by Frank Ryan
Symbioses, as they become established over long periods of time, will inevitably bring about genetic changes in the partners. Take, for example, some 319 species of hummingbirds, which are widely distributed throughout the warmer parts of the Americas—these live almost entirely on nectar, which is provided by flowers. Specialized joints in the wings of hummingbirds enable them to beat so fast they are practically invisible; this “adaptation” enables them to hover with pinpoint accuracy in front of the appropriate flower. In this symbiotic partnership, the Columnea plant has changed the shape of its flower to suit the elongated and curved bill of the violet sabrewing hummingbird that pollinates it; meanwhile the hummingbird has changed the length and shape of its bill to exactly fit the flower. If one sits back for a moment to think about this, bird and plant are now influencing one another's evolution to accommodate the symbiosis. To put this in evolutionary terms, natural selection is now operating, to a significant degree, at the level of the partnership—the holobiont.
The benefit of such a mutualism is clear. Only the violet sabrewing bill fits the Columnea flower: only the Columnea flower is likely to be fertilized by the dab of pollen transferred from flower to flower on the brow of the sabrewing hummingbird.
A third type of symbiosis, known as “genetic symbiosis,” is more powerful still as an evolutionary force.
The most abundant element in the atmosphere is gaseous nitrogen, which must be bound up into more complex chemical compounds to be useful for the internal chemical processes of life. The chemical fixation of atmospheric nitrogen is an essential step that makes the free atomic element available to every animal and plant, yet the ability to fix nitrogen is impossible for all animals and plants working by themselves. It is only found in bacteria. Legumes, such as peas and clover, form symbiotic unions with nitrogen-fixing bacteria, known as rhizobia, that live in nodules within their roots. The rhizobia get the high energy they need from their plant host while the host gets nitrogen in a suitable organic form for its internal chemistry from the bacteria.
But there is an additional wrinkle to the nitrogen cycle. Most species of the rhizobial bacteria that live in soil are not capable of fixing nitrogen. They only become capable when a “symbiotic island” comprising a package of six genes is transferred into their genomes from a nitrogen-fixing species. This transfer of pre-evolved and ready-to-go genes from one species to another is a very different mechanism of hereditary change from what we saw with mutation. It's an example of what is called a “genetic symbiosis.”
Unlike the accidental nature of mutations, genetic symbiosis adds genes with pre-evolved potential to a different evolutionary lineage. Some biologists will describe this as “horizontal gene transfer,” which indeed it is. But this is a generically collective term rather than a scientifically definitive concept. The concept of genetic symbiosis defines and explains exactly how the transferred gene came about and how the mechanism of transfer operates. Like mutation, this genetic change is hereditary: the offspring of the changed rhizobial species will inherit the symbiosis island. And again, just as with mutation, the genetic symbiosis will only become evolutionarily significant if and when it becomes incorporated into the evolving species gene pool by natural selection. Genetic symbiosis, working hand in glove with natural selection, has obvious potential for evolutionary change. At its most powerful level, where it involves the union of entire pre-evolved genomes, genetic symbiosis will create a novel “holobiontic genome,” which brings together the pre-evolved interactive genetic potential from two, or more, quite different evolutionary lineages.
Between three and two billion years ago, the Earth had no sign of the green life of plants we are familiar with today. It was populated by the first cellular life-forms, which comprised bacteria and bacteria-like organisms, called archaea. The atmosphere at this time contained no oxygen. But many of the genetic and biochemical pathways now common to life evolved during this microbial stage, so it isn't altogether surprising that all of life today has many genes and biochemical pathways in common. Then, about two billion years ago, life underwent two enormous changes that were described by the eminent evolutionary biologist John Maynard Smith as major transitions. A variety of ocean-bound bacterium, known as the cyanobacteria, evolved the ability to capture the energy of sunlight—the process we call photosynthesis. In time, those cyanobacteria, and a variety of other photosynthetic microbes, became part of the evolution of the kingdom of plants, where the microbes have evolved to the organelles in the cells of the leaves that we call chloroplasts. As a by-product of photosynthesis, the bacteria excreted gaseous oxygen into the oceanic water and ultimately the atmosphere. Today, most of the oxygen in the Earth's atmosphere finds its way through the photosynthesis of plants, algae, and the cyanobacteria that still grow with great abundance in just about every terrestrial and aqueous environment. But this proved to be a catastrophe for the sulfur-breathing bacteria and archaea that originally inhabited the surface waters of the oceans, for whom oxygen proved to be a lethal poison. Today, the descendants of these sulfur-breathers are forced to eke out an existence in places where oxygen cannot get to them, such as the insides of animal intestines or deep in anaerobic mud or between the layers of rock miles under the ground.
Perhaps two billion years ago, another species of bacteria made the leap to breathing oxygen. And now a second major genetic symbiosis came about, leading to all of the life-forms that breathe oxygen today, including plants, animals, fungi, and a variety of single-celled organisms.
How do we know about these extraordinary symbiotic events from the very far distant past? We know because the chloroplasts in the green leaves in plants still retain enough of their original microbial structures and genomes to tell us—and because the mitochondria in the cytoplasm of our human tissue cells also retain their bacterial shapes and structures and the residuum of their original bacterial genomes. We also know that whereas the evolution of chloroplasts happened again and again, involving different photosynthetic microbes, the symbiotic union that led to mitochondria only ever happened once. Or at least only one such union gave rise to the mitochondria that populate the cells of all animals, plants, fungi, and the oxygen-breathing protists that are found throughout biodiversity today. My late friend Lynn Margulis pioneered our understanding of the symbiotic origins of chloroplasts and mitochondria through the serial endosymbiosis theory, or “SET,” which she published in a pioneering book on the origins of nucleated cells.
This symbiotic origin of our human mitochondria is important to our understanding of how the two genomes, mitochondrial and nuclear, still function as a “holobiontic” union even today.
At the time of first symbiotic union, the ancestral bacterium would have probably possessed roughly 1,500 to 2,000 genes. Today, as a result of natural selection working at the level of holobiontic union, the genome of the mitochondrion has been whittled down to a residuum of 37 genes. At some stage in the past, approximately 300 of the original bacterial genes were transferred to the nucleus, where many continue to play a part in the nucleus-mitochondrial genetic linkage that is necessary for normal function. Our human mitochondria populate the cytoplasm, the part of the cell outside the nucleus, where they have evolved to sausage-shaped organelles that look exactly like the original bacteria. The mitochondria also reproduce themselves by bacterial-style budding independently of the reproduction of the nucleus.
This changes the inheritance of diseases that come about through mutations affecting the mitochondrial genes. Where the nuclear genome is inherited from both our parents, and follows the typical Mendelian laws of inheritance (including the patterns of recessive, dominant and sex-linked inheritance we saw in an earlier chapter), the mitochondrial genome is inherited exclusively from our mothers, and it follows non-Mendelian patterns of inheritance.
Mitochondria fulfill an enormously important cellular function—enabling our living cells to breathe oxygen. This is further linked to multiple cellular functions, including energy production; the g
eneration of toxic free radicals that are by-products of respiration; and the regulation of programmed cell death, or apoptosis, which is a necessary part of the cycling of cells in tissues and organs. Since the mitochondrial genome is much smaller than the nuclear genome—some 16,500 nucleotide pairs compared to 6.4 billion nucleotide pairs—we might anticipate fewer mutations and thus a low prevalence of genetically induced disease. However, where most of our nuclear DNA does not code for functional proteins, so that mutations are less likely to cause disease, nearly all of our mitochondrial DNA is coding, and thus mutations are much more likely to cause disease. Moreover, because it comprises bacterial genes, which are more error-prone than vertebrate genes, mutations in mitochondrial genes are about ten to twenty times more common than would be expected. This is further complicated by the fact that mitochondrial disease can also result from mutations affecting those 300 genes that crossed over into the nucleus. All of this means that we are particularly intolerant of mitochondrial mutations, which are apt to cause serious difficulties with the oxygenation of our living cells.
Mitochondrial diseases are complex and tend to be highly specific to the individual, or family, ranging in severity from mild to fatal. It is hardly surprising that the complexity of the underlying genetics, coupled with the variation in disease presentation, can make the genetic basis of such diseases hard to diagnose and trace. Roughly 1 in 7,600 births are affected by genetic abnormalities affecting the mitochondria, contributing a significant proportion of inborn errors of metabolism in newborn children. Mutations, leading to significant disease, have been identified in more than 30 of the 37 mitochondrial genes and in more than 30 of the related nuclear genes. The illnesses include “Complex I deficiency,” which accounts for roughly a third of all “respiratory chain deficiencies.” Often presenting at birth or in early childhood, affected individuals suffer a progressive degenerative disorder of the brain and nervous system, accompanied by a variety of symptoms in organs and tissues that require high energy levels, such as brain, heart, liver, and skeletal muscle. Another mitochondrial syndrome, presenting in adult life, is Leber's hereditary optic neuropathy, which is one of the most common inherited forms of eye disease. Most cases of Leber's syndrome are caused by mutations in mitochondrial genes.
There is growing evidence that mitochondrial dysfunction plays a significant role in a much broader spectrum of diseases and perhaps even the ageing process. Given the advances in genetics, we may in time develop effective gene-based therapy for some of these conditions, but any such therapeutic approach will need to consider the symbiotic evolutionary origins of mitochondria and the complex genetic and molecular dynamics that arise from such an inheritance.
There is another microbe that is quintessentially adapted, through the nature of its life cycle, to entering into holobiontic genetic unions with the genomes of its hosts: this is the rather strange, and in my view, rather extraordinary, microbe we know as a retrovirus.
When I am asked whether poliovirus is a non-living or a living entity, my answer is yes.
ECKARD WIMMER
Eckard Wimmer is a distinguished German-born virologist who has spent his professional life working in America. In 2002, he astonished the world when he and his group of colleagues reconstructed the polio virus from mail-order components they assembled in the laboratory. Twenty years earlier, Wimmer had been the first to sequence the polio virus genome. Even today, as his definition suggests, it is head-scratchingly difficult to define what we mean by a virus. This definition has not become any easier with the passing of the years, a difficulty compounded by the recent discovery of giant viruses with 1,000 or more genes, making them genomically more complex than small bacteria. Perhaps rather than attempting to define viruses, a more sensible approach is to examine some of their basic properties.
All viruses are coded by genomes—just as in all of life, from bacteria to mammals. Most viral genomes are DNA based, but some have genomes based on RNA. In fact, viruses are the only organisms that use an RNA code. This makes some biologists wonder if RNA viruses might date back to a purported stage in evolution known as the RNA world, which, if this theory is correct, would have preceded the present DNA-based world. RNA, unlike DNA, is capable of replicating without the help of protein enzymes. Thus it would have entailed a smaller step in the origins of life from the purported ambient soup of chemicals for RNA-based self-replicators to set the ball rolling. Viruses are obligate parasites; they are invariably born within the cells of their hosts. They can die—like bacteria, they can be killed through heating and a number of other toxic agencies. They also go through “life cycles” that involve a stage of reproduction, another basic characteristic of living organisms. The next, and perhaps most important, question is predictable: Do viruses evolve through the established evolutionary mechanisms?
The answer is yes—they most certainly do.
Viral genomes mutate faster than those of any other known organism. This is part of the explanation why our immune system finds it so difficult to counteract HIV-1 once it has got inside our bodies. Within a year or two of infection there are literally billions of different evolving strains of the virus within a single infected person. While viruses do not contain their own epigenetic inheritance systems, they will sometimes take advantage of host epigenetic systems when they invade the nucleus. Are they capable of hybridization? Again, they are the prime examples—it is the way in which new pandemic flu viruses emerge to provoke mayhem around the world. Are viruses capable of symbiotic evolution—in the jargon, genetic symbiogenesis? As I shall soon explain, they are the ultimate example of this.
Why then do some scientists insist that viruses do not belong in the tree of life? As far as I can see, this appears to derive from historical reasons dating back to mistaken notions of how viruses came into being.
When life was defined in about the middle of the twentieth century, at a time when we knew a lot less about viruses, a consensus of biologists took the view that the minimum requirement was an enclosing cell membrane containing the enzymatic and biochemical means of conducting its own internal chemistry. To my mind, this suggests that the definers took pains to invent a definition that specifically excluded viruses. Why should life demand a cell membrane as a defining boundary while excluding a viral envelope, which is the viral equivalent of a cell membrane? And as to the requirement for a life-form to carry out its own internal chemistry, only a limited number of so-called “autotrophic bacteria” are capable fully of carrying out their own chemistry. All other life-forms, including we humans, are dependent for survival on a host of other living entities for our essential amino acids, fatty acids, and vitamins. Others appear to have ruled out viruses as life-forms because they are inevitably parasites—this despite the fact that so too are many different types of bacteria.
Another mistaken idea adopted at the time of the cellular definition of life was the notion that certain viruses, such as bacteriophages and retroviruses, evolved from wandering pieces of the host genome that acquire transmissible characteristics. I think that given the present understanding of viral lineages, this is no longer credible. The evidence points to bacteriophages and retroviruses evolving out of exceedingly ancient viral lineages—albeit these viral lineages, like many others, have evolved in an intimate symbiotic interaction with their hosts—what virologists term “co-evolution”—throughout the eons. At the time of the original definition, biologists had no knowledge of the makeup of genomes. Now that we do have this information, there is a very simple way in which we can put this idea to bed once and for all. If phage viruses and retroviruses were truly offshoots of the host genome, the viral genome would largely consist of similar genes to the host genome. Instead we find the very opposite—the majority of viral genes are exclusively found in viral lineages. Viruses are incredibly creative evolutionary entities, capable of manufacturing new genes all by themselves. And where there are genuine genetic commonalities between virus and host, the exchange of genes is fa
r heavier in the direction from viruses to their hosts.
AIDS is the pandemic of our age. The causative virus, HIV-1, is a retrovirus. Even among the viruses, which have many strange and curious members, the retroviruses are remarkable. As the “retro” of their name suggests, they contradict the now-outmoded dogma of the inexorable progression from gene to protein via messenger RNA. Not only do retroviruses have a genome that is based on RNA rather than DNA, they also have their own enzymes capable of converting the viral RNA to its complementary sequence of DNA before they inject their converted genome into the host cell's nucleus. This is also the key to understanding how retroviruses are capable of changing the evolutionary history of the hosts that they infect. To put it in evolutionary terms, retroviruses can invade their host germ lines and thereby enter into genetic symbioses with their hosts through the creation of a new holobiontic genome—one that, in our case, is made up of a symbiotic union of retrovirus and the human genome.
HIV-1, the main cause of AIDS, spreads by unprotected sexual intercourse, whether anal, vaginal, or oral, when the virus finds a way through the surface tissues. It can enter the blood stream directly when people share contaminated injection equipment and can also be transferred from a mother to her baby during pregnancy or birth, or through breastfeeding. Even at this epidemic stage, when the virus is behaving as a selfish genetic parasite, a symbiotic pattern of evolution has already begun. An important international research investigation has shown that the rate of disease progression in infected people is linked to subtypes of a human gene known as HLA-B. This is one of the genes that determines immune responses and tissue during organ transplants. The distribution of HLA-B subtypes in the human population changes the evolution of the virus: meanwhile the virus, through lethality for specific subsets of the same gene subtypes, changes the human gene pool.