How plants borrowed genes from fungi and bacteria – 03/07/2024 – Fundamental Science

In the early days of evolutionary theory, Charles Darwin conceived of the diversification of life forms from common ancestors as a great tree, the tree of life. In this process, new branches arise from a branch that, in turn, connects to others, up to the fundamental trunk, the common origin of all organisms. In this view, evolution would be a process of vertical inheritance, in which genetic material would flow from one generation to the next, accumulating changes over time.

During the last century, this perspective has been challenged. In 1928, bacteriologist Frederick Griffith published his now classic experiment that proved the ability of bacteria to exchange genes. At that time, the results were difficult to understand, as the physical basis of heredity was not yet known, now identified as the nucleic acids DNA and, in some viruses such as Covid, RNA.

Griffith showed that genetic material from pathogenic bacteria – those with the potential to trigger disease in their hosts – isolated from cells could transform non-pathogenic bacteria into pathogenic ones. This indicated the possibility of horizontal inheritance of the genetic material responsible for pathogenicity, that is, between different lineages and without involving reproduction. The different bacteria were therefore capable of “swapping” genes.

For many decades, biologists considered this process rare, and restricted to bacteria. In the early years of this century, however, evidence began to emerge suggesting that eukaryotes (organisms whose cells have a nucleus and a more complex structure), especially unicellular ones, could also acquire genes from other organisms, in a process called horizontal gene transfer. The impact of this process on the evolution of multicellular eukaryotes, composed of different types of cells organized in tissues, such as animals and plants, has remained little explored and understood.

In February of this year, a partnership between my research group at UFMG and Michigan State University (USA) advanced this knowledge a little further. Through sophisticated analyzes and comparisons of the genomes of plants and algae of various types, we published an unprecedented and, in a certain way, unusual study: apparently, plants were also capable of exchanging genes with fungi and bacteria in their evolutionary process. But how did we arrive at this discovery?

Over the last 15 years, I have dedicated myself to investigating the evolution of the biochemical characteristics of plants, such as their ability to synthesize and degrade carbohydrates. This curiosity arose after realizing that most of our planet’s biomass is made up of vegetable carbohydrates, such as cellulose. It is estimated that terrestrial plants contain 80% of the living matter in the biosphere and that, in general, carbohydrates represent three-quarters of their dry mass.

This makes sense, since the process of photosynthesis, responsible for sustaining most life on Earth, produces sugars from carbon dioxide in the air. Therefore, it would not be an exaggeration to say that we live on a planet dominated by sugar molecules linked together in different combinations.

In our research, we decided to analyze the evolution of all types of enzymes capable of “breaking” chemical bonds of carbohydrates in plants. We already knew that they have at least 40 different types of genes that code for enzymes capable of breaking down carbohydrates. Each type of gene can have several dozen different copies, so much so that a current angiosperm plant, one that has flowers, dedicates more than 1% of its total genes to this function alone.

We also knew that when the first eukaryotic algae emerged, more than a billion years ago, the repertoire of enzymes capable of hydrolyzing carbohydrates was small, consisting of just a few dozen. Some of these older enzymes, for example, are linked to the breakdown of starch, the fundamental energy reserve of the plant lineage. This finding led us to an obvious question: If your remote ancestors had only a few types of these enzymes, where did the wide variety of those that break down carbohydrates in today’s plants come from?

To try to answer, we compared genomes from the plant lineage with all currently known genomes from the most diverse types of organisms. To our surprise, most of the enzymes that did not exist in the earliest plant ancestors have high similarity to enzymes from bacteria or fungi.

This result most likely indicates that, throughout plant evolution, multiple horizontal gene transfer events from fungi and bacteria shaped the biochemical capacity of these organisms to handle carbohydrates. Perhaps the ecosystems we know, which depend on plants fixing carbon from the air via photosynthesis, wouldn’t even exist if it weren’t for a little genetic help from microscopic bacteria and fungi.

We hypothesize that most of these events occurred when the ancestors of plants were still unicellular algae that were beginning to colonize the terrestrial environment, in microscopic ecosystems where they lived closely associated with fungi and bacteria. It is surprising to conclude that possibly all current forests descend directly from microforests, microscopic terrestrial ecosystems where microalgae acquired genes from other microorganisms with which they lived.

This is one of the first examples in modern biology that demonstrate that the highly elaborate cellular capabilities of complex eukaryotic beings may have originated through the serial acquisition of genes from different types of microorganisms. They would, therefore, have “borrowed” genes from different beings in their evolutionary processes.

Contrary to what Darwin imagined in the 19th century, life does not evolve exactly like a tree, but like a complex network in which very distant branches can interact by exchanging genes. This process of acquiring genes from different sources may have been extremely important in the transition from microscopic and unicellular life to macroscopic life composed of countless different types of cells, such as humans.

Perhaps we are beginning to discover that complexity can emerge through the fusion of many simple things. At their core, plants are made up of a bit of DNA from fungi and bacteria that helped them create the planet on which our primate ancestors evolved, jumping from branch to branch just like the genes on the tree of life.

*

Luiz Eduardo Del Bem is a geneticist and professor at the Institute of Biological Sciences at the Federal University of Minas Gerais (ICB-UFMG).

The Fundamental Science blog is edited by Serrapilheira, a private, non-profit institute that promotes science in Brazil. Sign up for the Serrapilheira newsletter to keep up to date with news from the institute and the blog.