The Web of Life

Apologies for silence for the past while. Work and life are busy, and I bought an electric guitar. There’s nothing like sitting around crunching power chords (badly) when looking to waste time.

Anyway, I digress. Moving away from my usual rants about the science of climate change and biodiversity loss, this post will deal with a scientific theory that I personally find intriguing – horizontal gene transfer, specifically between prokaryotes and eukaryotes. A nice new paper has emerged, though not without contest, that further supports it.

In science, everybody loves a good old feud, and careers can advance quite rapidly for those who pick a winning side. All areas have their high-profile spats; the field of palaeontology for example is currently embroiled in a mighty twist over the cause of the Cretaceous-Paleogene extinction event, otherwise known as the demise of the dinosaurs 66 million years ago (link). Physics always has several healthy feuds on the boil, the most notable currently being about the nature of dark matter (link). In biology there are also quite a few, such as the exact nature and circumstance of abiogenesis (the emergence of the very first living cells), the varying theories and controversies among which I meandered previously (link).

The theory of horizontal gene transfer (HGT) between bacteria and viruses and multicellular organisms is also a live one. As we know of course, for an organism to reproduce and evolve it must produce offspring, and the offspring receive genetic material from the parents from direct inheritance – vertical gene transfer. Genes from parents to young. These genes over time along successive generations and under a multitude of evolutionary pressures mutate and allow the organism to evolve along a given evolutionary timeline. Species develop into different ones. So far so simple, relatively speaking.

But we know for certain that, among bacteria at least (prokaryotic cells), genetic material is swapped between different species by methods of HGT, usually by conjugation, transformation and transduction. This is one of the primary methods by which bacteria can evolve increased virulence, or antibiotic resistance, for example. Genes for virulence or penicillin resistance move from one species into another more problematic species (in terms of human medicine) without direct reproduction.

But can genetic material pass from single celled bacteria to multicellular organisms, from bacteria to mammals? From viruses to a multicellular host? From parasites, either single celled or multicellular, to animal hosts? This is problematic in that it cannot yet be reliably proven that it does, hence the controversy. Yet, evidence is mounting, and it is becoming more accepted that HGT may have occurred widely and could be a significant force in the evolution of many eukaryotic lineages – plants, animals, etc (link).

Mullticelluar organisms are composed of eukaryotic cells, tough rigid structures that tightly control what material passes through the cell wall. Bacteria (prokaryotic cells) live relatively exposed to the materials of its surroundings and can take up genetic material via transduction and incorporate it into the genome by employing for instance, homologous recombination. If this confers an advantage on the cell this new material is passed on during cell division processes into subsequent generations. If it does not, the cell more than likely dies, and the material is not passed on.

But in eukaryotes it is far from being so straight forward. Adoption of new genetic material via HGT must ideally take place in the germ line cell development phase of an organism (development of sperm, egg, or even at fertilisation) for it to be established in further generations. For example, exposure of virus DNA to skin cell DNA during an infection would be unlikely to result in inheritable changes, in the event of HGT, as skin cells are isolated from reproductive processes so cannot be passed on. The incorporated genetic material would remain local (on the skin).

Yet evidence has been proposed, some quite convincingly, that HGT has occurred between bacteria and fungi (link), between bacteria and insects (link), bacteria and nematodes (an exciting idea for me given my speciality) (link), between viruses and plants (link), and between bacteria and animals (link). Even the human genome has been proposed to contain a myriad of HGT derived genes (link), though it is here that the debate rages like the swirling maelstrom of a mega hurricane. On that one, it is best to remain on the side-lines for now.

Given that life develops in extremely close quarters with many other different species from many different phyla, it is an attractive idea that over a long enough timeline genetic material gets somehow “swapped” between the associates. We humans for instance are swarming in bacteria (literally thousands of species), inside an out, as well as other commensal organisms such as mites and amoebas. Not to mention the countless viruses we live with, the countless parasites we become infected with and so forth. Over millions of years of evolution how much of our genome, or that of any given organism, derived its genes from other organisms via HGT? It seems likely that we are not part of a tree of life, as is commonly depicted, but part of an extremely complicated interwoven web of life. It is very likely that our genes are not just acquired vertically, accumulating variations along the way, from countless preceding generations of forebears, but also from innumerable other sources as well. I may have my father’s genes probably nestling beside those of a parasite, or a bacteria, or anything at all (warning; this is high conjecture, though informed conjecture).

However, the biggest problem in finding HGT genes is how to discern between experimental contamination (during genome sequencing, which is all too easy and common) and genuine genes that are the result of HGT. The publication sphere is littered with many examples of researchers making HGT claims, only to have them refuted by further work from others.

Enter the paper I discovered yesterday. Studying red algae (a single celled eukaryotic organism) that live in acidic hot springs researchers claim to have found that 1% of its genome is derived from foreign sources, possibly via HGT events, and most likely from bacteria (link). They show that the genes are involved allowing the algae to survive in its hostile environment and appear to have strong similarities to genes of non-eukaryotic origin – most likely from specialised prokaryotic extremophiles that co-exist in the host springs with the algae. To mitigate against claims that the putative HGT derived material may be contamination, they write that the HGT genes are clearly located between and within previously well understood algal genes. Convincing? Maybe. In science, and in molecular biology particularly so, what seems to be a general likelihood that something is something can often be proven otherwise.

Nevertheless, it is one of the stronger papers in the field lately. Further work is needed, and a widespread agreed scientific consensus that HGT is, or was, a common occurrence in eukaryotic evolution is far away on the horizon. All biologists can do at present is look at the available evidence and make up their own minds. I am a believer. Professor William Martin of the university of Dusseldorf is not. He published a paper in 2015 strongly suggesting that regular HGT between prokaryotes and eukaryotes is highly unlikely, probably only having occured very early in eukaryotic evolution, if at all (link). In response to this current publication, he states the following, “They go to great lengths to find exactly what I say they should find if (HGT to eukaryotes) is real, but they do not find it…..”.

And on it goes.

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