Genomes in flux

The ever-changing face of the bacterial genome

Evolution depends on diversity - and bacteria are past masters at shuffling their genomes.

The life of a bacterium is an uphill struggle; a species living inside the human body faces a constant battle against the immune system and antibiotics if it causes disease. It is engaged in a continuous biological arms race with its host, which is constantly developing new ways to expel it. In short, it must change or die.

And change it does: as more and more genomes are sequenced, the full extent of the adaptability of bacteria is becoming clearer. Some bacteria evolve so rapidly, even sequencing teams struggle to keep up.

At a recent meeting to commemorate the 25th anniversary of the sequencing of the first DNA genome the Wellcome Trust Sanger Institute's Dr Julian Parkhill described how sequencing projects have helped shed light on the tactics used by bacteria to adapt to their environment and outwit their hosts.

All change

Insights have come from several areas. Comparisons between different bacterial strains, or between related species, can reveal how genomes have changed over time. In addition, certain features of the DNA sequence can suggest mechanisms to promote genome shuffling - typically repeated sequences promoting DNA exchange between different parts of the genome. Finally, even sequencing experiments themselves can reveal strange goings-on inside the genome, with mysterious rearrangements or unexpectedly high variability between individual bacteria. A few examples are shown below.

It is tempting to think of an organism's genome as something immutable, cast in stone, yet nothing could be further from the truth. The sequence of a bacterial genome is like a snapshot of 'evolution in action'. It tells us what is happening in one organism, at one point in time. But as more sequences become available and comparisons between genomes are made, the genomes are turning out to be far less fixed than had been imagined.

Bacteria have been evolving for nearly four billion years - and for the first three billion years or so, they had the planet pretty much to themselves. Far from being 'primitive' organisms, bacteria are highly evolved, adapted to their specific ecological niches. And one of their most powerful attributes is the ability to create myriad new forms of themselves. As Darwin noted, evolution depends on diversity, and during their long history bacteria have developed a fiendish array of mechanisms to generate spectacular levels of diversity.

By providing insights into these mechanisms, pathogen genome sequencing is laying the foundations for a better understanding of these tenacious and flexible organisms and for new ways to outwit them. Yet it also reinforces the point that bacteria possess the means to be very challenging foes indeed.

Bacteroides fragilis

Residence: Human gut
Motive: To survive and propagate
Offence: Opportunistic pathogen causing potentially deadly systemic infections, particularly in patients undergoing gastrointestinal surgery

Bacteroides fragilis is a gut-dwelling bacterium that can be a killer when it finds its way into the bloodstream, attacking all the main organ systems. It comes in at least three forms, differing in key surface structures, which provides a mechanism for evading the host's immune response.

Anomalies in sequencing experiments suggested something odd was going on inside its genome, around regions where the genes encoding its key surface structures were found. Remarkably, B. fragilis appears to have short fragments of DNA able to rotate through 180° - a flip that switches its surface coat from one form to another.

Neisseria meningitidis

Residence: Human throat
Motive: To survive and propagate
Offence: 500 000 cases of meningitis and septicaemia worldwide each year

Neisseria meningitidis is a common inhabitant of the human throat, but rarely causes disease. To remain in place, Neisseria constantly changes its external appearance to present a continually moving target to the immune system. To do this, its DNA codes for many different surface structures - in fact, it devotes 25 per cent of its genome to the task.

But this is not the only way Neisseria can change its appearance. It also has a habit of picking up bits of DNA from its surroundings, and integrating these fragments into its genome (thanks to a preponderance of repeat sequences which promote DNA recombination).

Perhaps even more cunningly, Neisseria has a bank of gene-like sequences next to a gene for a surface protein. The presence of DNA repeats appears to promote recombination in this region, creating new genes and hence new surface proteins with different characteristics.

Salmonella typhi

Residence: Human gut, liver, spleen, bone marrow
Motive: To survive and propagate
Offence: typhoid fever, killing 600 000 people annually

Salmonella typhi evolved from a relatively harmless gut-dwelling bacterium about 30 000 years ago - a blink of an eye in evolutionary terms. It is a distant relative of E. coli (only a little more closely related than humans and mice), and yet the two have very similar genome structures, with genes with similar functions ordered in the same way along their chromosome. What non-pathogenic E. coli lack are the large chunks of DNA known as 'pathogenicity islands', which code for an array of genes that together make S. typhi a very nasty bug to encounter.

Pathogenicity islands are large, but seem to move about genomes en bloc. By contrast, most of the differences between E. coli and S. typhi are minor changes speckled throughout the genome. But even tiny changes to DNA can have a profound biological impact. Unlike S. typhi, which infects only humans, its less deadly relative, S. typhimurium, infects a range of mammalian hosts. Yet comparisons between genome sequences reveal that host specificity may be dependent on changes as small as a single base pair.

In its more restricted lifestyle, S. typhi has little need of many of its genes, which begin to waste away and turn into non-functional 'pseudogenes' - of which S. typhi has at least 204. There is no selective pressure to maintain genes of redundant function, and it may even be advantageous if such genes are inactivated.

Campylobacter jejuni

Residence: Human and avian gut
Motive: To survive and propagate
Offence: 60 000 cases of food poisoning per year in the UK alone, occasionally followed by a neuro-muscular paralysis termed Guillain-Barré syndrome

Campylobacter has regions within its genome where strings of repeated single bases or longer sequences appear. These 'polymeric tracts' often appear associated with genes coding for cell surface proteins. Polymeric tracts are hard to copy - DNA-copying enzymes often slip, adding or removing bases by mistake. These mistakes change the DNA sequence of the gene, and hence the type of protein produced.

This is a random process, but means that a proportion of bacterial cells in a population will have different surface characteristics. This is a useful survival mechanism for the bacterium: even if most of the population is recognised and killed off by the host's immune response, there will be a few cells with different coats that can expand to fill their place.

Oddly, although Neisseria has a similar number of genes containing polymeric tracts, slippage is much more common in Campylobacter.

Yersinia pestis

Residence: Human bloodstream, lymph and fleas
Motive: To survive and propagate
Offence: The Black Death and the annihilation of a third of the European population during the 14th century

Yersinia pestis is an even younger pathogen - perhaps just 1500 years old. Surprisingly, this organism also originated from a relatively harmless gut-dwelling bug, Y. pseudotuberculosis. A turning point in the evolution of Yersinia appears to be when one of its ancestors commandeered genes from bacterial and viral insect pathogens, allowing it to infect insects. But on its own this was not sufficient to turn Yersinia into a killer - both Y. pestis and Y. pseudotuberculosis contain these genes.

It was only when the bacterium acquired pieces of DNA that allowed it to develop a continuous life cycle including both mammals and fleas that it was able to spread quickly through a population living in flea-infested conditions. That change had a profound effect on human history.

Yersinia continues to evolve even today. Sequence analysis suggests that the bacterium has flipped the orientation of stretches of DNA. In fact, sequencing has revealed that Yersinia is constantly inverting chunks of DNA, even during the course of laboratory experiments. Although there appear to be no immediate consequences, it may act to increase the overall flexibility of the genome.