Does the term 'protein expression' refer to the production of proteins only or also their regulation?

Question

I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific website it states that "Protein expression refers to the way in which proteins are synthesized, modified and regulated in living organisms". However, on the National Cancer Institute website it states that protein expression "Refers to the production of proteins by cells".

I was wondering, between these two definitions, which one is more correct? Can protein expression also be used to refer to how proteins are regulated (e.g. can you use the term protein expression when discussing how one protein regulates the activity of another)? Any insights are appreciated.

Answer 1

There are no formal definitions accepted in science for ambiguous phrases such “protein expression”.

If you wish to know what a particular author who uses such a shorthand phrase means you need to examine the context. If you wish to write scientific reports that are comprehensible to others you must express yourself precisely, defining any shorthand phrases that are necessary to avoid clumsiness.

In the context of the question, all that “protein expression” means to me is “expression of protein” — the synthesis of the protein from some entity that has the potential to do so. It a fundamental level that would be a gene or mRNA that encodes a protein (or proteins — that too is unclear), in which case this might be less ambiguously expressed as, for example:

“…expression of protein from gene X inthe plasmid construct Y…”

“…expression of proteins from mRNA in vitro…”

(I would generally retain the preposition. Be kind to it, poor little thing!)

To indicate that one was interested in the potential of tissues to synthesize proteins, then (with all due respect NCI, who are probably simplifying for the layman) one would need to write something like:

“…expression of protein in liver cells (after prolonged starvation etc.)…”

Under no circumstances would I imagine the term “expression” to imply or include “regulation” or “post-translational modification”. To illustrate why, consider the following example of a perfectly valid use in this sentence:

“A problem with expression of mammalian proteins in bacteria is that the required post-translational modification does not occur.”

If I wished to indicate I was also writing about regulation I would say so specifically:

“The expression of haemoglobin in reticulocytes and its regulation”

(and expect others to do so too.)

The fact that, as a professional molecular biologist, I disagree with @MattDMo, who is likewise a professional scientist, only demonstrates that the term is ambiguous. We would both like the context.

Answer 2

The Thermo Fisher definition is more explicitly accurate, although one could argue that the term "production" in the NCI definition implies regulation and post-translational modification (PTMs) as well. Either way, protein expression definitely includes regulation. Typically, when you measure protein expression, such as via Western blot, you are looking at the total amount of your target (regardless of whether you're using an antibody for total protein or PTM-specific) at a single timepoint. That amount has been influenced by regulation of various kinds.

EDIT As David talks about in his answer, context is key. Given your recent questions about Western blotting using mammalian extracts, I implicitly assumed that context in my answer above, when in fact there could be other, very different contexts (such as bacterial or cell-free protein production where there is no regulation other than the promoter(s) present).

Answer 3

Adding a third viewpoint, I'm primarily an electrophysiologist in neuroscience. In my corner of the world, I have to say we can be a bit sloppy about terminology from molecular biology.

There might be more precise meanings intended in other areas, but when someone writes "protein expression" I typically translate this roughly to "we measured protein". It's sometimes presented as a contrast to "gene expression" which roughly translates to "we measured mRNA", or as "activation/activity" of some protein which means "we measured phosphorylation/we measured enzymatic activity by looking at products/reactants".

In this way, like in MattDMo's answer, "protein expression" includes everything leading up to translation of proteins and everything after in terms of modification and regulation, because what's actually being measured is protein level at some moment in time. That also might be all we care about, if the goal is to infer something about that protein's role in some cellular process. The details of how exactly you got to those protein levels might be important to someone else, but are left out when using a vague term "expression".

If this is what is meant, why not just say "protein", instead of "protein expression"? I think this is because it shifts the "agency" of what's going on from protein molecules to a more wholistic view of cell biology. When we talk of changes in protein expression, it is meant to imply that there is a regulatory change, not just some stochastic variation in protein levels: it's an active process that the cellular machinery is involved in, even if the specific steps involved are not mentioned. Additionally, this terminology leaves open the possibility that an observation involves other downstream effectors.