LATERAL GENE TRANSFER

“A zebrafish larva fluorescing due to DNA it took up with
the help of a zap from an electric eel. Sakaki et al. 2023″

aka HORIZONTAL GENE TRANSFER
https://ncbi.nlm.nih.gov/pmc/articles/PMC10702328/
https://newscientist.com/electric-eels-genetically-modify-other-animals
Electric eel zaps can genetically modify other nearby animals
by Melissa Hobson / 11 December 2023

“A pulse of electricity from an electric eel can make other fish take up DNA from the water in a tank. If this process occurs in nature, it could help organisms acquire new traits and evolve in unexpected ways. In laboratories, scientists use electricity to create temporary pores in a cell membrane – a process called electroporation – which allows genetic material to be transferred into cells. Atsuo Iida at Nagoya University in Japan wondered whether this might also happen in nature. In the wild, electric eels emit weak electrical pulses for sensing and stronger pulses to stun their prey or to defend themselves.

Iida and his colleagues placed electric eels and zebrafish larvae in a tank of water containing DNA that codes for a green fluorescent protein. They fed an anaesthetised goldfish to an eel, which prompted it to emit pulses with an amplitude of around 185 volts. After one day, some of the zebrafish larvae began to glow, showing that they had taken up the fluorescent protein gene. When team member Shintaro Sakaki told Iida the result, he didn’t believe it at first. “So, we observed it together. Then, I was very excited,” he says. The fluorescence lasted for between three days and one week. The findings suggest electric eels and other organisms that generate electricity could stimulate a kind of genetic modification in nature, says Iida, but further research is needed to confirm this. Tadej Kotnik at the University of Ljubljana in Slovenia says the result isn’t surprising, as any type of electricity can make microscopic holes in cell membranes that molecules can pass through. “Let’s say you drop a hairdryer into the bathtub – you will get this because electroporation is physics,” he says. His own work has suggested electroporation can be triggered by lightning.

One important question is whether the zebrafish could pass the genes on to the next generation, says Kotnik. He thinks this is unlikely because of how quickly DNA degrades. But even if only one zebrafish in a million passes the DNA on to their offspring, it would be highly significant, he says, because “such discharges by electric eels could eventually generate new species or increase diversity”. Iida is planning follow-up studies looking at whether electric eel discharges can make smaller organisms, such as bacteria and plankton, take up DNA. Bacteria commonly exchange DNA through a process called horizontal gene transfer, says Kotnik. “Electric eels floating around a diverse set of bacteria could speed up the process of them cross-acquiring various traits, including [antibiotic] resistance.”

“Archaea in the genus Methanoperedens produce methane
and are found in places with low or no oxygen”

RESISTANCE is FUTILE
https://nature.com/articles/s41586-022-05256-1
https://astrobiology.com/methane-eating-borgs-assimilating-earths-microbes
Methane-eating ‘Borgs’ Have Been Assimilating Earth’s Microbes
by Keith Cowing / October 19, 2022

“Last year, a team led by Jill Banfield discovered DNA structures within a methane-consuming microbe called Methanoperedens that appear to supercharge the organism’s metabolic rate. They named the genetic elements “Borgs” because the DNA within them contains genes assimilated from many organisms. In a study published today in Nature, the researchers describe the curious collection of genes within Borgs and begin to investigate the role these DNA packages play in environmental processes, such as carbon cycling. Methanoperedens are a type of archaea (unicellular organisms that resemble bacteria but represent a distinct branch of life) that break down methane (CH4) in soils, groundwater, and the atmosphere to support cellular metabolism. Methanoperedens and other methane-consuming microbes live in diverse ecosystems around the world but are believed to be less common than microbes that use photosynthesis, oxygen, or fermentation for energy. Yet they play an outsized role in Earth system processes by removing methane – the most potent greenhouse gas – from the atmosphere.

Methane traps 30 times more heat than carbon dioxide and is estimated to account for about 30 percent of human-driven global warming. The gas is emitted naturally through geological processes and by methane-generating archaea; however, industrial processes are releasing stored methane back into the atmosphere in worrying quantities. Banfield, a faculty scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and professor of Earth & Planetary Science and Environmental Science, Policy & Management at UC Berkeley, studies how microbial activities shape large-scale environmental processes and how, in turn, environmental fluctuations alter the planet’s microbiomes. As part of this work, she and her colleagues regularly sample microbes in different habitats to see what interesting genes microbes are using for survival, and how these genes might affect global cycles of key elements, such as carbon, nitrogen, and sulfur.

The team looks at the genomes within cells as well as the portable packets of DNA known as extra-chromosomal elements (ECEs) that transfer genes between bacteria, archaea, and viruses. These elements allow microbes to quickly gain beneficial genes from their neighbors, including those that are only distantly related. While studying Methanoperedens sampled from seasonal wetland pool soil in California, the scientists found evidence of an entirely new type of ECE. Unlike the circular strands of DNA that make up most plasmids, the most well-known type of extra-chromosomal element, the new ECEs are linear and very long – up to one-third the length of the entire Methanoperedens genome. After analyzing additional samples from underground soil, aquifers, and riverbeds in California and Colorado that contain methane-consuming archaea, the team uncovered a total of 19 distinct ECEs they dubbed Borgs.

Using advanced genome analysis tools, the scientists determined that many of the sequences within the Borgs are similar to the methane-metabolizing genes within the actual Methanoperedens genome. Some of the Borgs even encode all the necessary cellular machinery to eat methane on their own, so long as they are inside a cell that can express the genes. “Imagine a single cell that has the ability to consume methane. Now you add genetic elements within that cell that can consume methane in parallel and also add genetic elements that give the cell higher capacity. It basically creates a condition for methane consumption on steroids, if you will,” explained co-author Kenneth Williams, a senior scientist and Banfield’s colleague in Berkeley Lab’s Earth and Environmental Sciences Area.

Williams led research at the Rifle, Colorado site where the best characterized Borg was recovered, and is also chief field scientist of a research site on the East River, near Crested Butte, Colorado, where some of Banfield’s current sampling takes place. The East River field site is part of the Department of Energy’s Watershed Function Scientific Focus Area, a multidisciplinary research project led by Berkeley Lab that aims to link microbiology and biochemistry with hydrology and climate science. “Our expertise is bringing together what are often thought of and treated as completely disparate fields of inquiry – big science that links everything from genes all the way up to watershed and atmospheric processes.”

Banfield and her fellow researchers at UC Berkeley’s Innovative Genomics Institute, including co-author and longtime collaborator Jennifer Doudna, hypothesize that the Borgs could be residual fragments of entire microbes that were engulfed by Methanoperedens to aid metabolism, similar to how plant cells harnessed formerly free-living photosynthetic microbes to gain what we now call chloroplasts, and how an ancient eukaryotic cell consumed the ancestors of today’s mitochondria. Based on the similarities in sequences, the engulfed cell could have been a relative of Methanoperedens, but the overall diversity of genes found in the Borgs indicates that these DNA packages were assimilated from a wide range of organisms. No matter the origin, it is clear that Borgs have existed alongside these archaea, shuttling genes back and forth, for a very long time.

Notably, some Methanoperedens were found with no Borgs. And, in addition to recognizable genes, the Borgs also contain unique genes encoding other metabolic proteins, membrane proteins, and extracellular proteins almost certainly involved in electron conduction required for energy generation, as well as other proteins that have unknown effects on their hosts. Until the scientists can culture Methanoperedens in a laboratory environment, they won’t know for sure what capabilities the different Borgs confer, why some microbes use them, and why others don’t. One likely explanation is that Borgs act as a storage locker for metabolic genes that are only needed at certain times. Ongoing methane monitoring research has shown that methane concentrations can vary significantly throughout the year, usually peaking in the fall and dropping to the lowest levels in early spring. The Borgs therefore provide a competitive advantage to methane-eating microbes like Methanoperedens during periods of abundance when there is more methane than their native cellular machinery can break down.

Plasmids are known to serve a similar purpose, quickly spreading genes for resistance to toxic molecules (like heavy metals and antibiotics) when the toxins are present in high enough concentrations to exert evolutionary pressure. “There is evidence that different types of Borgs sometimes coexist in the same host Methanopreredens cell. This opens the possibility that Borgs could be spreading genes across lineages,” said Banfield. Since posting their article as a pre-print last year, the team has begun follow-up work to better understand how Borgs may affect biological and geological processes. Some researchers are combing through data sets of genetic material from other microorganisms, looking for evidence that Borgs exist in association with other species. While her colleagues are using lab-based methods, co-author Susan Mullen, a graduate student in Banfield’s lab, will be getting her feet wet with some very picturesque field work. She recently started a project to sample microbes from the floodplains of the East River throughout the year to assess how seasonal changes in Borg abundance and other microbes known to be involved in methane cycling correlate to seasonal fluxes of methane.”

“A bacterial gene helps make vertebrate vision possible”

GENE SWAPPING
https://pnas.org/doi/full/10.1073/pnas.2214815120
https://science.org/ancient-gene-stolen-bacteria-set-stage-human-sight
An ancient gene stolen from bacteria set the stage for human sight
by Elizabeth Pennisi / 4.10.23

“The eye is so complex that even Charles Darwin was at a loss to explain how it could have arisen. Now, it turns out that the evolution of the vertebrate eye got an unexpected boost—from bacteria, which contributed a key gene involved in the retina’s response to light. The work, reported today in the Proceedings of the National Academy of Sciences, drives home the evolutionary importance of genes borrowed from other species. “Their findings demonstrate how complex structures like the vertebrate eye can evolve, not only by modifying existing genetic material but also by acquiring and integrating foreign genes,” says Ling Zhu, a retinal biologist at the University of Sydney’s Save Sight Institute who was not involved with the work. “It’s incredible.”

Bacteria are known to readily swap genes, packaged in viruses or mobile pieces of DNA called transposons, or even as free-floating DNA. But vertebrates, too, can incorporate microbial genes. When the human genome was first sequenced in 2001, scientists thought it contained about 200 bacteria-derived genes, though the microbial origins of many did not hold up. Hoping to improve on those earlier efforts, Matthew Daugherty, a biochemist at the University of California San Diego, and colleagues used sophisticated computer software to trace the evolution of hundreds of human genes by searching for similar sequences in hundreds of other species. Genes that seemed to have appeared first in vertebrates and had no predecessors in earlier animals were good candidates for having jumped across from bacteria, particularly if they had counterparts in modern microbes.

Among the dozens of potentially alien genes, one “blew me away,” Daugherty recalls. The gene, called IRBP (for interphotoreceptor retinoid-binding protein), was already known to be important for seeing. The protein it encodes resides in the space between the retina and the retinal pigment epithelium, a thin layer of cells overlying the retina. In the vertebrate eye, when light hits a light-sensitive photoreceptor in the retina, vitamin A complexes become kinked, setting off an electrical pulse that activates the optic nerve. IRBP then shifts these molecules to the epithelium to be unkinked. Finally, it shuttles the restored molecules back to the photoreceptor. “IRBP,” Zhu explains, “is essential for the vision of all vertebrates.”

Vertebrate IRBP most closely resembles a class of bacterial genes called peptidases, whose proteins recycle other proteins. Since IRBP is found in all vertebrates but generally not in their closest invertebrate relatives, Daugherty and his colleagues propose that more than 500 million years ago microbes transferred a peptidase gene into an ancestor of all living vertebrates. Once the gene was in place, the protein’s recycling function was lost and the gene duplicated itself twice, explaining why IRBP has four copies of the original peptidase DNA. Even in its microbial forebears, this protein may have had some ability to bind to light-sensing molecules, Daugherty suggests. Other mutations then completed its transformation into a molecule that could escape from cells and serve as a shuttle.

Not everyone agrees that the evolution of IRBP was crucial for vertebrate vision. “I don’t think it had to happen” in order for vertebrates to see well, says Sönke Johnsen, a biologist at Duke University. Invertebrate eyes make do without IRBP, he notes. Instead of shuttling back and forth, the vitamin A complex stays put in the retina, where one wavelength of light bends the light-sensing molecule, while another unbends it. Some researchers have speculated that mechanism hampers invertebrates’ night vision. Yet “there are plenty of extremely good invertebrate eyes,” Johnsen says. Daugherty agrees that vertebrates’ reliance on IRBP could simply be a historical accident. “We are sort of stuck with it,” Daugherty says. Either way, the work supports the idea that horizontal gene transfer can help to endow organisms with new functions, says Julie Dunning Hotopp, a genome biologist at the University of Maryland School of Medicine’s Institute for Genome Sciences. Once these genes take root in a new species, evolution can tinker with them to produce totally new abilities or enhance existing ones. “It is the biological equivalent of upcycling that happens in my Buy Nothing Group.”

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