I and II. The heat causes incorrect chromosomal division as the incorrectly assembled fibers are unable to pull the chromosomes apart in a correct manner. As a result, dyads (1 chromosome) and triads (3 chromosomes) form instead of the typical tetrads (2 chromosomes). This ultimately causes incorrect chromosome numbers after meiosis II, increasing polyploidy rates.
During cytokinesis, the final stage of cell division where the two cells split apart with their now developed nuclei, heat stress has also been observed to hinder the construction of the cell wall, preventing the physical cell split. This causes the cell to now have two nuclei and therefore be a polyploid cell. Not only does heat stress increase polyploidy rate, it also increases rate of nonhomologous recombinations. Nonhomologous recombination describes when two pieces of unrelated double strand DNA recombine, instead of related ones (homologous recombination), often causing broken genes and expression. It was observed that the presence of heat stress hinders the formation of the synaptonemal complex, the protein complex that joins homologous chromosomes for recombination. This leads to an increased rate of nonhomologous recombination. In most other cases, both incomplete formations would trigger arrest of cell division, but under heat stress the signaling molecule telling the plant to continue dividing remains unaffected, allowing for nonhomologous recombination and creation of multinucleate, polyploid cells to continue [4].
Heat and Transposable Element ONSEN
Transposable elements (TEs), mobile sections of DNA that can cut out, copy, and insert themselves within a genome, are another source of mutation in plants and other organisms. TEs can be suppressed in plants through a variety of mechanisms, but in the presence of environmental stress, they can become activated.
Specifically, ONSEN, a copy/paste transposon, becomes activated during plant heat stress response due to the activation of a response promoter that simultaneously releases ONSEN, which the plant can not repress without deactivating its heat response [5]. ONSEN, once activated, selectively inserts itself into specific coding exon regions of chromatin tagged with the H2A.Z and H3K27me3 histone variants while avoiding centromeres and other TEs. These insertions can have many consequences with strong fitness effects on genes, creating knockouts, exonization, alternate expression, and truncation. In addition,TEs possess the ability to rapidly expand the genome size of an organism [6]. Moreover, ONSEN and its insertions specifically can act as a heat response promoter and enhancer, and make neighboring non-heat responsive genes become heat responsive after insertion, due to the heat responsiveness of ONSEN’s long terminal repeats spilling over [6].
It’s also been observed that ONSEN insertions in Arabidopsis can create increased drought tolerance. 23 lines of Arabidopsis thaliana were exposed to heat stress over multiple generations in a lab setting. In five of twenty-three Arabidopsis lines, increased drought tolerance occurred. In all five of these lines, there was an exonic ONSEN insertion, causing the loss of function in ribose-5-phosphate-isomerase gene, which codes for a protein involved in the Calvin cycle. It leads to decreased plant size, water loss, and photosynthetic rate, but at the same time, decreased necrotic tissue after exposure to drought conditions also occurred. This increased drought tolerance has not been seen to occur in the wild yet, but this is attributed to the fact that the population of wild Arabidopsis, as with any species, is too large to ever truly know every single genetic variation event that has occurred, especially if one has only occurred at a small scale so far [7].
The implications of this drought tolerance are far reaching. Transposable elements are primarily considered harmful to organisms, as they mutate and degrade functional genes, but ONSEN creating drought tolerance during periods of heat stress contradicts that. Understanding ONSEN and other TE activation and behaviors will increase our knowledge of how plants adapt and evolve and could pave the way for developing heat-tolerant crops or leveraging its insertion patterns to introduce beneficial traits into plants. These transposable elements could be used in applications such as plant breeding to increase desired traits, and in identifying target genes, like ribose-5-phosphate-isomerase.
Future Directions
Heat has been a known factor increasing mutation rate in plants, but due to recent advances in technology and increased concern about the effects of climate change, heat-induced mutation in plants has become a reinvigorated topic of study. In the original Datura seed study, they determined mutation rate by looking at the pollen abortion index, or amount of univable pollen created [1]. Nowadays, mutation rate determination uses technology such as long read sequencing and bioinformatics, which allow for greater accuracy, detail, and efficiency and are more affordable than in the past. This greater accessibility has made the field of mutation, genomics, and epigenomics a hot topic of study, opening up many new questions.
One potential path yet to be explored is thinking of mutation rate as a phenotype, rather than a process like genetic drift or natural selection. Mutation has long been dogmatized as a completely random process that creates completely random genetic variation. Yet, the dogma of random mutation is starting to have more and more holes, as new research comes out. Mutation rate isn’t universal between organisms. Some species have much higher mutation rates than others. As this review has explored, heat can change mutation rate. It’s also been shown that different regions of the genome have higher mutation rates, and others have preferential DNA repair, creating mutation bias. If mutation was truly as random as it has been accepted to be so far, there would be no mutation bias, and mutation rate would be static across the entire tree of life. Thinking of mutation rate as a phenotype, the sum of the genome and its regions’ likelihood to mutate and ability to fix itself, offers a greater and more complex understanding than thinking of mutation rate as just how often a C becomes a T or a nucleotide is deleted. By thinking of mutation rate as a phenotype we then can determine the genotypes that lead to these differential rates.
This knowledge would be extremely valuable to applications such as plant breeding: being able to select for decreased mutation rate could be beneficial in creating a more uniform crop whereas selecting for increased mutation rate could be a contributor to increasing the number of landrace genomes. Further research into this area could provide critical insights into plant adaptation mechanisms, opening doors to new innovative breeding strategies.
About the Author: Percival Singson
Percival Singson is a second year Plant Sciences major with a concentration in Plant Breeding, Genetics, and Genomics, and dual minors in Evolution, Ecology, and Biodiversity and History. He originally wrote this review for his PLS 152 (Plant Genetics) midterm, inspired after asking his professor a question about heat-induced mutation in class. He now works in this professor’s lab, the Monroe Lab, studying methylation, mutation, transposable elements and climate adaptation in Arabidopsis thaliana. When he’s not thinking about how cool plants are, he’s usually out marathon training with the XCTF club or working on his next stand up comedy routine.
Author’s Note
This was originally my midterm for my plant genetics class. Our task was to write a miniature literature review on any topic related to the field of plant genetics. I specifically chose to do the review on the effect of heat mutation in plants, as a form of preparation for when I joined my PI’s lab, which studies these topics. I think it’s an incredibly relevant field, especially due to climate change implications and it has so many open questions left, as most papers I encountered on the topic have come out within the last 4 years. This due to the recent advances in genomic technology that have made the study of whole genomes easier. I want readers to also become interested in studying this topic, because if we want to be able to prepare our crops and ecosystems for climate change, then we need to know more about how heat can affect the evolution and adaptation of plants.
References
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Lu Z, Cui J, Wang L, et al. 2021. Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposures to high temperatures. Genome Biol [Internet]. 22(160).https://doi.org/10.1186/s13059-021-02381-4
Belfield EJ, Brown C, Ding XJ, et al. 2020. Thermal stress accelerates Arabidopsis thaliana mutation rate. Genome Res [Internet]. 31(1):40-50 https://doi.org/10.1101/gr.259853.119
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Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, et al. 2014. How a Retrotransposon Exploits the Plant’s Heat Stress Response for Its Activation. PLoS Genet [Internet]. 10(1). https://doi.org/10.1371/journal.pgen.1004115
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Thieme M, Brechet A, Keller B, Bucher E, Roulin A. 2022. Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana. New Phytol [Internet]. 236:182-194. doi:10.1111/nph.18322