The Curious Case of Horizontal Gene Transfer

By- Suhani Sharma

(10 min read)

Which organisms comes to mind when you think of Horizontal Gene Transfer? Bacteria? No! It’s Plants AND Bacteria!

Independent searches in Grasses and Cuscata have found that the species take up genes from their hosts or neighbouring organisms to speed up evolution, making them “Naturally Genetically Modified“. Another astonishing find is that usually the horizontal gene transfer does not exceed a couple percentages but in this case they exceeded over 40%.

Horizontal Gene Transfer(HGT) or Lateral Gene Transfer(LGT) is the transmission of genes from one organism to another without actually reproducing. It is known to take place through different methods like Translation, Transduction and Conjugation.

The incoming DNA or RNA can replace existing genes, or can introduce new genes into a genome.Extensive exchange of genetic information between mitochondrial genomes of plants is now well documented, providing the highest known levels of eukaryote–eukaryote transfer.

In many instances, genes acquired by HGT have clear functional or ecological implications for their new host. For example, several highly derived anaerobes have acquired many metabolic genes from bacteria that probably contribute to their adaptation to anaerobic environments.

Grasses

The research, led by the University of Sheffield, studied grasses, which include some of the most economically and ecologically important plants, such as the most globally cultivated crops wheat, maize, rice, and barley.

Dr. Luke Dunning, senior author of the research from the Department of Animal and Plant Sciences at the University of Sheffield, said: “We found over 100 examples where the gene had a significantly different history to the species it was found in.”

“The findings may make us as a society reconsider how we view GM technology, as grasses have naturally exploited a very similar process. If we can determine how this process is happening it may allow us to naturally modify crops and make them more resistant to climate change.”

Samuel Hibdige, first author of the research and PhD Researcher from the University of Sheffield, said: “We still don’t know how this is happening or what the full implications are. But, we know it is widespread in grasses, a family of plants that provide a majority of the food we eat.”

The study detected a statistical increase in species which possess certain kinds of modified stems called ‘rhizomes’. The causes for this are still under study.

Cuscata

The DNA of the most mysterious flowering plant, Rafflesia arnoldii, has the largest flowers in the world weighing around 10kgs. 

Jeanmaire Molina, an evolutionary plant biologist at Long Island University in Brooklyn, in a paper released in 2014 in the ‘Molecular Biology and Evolution’ was unable to detect any functional genes from its chloroplasts. The plants seemed to have simply ditched their entire chloroplast genome.

“That was almost unthinkable. Chloroplasts are best known for using light to make food, but like all the food-making organelles called plastids, they contain genes that are involved in many key cellular processes. Even malaria parasites still carry a plastid genome”, Molina noted, “and their last photosynthetic ancestor lived hundreds of millions of years ago.”

Rafflesia arnoldii

This study is now confirmed by a team at Harvard University showing how far parasites can go in shedding superfluous genes and acquiring useful new ones from their hosts. It also deepens mysteries about the role of highly mobile genetic elements that don’t encode proteins in enabling evolutionary changes.

A study by Charles Davis and his student Liming Cai concluded that parasites have to delete many of their genes considered essential to its free-living relatives. Because they steal(or borrow) from their hosts, they essentially outsource the labor of metabolism, so they don’t need all the moving biochemical parts of an independent plant cell.

Still, Davis was shocked to see that nearly half of the genes widely conserved across plant lineages had disappeared from Sapria. That’s more than twice as many genes as are lost from the parasitic plants called dodders (genus Cuscuta), and four times the losses in cereal-killing witchweeds (genus Striga).

 “We knew that there would be loss,” he said, “but we didn’t think it would be on the order of 44% of its genes.”

In addition the plants have deleted the noncoding stretches of DNA within many genes. These regions, called introns, are interspersed among the parts of genes that code for the actual protein that is produced.

It might look as though Custata’s genome is reduced but that’s not true. It’s genome is in fact as big as ours. How?

Well, for starters, it is loaded with borrowed genes particularly from its hosts, past and present.

“Because these parasites have been stealing (or borrowing) genes for millennia”, Cai noted, “their genome is like a huge graveyard of DNA.” And this type of ecological history is all but impossible to deduce from fossils.

Another thing to consider here is that Sapria’s genome is composed of 90% repeated elements. Most of these extra elements are DNA transposons or Jumping Genes.

Their presence in such large numbers is somewhat unusual because they are considered as “selfish” genes; they replicate even at the expense of the genome they occupy. For that reason, host genomes usually rein in their expression.

“Most of the time, they’re targeted for silencing,” said Shahid. It seems that either regulation has somehow gone awry in the Rafflesiaceae, or the parasites find some benefit in letting these elements jump around.

A couple of possible reasons for this were proposed, one being that the transposable elements simply ‘accumulate through time‘ due to their isolated lives, another being that they basically function as an ‘invasive species’ since most of them come from the host. 

But to Shahid, it doesn’t make sense that a genome showing so many signs of streamlining — with the loss of genes, noncoding sequences within genes and an entire plastid genome — would be blasé about genomic dead weight. Worse, transposable elements are dangerous.

You must spend a lot of energy in order to silence them,” she said, lest they lay waste to everything. She finds it more likely that these transposons are doing something for the parasite; the question is what.

Their presence might be tied to all those stolen genes. When transposons jump, Shahid explained, they often bring bits of nearby DNA with them. “These transposable elements might be helping them to carry gene fragments, and then insert them into their own genome,” she said.

The transposons might then be the engines driving horizontal gene transfers that the parasite needs to survive. For example, they might help the parasites steal some of the host’s important gene regulators.

Transposable elements can cause chunks of the genome to move around, too, which can be dangerously destabilising — but can also lead to gene duplication and innovation, Shahid said. That might help parasites stay a step ahead of their hosts’ defenses. 

Transposons could also be responsible for some of the unique features of the Rafflesiaceae: Molina has started to wonder if they have “something to do with the large flowers.”

For now, though, these parasites that stretch the definition of what plants can be are keeping their secrets. Researchers are hoping that these secrets are not lost forever because these plants are critically endangered and all the efforts towards their conservation are falling short. 

References-

  1. https://www.britannica.com/science/horizontal-gene-transfer
  1. https://www.nature.com/articles/nrg2386
  1. https://scitechdaily.com/naturally-gm-crops-steal-genes-from-other-species-to-accelerate-evolution/
  2. https://www.quantamagazine.org/dna-of-giant-corpse-flower-parasite-surprises-biologists-20210421

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One thought on “The Curious Case of Horizontal Gene Transfer

  1. Parasites retain whatever is useful. Mosquitoes (doi: 10.12688/f1000research.7534.1) and many sap sucking insects (a recent paper – think it is from Cell – wrongly reported as the first time in Nature) take in plant DNA and if the expression gives them evolutionary advantage, the genes are retained. Even some molluscs have plant genes.
    In the 70’s when we learned about RNA viruses being responsible for HGT in plants, it was new. When reports on fungi acquiring plant genes started appearing in the 90’s, we were excited. Now we are waiting for reports on vertebrate (hopefully mammalian) genes in mosquitoes.
    Anyway, good work, guys. Keep it up.

    Liked by 1 person

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