When less might be more: The evolution of reduced genomes

The advent of affordable genome sequencing has provided us with a wealth of data. Researchers have sequenced everything from Escherichia coli (4.6 Mbp genome size), to sea urchins (810 Mbp), chimpanzees (3.3 Gbp), and humans (3.2 Gbp). Then there are the massive genomes, which have been identified, including that of the rare Japanese flower (Paris japonica) with a genome of 149 Gbp. But, what does that mean? Maybe it’s more interesting to switch our focus from the large and in charge genomes to those of the small free living prokaryotes who have taken the opposite route.

Two recent articles, one by Luo and colleagues and another by Baumgartner et al., used different approaches to understand the basis and function of reductive genome evolution and how it is related to the adaptation of bacteria to unique niches in the environment.
Genome reduction is what it sounds like, it leads to smaller genomes and there are a handful of theories about why it might occur. Lugging around extra DNA encoding stuff that’s never used, might not be very efficient. A smaller genome, could lead to smaller cell sizes, allowing for more efficient uptake of nutrients. Population genomics theory suggests that in organisms with large effective population sizes, selection is efficient, which could lead to the loss of unnecessary regions of the genome.
Genome reduction occurs in obligate intracellular bacteria such as Buchnera aphidicola, which is an intracellular symbiont of (any guesses?) aphids. The genome of the host and bacterium revealed that B. aphidicola provides an essential amino acid (arginine) to the aphid, while the aphid produces other amino acids that the B. aphidicola doesn’t make, a deal for both sides.
Genome reduction is also seen in marine bacterioplankton, and is often referred to as genome streamlining, suggesting that reduction in genome size is beneficial and driven by positive selection. The functional genes retained after genome streamlining in symbionts and free living marine bacteria are different, however, in both cases they have been shown to be linked to their ecological niche.

In their article, Luo and colleagues analyzed genomes from the most abundant cyanobacteria:  Prochlorococcus, where genome reduction is apparent. These picophyotplankton include different lineages that have been divided into groups (ecotypes) inhabiting distinct niches. They also focused on other incredibly abundant bacteria, including the alphaproteobacteria SAR11, and the gammaproteobacteria SAR86.
Not all of the groups within Prochlorococcus have the same size genome, there is actually a consistent stepwise decrease in size. However, in the SAR11 and SAR86 clades, members have streamlined genomes across the board. Luo et al. compared rates of the ratio of radical substitutions (changes in base pairs that code for different amino acids), to conservative substitutions (changes in base pairs that don’t lead to different amino acids), in different subgroups of these globally abundant lineages.This is a pretty cool study in which the authors tried to figure out what the selective pressures were that originally led to genome reduction.

Interestingly, they found that there was an excess of radical changes in the organisms with streamlined genomes compared to relatives with larger genomes. They also find that both the loss of large segments of DNA as well as genetic drift have driven genome reduction in marine bacterioplankton.
Another interesting story presented by Baumgartner and colleagues, focused on a fresh water bacterium (Sphingobium sp. Z007) isolated from Lake Zurich. Previous studies have suggested that genome reduction in this lineage is linked to switches to environments lacking substrates. They grew bacteria for about 600 generations in thelab either with or without a flagellate that would graze on them, allowing them to either evolve with or without predators. Interestingly, they found three strains lost a big chunk of their genome during their evolution in culture with the predators.
These three strains grew better compared to other strains that had undergone the same predator treatment, although they had shifted to growing as cell aggregates, which are also resistant to grazing. Additionally, when the three isolates were grown in another co-culture with predators, they did better than both the original ancestral strain and the strains evolved without predators. There were some drawbacks to the reduction in genome size, however, since they were not able to grow in the presence of one compound which they had lost the degradation pathway for.
There are a variety of aspects to genome structure and function that we are only able to unravel now that sequencing is affordable and fast. The model organisms discussed by both of these recent studies provide unique windows into the evolution of reduced genomes.
Baumgartner, M., Roffler, S., Wicker, T. and Pernthaler, J., 2017. Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment. The ISME Journal. doi: 10.1038/ismej.2017.87
Luo, H., Huang, Y., Stepanauskas, R. and Tang, J., 2017. Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nature microbiology, 2, p.17091. doi: 10.1038/nmicrobiol.2017.91.
van Ham, R.C., Kamerbeek, J., Palacios, C., Rausell, C., Abascal, F., Bastolla, U., Fernández, J.M., Jiménez, L., Postigo, M., Silva, F.J. and Tamames, J., 2003. Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences, 100(2), pp.581-586. doi: 10.1073/pnas.0235981100

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