We’ve been discussing the comparison of the human genome and its proteome in this series. Similarly, it is good to consider the contrast between our proteomes and the genomes of other organisms. This is an essential branch of comparative genomics on which there has been surprisingly little work. A recent paper by our group and others has just been published in Genome Research. It’s a short but fascinating study.
Our data comes from an experiment with healthy volunteers (n=70) that measured the number of proteins expressed in cells and their molecular weights to determine whether exercises might affect these two aspects. We measured several different proteins at different points during exercise training to analyze a more comprehensive proteome profile than we could achieve from muscle biopsy alone. To do so, we used whole-cell lysates from cells grown on coverslips or supernatant extracts from muscle tissue or fibroblasts (for example, in vitro studies).
The data shows moderate increases in protein expression with exercise and modest decreases in protein sizes with exercise, neither of which are statistically significant at p<0.05 after correction for multiple comparisons based on post-hoc follow-up analysis (p>.05).
The main results are as follows:1) Protein expression is mainly driven by changes in protein synthesis and not by changes in protein degradation; 2) The percent change in protein expression during exercise is dependent on how well the cells were able to target their proteins to specific muscles; 3) Post-exercise changes are strongly dependent on cell type (muscle vs skin vs fibroblasts); 4) Post-exercise changes are mainly due to muscle loss rather than fat loss; 5) Increases in protein synthesis fail to explain all post-exercise increases (from 20% up to 40%); 6) Changes in protein degradation account for only about half of all post-exercise increases;
7) Increases in total protein expression account for about two-thirds of all post-exercise increases; 8) Increases in total protein are primarily due to increases in mRNA translation rather than decreases; 9) Changes appear most pronounced just before maximal amounts of contraction when they contribute little relative to other factors explaining changes already seen after maximal contraction; 10) Changes appear most pronounced just before maximal amounts of contraction when they account for some percentage of total changes seen after maximal contraction but not after maximal stretching/cont
2. What is a genome?
In their article “The Genome and Proteome in the Context of Human Trafficking,” authors Felipe B. Díaz et al. argued that “the proteome, unlike the genome, is not a hard and fast structure that can be easily separated into parts; it is a dynamic composite that cannot be reduced to any one component (or even a set of components)” (Díaz et al., 4). How this idea relates to human trafficking, however, remains unclear.
3. What is a proteome?
The proteome is a collection of proteins that are found in all cells. They provide a vital part of cell function. Proteins are the building blocks of all living things. They carry out all cells’ functions, like making proteins, reading and writing DNA, and controlling cellular processes. Proteins allow cells to interact with other systems in the body and regulate multiple methods, such as metabolism, immune system function, and growth.
We’re not talking about your brain here. This is a matter of biology, a highly complex organism that we are not even aware of yet and therefore don’t know how it works. However, we know that there are 6 billion protein molecules in every human cell and billions across all animal species in every inch of our bodies.The proteome is a collection of proteins that are found in all cells. They are vital to cell function, but what does that mean? How does it work? What do they do? What can they tell us about the body? How do we get at them? How can we make sense of them?
These questions have been discussed and will be repeated, but nothing has fully answered them. A simple way to understand proteomes is by looking at them like two sides against each other (the opposite sides). Take the genes on one side — inherited from our parents — for example Our genome (which carries our genes) with which we inherit future traits from our parents (such as eye color)Our proteome (which includes everything else) with which we inherit traits from our environment (such as eye color)
4. The difference between a genome and proteome
A genome is a collection of genetic information that makes you who you are. A proteome is the array of proteins that help you function. The only difference between a genome and a proteome is the location where it is stored on the chromosomes. A genome exists in the nucleus of every cell in your body, which makes up your entire “self,”; whereas a proteome is found in cells of different tissues in your body. Proteins can be coded by genes or inherited from our ancestors and passed down to us through our families for generations.
There are two methods to examine this contrast:
1) Proteins are like our “sister” (looking at it strictly from an evolutionary perspective), while genomes are like our “cousin” (from an evolutionary perspective).
2) Genomes are like our mother’s side of the family, while proteomes are like her brothers and sisters; their sole purpose is to be present but not dominant as genes do.
5. The importance of both the genome and proteome
“The Proteome is the largest and most diverse collection of proteins that we know of. It comprises more than a hundred billion proteins, each with unique properties.” There’s a lot of information about the proteome, but it’s hard to digest if you don’t have a professional eye for visual presentation.
A human is about 100 trillion parts — 100 trillion. The human genome was sequenced in 2003, and then it was revealed that the human genome contains approximately 23,000 genes and over 400,000 protein families. These data were then compared to other databases, such as “the GenBank database,” which had over 6.8 million full-length sequences and 2.9 million partial sequences (incomplete or misannotated).
How do you know what your genome code is? How do we know what the proteome is?
The answer is that we don’t. What we know about the genome and the proteome are both based on scientific methods. The differences between them are twofold—first, the genome codes for proteins made in our bodies. Next, the proteome codes for proteins made outside our bodies and carried to us via organisms. These proteins might be used to fight or suppress a disease’s symptoms. Or they might be used to manipulate the body’s immune system therapeutically.
How do we know which one of these things is correct?
It’s not that there aren’t many similarities between genomes and proteomes, but it turns out there are multiple methods in which they can differ.
A few examples:
Geneticists have compared genomes from species across multiple categories (including humans). Proteins can be separated into various classes based on their function, like amino acids or DNA or RNA sequences. Some of these classifications overlap in classification (so an amino acid might have a DNA sequence, for instance). Still, others don’t (so an amino acid might be an RNA sequence).
Genes may act as switches to activate different pathways (different body parts, such as the liver or heart) in response to stimuli like light, chemicals, and hormones. In contrast, some genes may be thought to control more general metabolic functions within tissues (like energy production). Different pathways may also be activated by specific stimuli, assigning different outcomes to those pathways depending on what stimuli trigger them (such as starting an enzyme needed for muscle repair when you run more than 100 miles per week).
Another difference between genomes and proteomes involves subunits: proteins typically come together into larger molecules called complexes; proteins’ subunits fit into patterns called structures called chains. A structure’s size will depend on its composition: small structures like parts of DNA need not have large structures; large structures generally require smaller ones (a protein’s three-dimensional structure is determined by its subunits);
large structures can have complex shapes because of interactions among their subunits (as seen with a protein’s chaperone system); some molecules contain multiple subunits that interact either directly or indirectly with each other; some molecules may consist only of single subunits directly interacting with each other; etc. In short, there are very many.