Economics in Mind, Evolution Has Allowed Some Bacteria to Evolve Sublime Genomes

Pelagibacter ubique is one of the most abundant bacteria on the planet and has also evolved to possess one of the smallest genomes in nature. Is there a link between these traits?

Our lives are often governed by economics. The government or a private company has to balance the inflow of resources with expenses, and how well they perform is often determined by the outcomes, which in turn depend on the inflow of funds – be it through taxes or large investments from other sources, and the mechanisms by which these resources are utilised.

The government finds ways to use its resources to build agents of delivery, including, say, highways or power stations, which eventually result in a tangible output such as seamless transportation and electrification. There are regulatory bodies that balance various parameters while establishing these agents of delivery. The more complex a system, the greater the need for regulatory checks over resource utilisation. The success of these endeavours is often determined by the efficiency with which resources are managed while producing an output.

While these macro-scale economics are obvious to many of us, the fact that within our bodies, cells operate on similar economics is not always apparent. Any living cell receives nutrients and utilises them to produce one or more outcomes, which may for example include the transmission and interpretation of electrochemical signals resulting in sensory responses and may be consciousness; or at a more humble level for tractable, bacterial cells, increasing population sizes by reproducing as often as possible.

For bacteria, it is a complex setup. Their environments are often diverse, and the nature and availability of nutrients variable. Bacterial cells should reproduce, as should most other cell types on the planet, for which they require a genetic material, a large polymeric chemical. They should be able to produce large molecules such as proteins that help the cell perform thousands of chemical reactions that eventually help it convert simple nutrients into a complex progeny cell. The production of the genetic material and proteins involves a series of complex chemical reactions. These chemical reactions, which make life, are costly and require loads of currency in the form of energy. And in the face of competition with innumerable neighbouring cells for often limiting resources, (nearly) every cell faces the necessity to optimise nutrient utilisation, which is something it achieves over the course of evolution.

First, let us look at the construction of the genetic material itself. The DNA polymer is a string of a four-letter alphabet. It includes genes that code for information that dictates the production of the cell’s agents of delivery, primarily proteins. In addition, there are segments adjoining each gene, which tell the cell when to produce the respective agent of delivery. Many cells, especially those of plants and large animals like us include gene deserts, and other sub-optimal vestiges of evolution that have not been pruned out by natural selection. These are often called “junk” DNA.

Bacterial genomes (the word ‘genome’ means ‘genetic material’), thanks to their large population sizes and fast reproduction rates and the resultant accelerated evolution, rarely contain junk. Of course, there are some exceptions. So, natural selection in combination with other evolutionary forces has resulted in bacteria carrying information-rich and streamlined genomes. In turn, bacteria waste little in constructing their genetic material and often keep a tight control over selfish and infectious DNA elements such as the genetic material of viruses, which may enter the cell by horizontal gene transfer.

Often, the size of the genetic material of a bacterium is an indicator of its adaptability and its ability to survive in a multitude of environments. Soil bacterial such as the Streptomyces utilise a range of nutrient sources, deal with a multitude of toxins and produce a variety of other molecules including antibiotics, and therefore contain large genomes (by bacterial standards), whereas certain other organisms which reside in unchanging, cosy environments – e.g., in a symbiotic relationship with a larger cell – have limited metabolic needs and therefore are endowed with small genomes. Such a relationship between genome sizes and adaptability is not clearly established for larger, multicellular organisms.

Each letter that makes up the genetic material is a molecule and differs from another in its atomic composition. Why is this important? At the most basic level, cells need a lot of carbon, nitrogen and phosphorus as nutrients. Not all environments contain all these three elements in abundance. For example, oceans are particularly poor in nitrogen. Oceans, constituting over 70% of the Earth’s surface, represent the single largest habitat-type for life, including bacteria. And there are certain types of bacteria which are particularly abundant in the oceans.

One such bacterium is called Pelagibacter ubique. It is found copiously in both fresh and saltwater habitats. It was first discovered in 2002 in Sargasso sea in the Atlantic ocean bordering the US, and has been found regularly in oceans since. It is a small bacterium but may in fact be the most abundant bacterium on earth, with its population estimated to be a number equal to one followed by twenty eight zeroes (10 billion billion billion). It might play a central role in converting organic carbon into carbon dioxide, which can then be used by ocean algae to produce and release oxygen. The importance of this bacterium to oxygen-loving life on earth can be seen from the fact that oceanic algae and other marine plants contribute over 70% of the total oxygen on the planet!

This important bacterium now has to deal with a severe lack of an essential nutrient: nitrogen. In a cell, one of the more nitrogen-rich molecules is the DNA. So nitrogen is non-negotiable. Now, among the four types of letters that make up the DNA, one pair contains fewer nitrogen atoms than the other. Pelagibacter ubique makes good use of this. Besides having one of the smallest – if not the smallest – genome of any free-living bacterium on earth, the bacterium preferentially uses that particular pair of DNA-constituting letters that requires less nitrogen. It has been hypothesised that this striking property of this organism’s genome is a result of natural selection imposed by nitrogen limitation.

Evolutionary adjustments often involve trade-offs. As the sequence composition of the DNA becomes less diverse, for example by being extremely rich in one pair of letters and poor in the other, the amount of ‘information’ it contains decreases, which is not always a great thing. This enforces changes in the organism’s molecular composition and lifestyle, something that evolution has to account for.

Besides optimising for nitrogen utilisation, the genome of Pelagibacter ubique is an exemplar of efficiency. There is hardly any signature of dead-weight in the genome: very little beyond what is needed to produce important metabolic proteins, and very little selfish genetic elements that can hijack the cellular machinery for non-productive purposes. This genome became the first ‘streamlined’ bacterial genome to be described in the mid-2000s. Pelagibacter ubique is definitely not alone in facing the need to streamline its genome; it may in fact be a representative of a paradigm.

Efficiency is built not only into its genetic material, but also in its size. Being one of the smallest bacterium known to us, it offers a high surface to volume ratio, thus permitting more efficient absorption of nutrients. This is also reflected in the fact that over two-thirds of all protein produced by a Pelagibacter ubique cell are involved in transporting molecules across the cell boundary, which might ensure that limiting nutrients in the immediate environment of the cell are maximally consumed. Thus, the genetic material of an organism, especially fast-evolving organisms, is determined not merely by a checklist of supply and demand, but also by how nutrient supply is efficiently channeled through various demands to ensure prolonged sustenance and reproduction.

(In the next instalment of this series, we will see how bacteria use regulatory agents to manage their economics.)

Aswin Sai Narain Seshasayee runs a laboratory researching bacterial biology at the National Centre for Biological Sciences, Bengaluru. Beyond science, his interests are in classical art music and history.