Crosstalk between transcriptomics and metabolomics

Author: Juan José González Plaza, PhD collaborator from ICCRAM Universidad de Burgos- researcher in NANOCOMP project.

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An application to cell-surface interaction studies.

The educational growth of a biologist includes several stages of confrontation and assimilation of knowledge. That includes exposure to the scientific method, learning of a series of theories, diving into disciplines and fields of knowledge, as a set of tools for dissecting organization and evolution of life. The array of possibilities of what can be studied is vast. Among other key concepts or lessons learned, we are confronted with the difference between genotype, and phenotype.

We define genotype as the set of genes that a living being has been “awarded” with. Every organism has DNA, which is a complex of genes and other genetic material. While genes mostly code for proteins (not always), the DNA between genes does not.  DNA can be explained as an instruction manual for an organism, an encyclopaedia of the being. This represents an unlimited potential for being, but always obeying to the constraints of what it is present. For instance, one cannot develop green eyes, if the gene/s responsible for this trait are not there. It does not appear “out of the blue”. While still being more complex than that, I aim only to illustrate the concept.

But as we cannot escape constraints imposed by physics, genotype is a potential, a concept, a dream. When it encounters reality, and by reality, I mean the environment, genotype becomes what it is meant to be at those particular conditions or stage of development. In that case, we talk about phenotype, equalling to the sum of genotype and environment.

While genes and the genotype are fixed since our first to the last moment on Earth, the phenotype is plastic, flows, changes, adapts. Not everything that is possible at the manual of instructions of a cell or particular living being, will happen at that environment. And all that was for a particular bacteria at a tropical environment, is not exactly what will occur to that same bacteria in the in a polar environment.

Real example

I like to illustrate that with an example from everyday life: imagine yourself visiting a Thai restaurant. You are presented with a restaurant menu. There you have all possible choices for Thai food, different possibilities of rice or noodles, or even meat. Notice that since you are at that specific restaurant, you cannot find Spanish cuisine. The restaurant menu represents the concept of the genotype (its specific DNA), where some genes (Spanish dishes) are not present (different DNA mixture for different organisms). You and I both agree now that, unless terribly hungry, you will not order all possible dishes. That you will select a first course, main dish, and probably dessert, if at lunch. That restaurant order will be different at any other time of the day, for instance a lighter meal for dinner because you do not want to go to bed with heavy stomach. Additionally, your order will be distinct if you visit the restaurant during Winter (probably heavier dishes and warmer food) or Summer (lighter and fresher meals). That specific order that you make, which depends heavily on the time of the day, or the season, or even if you are an adult or a kid, that is the concept of the phenotype (remember this for later, RNA). The environment (time frame, season, age, limit on what you can eat) has affected on what it finally was, despite of the huge selection at the restaurant (the potential of being). Take this illustrative example and bring it to actual living beings. Bacteria (Pad Thai restaurant) has a different genotype (restaurant menu, DNA) than archaea -single-celled organisms without a nucleus- (Spanish restaurant, DNA in different composition of genes and other material), and while this genotype has numerous possibilities, the environment affects and interacts to what is present to determine the phenotype (your order at the restaurant).

The RNA

I have mentioned RNA. Well, you must have heard of RNA. We mentioned that DNA is the basic molecule that retains the information of an organism, with different composition of genes. Some genes are used (at specific times), and some code for proteins. But for getting from gene to protein we need an intermediate step, the RNA. RNA is a different flavour of DNA, specific for each gene, and with a time liability. In general (because there are fascinating exceptions), it is a translation tool between DNA and protein (since these two are different “languages”). In the restaurant example above, RNA can be described as the different elements of your order. It tells us which of the genes (dishes) were selected, and we can infer how is the environment (ice-cream probably means hot weather). While in our case this is more complex, we rely on powerful statistical tools, intuition, and the previous knowledge. We build on top of previous research, adapt it, and modify it. When we talk about RNA research, we refer to it as “transcriptomics”. A transcript is the RNA version of a gene (what is written in the restaurant order). The transcriptome, is then the whole order (all of the transcripts given at a specific time and developmental stage in response to the environment). If it helps you to understand, transcriptome is a sort of plural of transcript, but meaning that those are a product of reaction of genotype and environment. 

Metabolites

Phenotype is also “composed” of metabolites. These are small molecules, such as sugars, alcohols, … They are present in every living being, and are products of the metabolism. If we define one of them as a metabolite, the whole group of metabolites at a certain condition is known as the metabolome. The metabolome is related with the transcriptome, but is a step ahead. Coming back to the restaurant, if the transcriptome was the whole order, the metabolome are the dishes on the table after the meal. If we were detectives, by checking those dishes we could infer as well many things about the person who ate, and its “environmental” conditions.

But how does all this phenotype, and orders at a restaurant according to the season or time of the day, relates with a cell-surface interaction project? Instead of different restaurant orders according to time of the day or season, we focus on how different treatments affect the gene expression (RNA), or the metabolism (metabolites). We study what conditions make cells to aggregate, or to form what is known a biofilm (a 3D layer of cells in a biological matrix, providing them enhanced chances for survival and access to nutrients).

While some of the researchers at SurfBio are very interested in studying the genotype, there are others that are more focused on the phenotype (RNA and metabolites are fascinating molecules!). Cell-surface interactions are very dependant on the environment, which among other factors includes the type of surface, availability of nutrients, or stressor factors. Studying why some cells attach to a metallic surface and persist can have deep implications. Microorganisms living inside of a pipe protect themselves forming thin layers at the inner pipe walls. These layers can grow, can damage the pipe, they could start to produce molecules that are harmful for humans, and those molecules could flow on the stream and come to our homes.

Another example, antibiotic resistance. The threat is posed when cells group themselves (biofilm) in hospital surfaces, resist cleaning, use it as a fortress, and from there advance and cause infections. Unfortunately, some are deadly ones. Studying their phenotype (what makes these bacteria to resist, how do they react against different cleaning treatments), can give us clues into interventions (based on the knowledge generated during phenotype study we can propose a better solution to eliminate or control the spread of those cells).

How can we as scientists study the phenotype?

Studying transcripts and metabolites required specialized isolation (or extraction) protocols, besides precise and accurate instruments. When working with both, we work at very low temperatures, as we want to stop the conditions as quick as possible. RNA and metabolites are very sensitive to the conditions, and dozens of seconds are a world difference! We want to preserve them. In that regard, we have the aid of liquid nitrogen. This gas, when liquid, has a temperature of –196 ºC, and ensures that “time stopped” for our samples. Then we can study what was happening at that specific environment on the right conditions.