91Â鶹ÌìÃÀ

If genes are the sheet music, proteins are the melody. In living organisms, genes are transcribed and translated into proteins, which carry out all the functions necessary to keep a cell, and the organism, alive and well. An organism’s repertoire of protein-coding genes allows it to thrive in its environment, as well as adapt accordingly to changes in external conditions. While humans have about , bacteria tend to have just a fraction of that, usually in the .

Despite their relatively small genomes, bacteria can undergo a process known as genome reduction, whereby they do away with sections of their genome that are not strictly necessary for survival. Bacteria can get rid of both protein-coding and non-coding stretches of the genome during genome reduction, which reduces the overall size, as well as the functional diversity, of their genome.

Stripping down an already-small genome may seem foolhardy, but there are some situations where it makes sense. The ‘genomic streamlining theory’ suggests that bacteria and other prokaryotes that have smaller genomes experience an as a result. This advantage can be particularly significant in nutrient-scarce environments, where ruthlessly squeezing out unnecessary genes can help the bacteria outcompete its neighbors by increasing the efficiency of how the cell runs.

Mechanisms of Genome Reduction and Streamlining

Genome reduction usually happens when a bacterium finds itself in a relatively constant environment with few external stressors—suddenly, its arsenal of genes used to deal with all kinds of situations are rarely called upon and, for the most part, become less critical. When mutations arise in genes that do not affect the bacterium’s fitness, these mutations are retained, and, over time, can lead to gene erosion, whereby genes accumulate inactivating mutations. In bacteria, , which rapidly reduce genome size, can also occur, provided that the deleted genes were not paramount for the bacterium’s survival.

One relevant context for genome streamlining is the open ocean. There, bacteria of the SAR11 clade play a major role in the marine carbon cycle by converting carbon dioxide (CO2) captured by photosynthetic organisms back into atmospheric CO2. SAR11 bacteria also have rather small genomes of , with hallmarks of genome streamlining, such as having , e.g., pseudogenes (nonfunctional DNA sequences that resemble functional genes found elsewhere in the genome). SAR11 bacteria are also missing genes for the biosynthesis of some important enzyme cofactors. This is rather unusual for a free-living organism, as it would need to evolve alternative ways of acquiring these cofactors. Indeed, SAR11 bacteria have likely evolved for cofactors, or their precursors, such as thiamine (vitamin B1).

Researchers believe that streamlining of the SAR11 genome has maximized the organism’s efficiency for cellular replication. The smaller your genome, the less you need to replicate; small genomes save on carbon, nitrogen and phosphorus requirements, which can be limited in the open ocean. However, not all marine bacteria have streamlined genomes, and scientists have yet to understand why such processes affect some microbes but not others.

What Selective Pressures Favor Streamlining?

Streamlining is observed inconsistently—though examples are found in many habitats, not all bacteria, in a given habitat or with similar life histories, have streamlined genomes—raising the question of why it occurs in the first place. What are the selection pressures that favor streamlining? This can be difficult to disentangle from other factors that are important in different habitats and bacterial groups.

One environment where genome reduction is particularly relevant, and well-studied, is insect-bacteria symbioses. Many kinds of insects rely on endosymbiotic bacteria with whom they have , to the point that both insect and bacteria are heavily dependent on one another. While SAR11 seems to have streamlined to enhance the efficiency of genomic replication in the open ocean, where building blocks for nucleic acids and proteins can be hard to come by, insect symbionts seem to lose genes that become irrelevant for a comfortable life inside their host.

The insects largely depend upon their bacterial symbionts for nutrients that are lacking in their diet, such as certain amino acids. While the genomes of insect symbionts can be very small, they retain genes that are essential for providing these nutrients, in exchange for room and board. Meanwhile, they often lose genes involved in responding to external stresses, as the host environment is relatively constant and stress-free. They might also lose catabolic genes used to break down carbon sources, as they often receive simple carbon sources from their insect hosts.

Why Does Streamlining Occur? 

Computational models have emerged as a clever way to investigate the question of why streamlining evolves. One model suggests that an of population sizes and mutation rates are key pressures for streamlining; the genome’s structure changes depending on the magnitude of influence of either factor, making it possible to infer from a given organism’s streamlined genome why it might have evolved that way. Different values for population sizes and mutation rates lead to diverse outcomes for the genome, depending on whether coding or non-coding genes are the focus.

For example, the genome of Buchnera aphidicola, an aphid symbiont, has conserved the coding portion of its genome, but cut down on non-coding in-between sequences dramatically. Using the streamlining model, this can be explained by an increase in mutation rate proportional to a decrease in population size, which the organism would have experienced when it moved into its insect host and became cut off from the outside world.

Likewise, a close relative of the SAR11 clade, Prochloroccocus, also has a streamlined genome. Procholorococcus seems to have experienced large population sizes and a slightly elevated mutation rate during its evolution, as its genome is characterized by a loss of both coding and non-coding sequences, though skewed towards non-coding sequence loss. The advantage is probably similar to that of SAR11, given that the 2 relatives both inhabit the open ocean.

Streamlined Too Hard?

Genome streamlining is not without its consequences. Among genes that are absent across members of the SAR11 clade are genes involved in controlling the cell’s cycle of growth and division. A preprint (not yet peer reviewed at the time of this article’s publication) suggests that when exposed to stressors, such as excess nutrients or high temperatures, a representative SAR11 strain , whereby the cells have an abnormal number of chromosomes. Bacteria usually have a single circular chromosome, but the perturbed SAR11 strain had 2, or even more, chromosome equivalents when exposed to stress.

There is a trade-off at play here—after millions of years of adaptation to the ocean’s nutrient-dilute, but stable, conditions, certain SAR11 bacteria seem to have streamlined their genomes to the point where they cannot properly counter “new” stressors.  The SAR11 strain has seemingly sacrificed flexibility for dominance, being among the most abundant organisms in the open ocean. Notably, some stressors may intensify as an effect of climate change, and it remains to be seen how this affects the microbe’s future success.

Beyond its ecological importance for the success of bacteria in diverse environments, the concept of reduced genomes has led to other interesting ventures. One of these is developing a with the smallest possible genome, which can provide insights into basic biology as well as be used as a chassis organism for biotechnological applications. Minimal cell research does raise questions about essentiality in context, as different genes can be essential or non-essential for survival, depending on the environment a bacterium finds itself in. However, the study of genome reduction and gene essentiality can also provide insight into the processes that are critical for life to persist, or even emerge in the first place, which are equally interesting subjects of study.

---

What is known about the history of life on our planet? Advances in technology and cross-disciplinary collaboration are helping to address some of life's most foundational questions. From simple, non-living chemical compounds to the vast diversity of unicellular and relatively complex multicellular organisms we see today, examine what is known about early microbial life (EML) in this collaborative report between the American Academy of Microbiology and the .