Investigating Gene Interaction Through ‘Horizontal Science’

To understand the cell can be perceived as a simple task, it is the most basic and fundamental part of life. Yet often understanding something is more complex than first thought. The current approach to understanding the cell as a whole, is to break down individual parts or pathways, and investigate these in isolation. In theory, once we completely understand each element, we can combine our knowledge and appreciate the cell in its entirety.

Understanding the cell is one of the greatest challenges facing biological research. An individual cell is more than a series of elements and pathways, and it’s how these pieces fit together that complicates the cell. When looking at an individual pathway, it is easy to say that altering a variable has a known effect. In reality, the cell is able to compensate by altering other pathways that you just can not consider in isolation. This is one of the largest barriers to successful computational models, in that we simply do not fully understand the compensatory mechanisms within the cell to enable modeling.

Specific examples within industry include using bacteria to produce synthetic rubber. Utilising synthetic monomers offers many advantages over traditional methods, however, our understanding of the cell is still the bottleneck. As we develop synthetic biology and try to artificially increase our desired products, the cell seeks stability and reacts. We still do not understand the implications that this may have, will increasing the production of our target cause a reduction in metabolism and therefore decrease overall production? The cell always tries to remain balanced and only once we fully understand the cell, can we manipulate them to be beneficial. But how do we further our understanding? How do we realise which genes are essential, and which are not – which can we modify without damaging the cell?

E. coli (K-12) has around 358 known essential genes out of a total of 4,377 genes in rich medium. Developing this understanding of essential and non-essential gene interaction is one of our priorities. Utilising homologous recombination, we mate two strains each containing a single gene deletion, and an antibiotic resistance marker. This produces a library of mutants, each with two gene deletions and resistance markers for two antibiotics. Investigation into which mutant strains grow and therefore develop provides us with ideas about the genetic network, which includes isozymes, compensatory, or bypass pathways relations.

Using the ROTOR+, we are able to produce thousands of mutants each day, and also investigate a variety of conditions and carbon sources (French et al, Molecular Biology of the Cell, 2016). Still, to exhaustively test every combination is estimated to take up to 10 years. One of the worries is that other researchers could be investigating the same area, which could be seen as wasteful of both time and resources. Many researchers work independently, which can be referred to as ‘vertical science’, where one group of researchers exclusively work on their individual research. The Mori group’s research is ‘horizontal science’, where using high-throughput techniques (HTP), his group generates lots of data across multiple strands of research. The concern is that vertical scientists and horizontal scientists may not be aware if they are producing the same data, and are therefore not utilising resources. Collaboration is a key value, with this, a view that researchers should communicate their ideas and build relationships with other researchers, to avoid the accumulation of unanalysed data. Of course, in these situations funding can be limiting, preventing the opportunity to collaborate, although communication should still be sought.