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Are transcription factors and protein kinases only expressed at low levels in eukaryotes?

As regulatory proteins, I would expect their abundance to be lower than most other proteins, but I cannot find any published research to support that.

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  • $\begingroup$ @l0110 Replacing makes the question "Are transcription factors..." $\endgroup$
    – Armand
    Jul 3 at 19:48
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    $\begingroup$ You are grouping genes by overall function "important cellular regulators" but asking a question about a putative shared characteristic "expressed at low levels" for genes which act via very different mechanisms. I would think looking into their mechanisms would help answer your question. $\endgroup$
    – Armand
    Jul 3 at 19:53
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Summary
The abundance of protein kinases and transcription factors vary among and between these broad classes of protein.

General Considerations
Let us first think what might be expected for the abundance of transcription factors and protein kinases.
Protein kinases: These would be expected to be less abundant than their substrate proteins as they are enzymes catalysing a reaction. However some protein kinases are part of amplification cascades (e.g. MAP kinases) so the abundance of individual member would be expected to differ.
Transcription factors: Transcription factor is a portmanteau term that includes both proteins that act generally on promoters (e.g. the TATA-binding proteins TFIIA, TFIIB etc.) and ones that are specific for the promoters of particular genes or classes of genes (e.g. heat shock factor). The abundance of transcription factors might be expected to be inversely proportional to their specificity.
Correlation between Protein Kinases and Transcription Factors: I can see no reason to group these two classes together as the regulation of metabolic activity and gene expression are very different processes. All I would expect is that they would to less abundant than structural proteins such as actin or ribosomal proteins (although differing in abundance among themselves).

One Possible Approach
To the man with a hammer, everything looks like a nail. My particular hammer may not be the best tool for this particular nail, and there are certainly other tools available which other answers may mention, but it’s something you can do at home (without even adult supervision). The hammer is called FlyAtlas 2 and can be accessed at http://flyatlas.gla.ac.uk/FlyAtlas2/index.html. It allows one to examine the extent of expression of different genes in the tissues of the fruit fly, Drosophila melanogaster.

Some Words of Caution
Before looking at experimental data, one should be aware that the abundance of enzymes will vary depending on the particular tissue examined and the physiological conditions. One should also be aware that the data are for abundance of mRNA transcripts, which may not always be proportional to the amount of the encoded protein. Further, although the resource has been published in a peer-reviewed journal, as is normal in science, the referees have not repeated the experiments.

How to Proceed

FlyAtlas 2 selections

  1. Connect to http://flyatlas.gla.ac.uk/FlyAtlas2/index.html
  2. There are two ways of proceeding here. One can go to the Category page, type in a term in either as a Category or Free Search, and select from the menu, as shown.
  3. Alternatively go to the Gene page, click (or tap) on Gene Name and choose from the autocomplete. This gives fewer results than 2, but they tend to be grouped in a way that makes it easier to make repeated searches.
  4. Click Search and tick Whole Body in the results (which may be downloaded in a spreadsheet-friendly format). An example is shown.

FlyAtlas 2 results

Results
A quick application of this approach shows that:

  1. Protein kinases are expressed in whole flies in a ten-fold range, from just detectable (e.g. Cyclin-dependent kinase 2) to 20–40 FPKMs (protein kinase A, calmodulin-dependent protein kinase).

  2. Some protein kinases are highly expressed, but only in specific tissues (e.g. Erk7 in testis).

  3. Transcription factors are expressed in whole flies in a range from just detectable (e.g. Transcription factor AP-2) to about 10 FPKM (TF IIB, heat shock factor)

  4. Some Transcription factors are tissue-specific (e.g. TF B4 in ovary and testis).

  5. Comparative values of cellular enzymes are glycogen phosphorylase (c. 100), phosphofructokinase (c. 50), enolase (c. 200).

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  • $\begingroup$ Thanks David. I usually use R or Python for these analysis but it is nice to know there is a website to do it. My own analyses showed these two groups of genes are expressed at low levels for mRNA and protein when comparing to other groups of genes in plants. Since I want to know if there is a reference there (that was the original question), I up-voted your answer but not accept it. But thanks again for your time and effort! $\endgroup$
    – l0110
    Jul 5 at 2:39
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    $\begingroup$ @l0110 The website is, like others of its type, a front end to a relational database, providing the general user with the ability to make a restricted range of queries. It also provides APIs for the programmer to make queries in whatever language he prefers (see online Docs). Although perhaps not of interest to you as a plant scientist, queries using the recent categorization of fly genes into classes on FlyBase might be a better way to approach the question. I imagine there are similar resources for Arabidopsis. Btw. I have deleted my comments on your question now. $\endgroup$
    – David
    Jul 5 at 8:25

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