Cells couple the amount of histone proteins to genome content not to cell volume

For cell survival, it is at utmost importance that proteins are constantly available at accurate concentrations to ensure that all cellular processes run smoothly. For most proteins, the synthesis rate is coupled to cell volume and increases with cell growth. However, for a subset of proteins, this machinery-limited regulation would have severe side effects. Analyzing the homeostasis of histone proteins through the cell cycle, Claude et al. could solve this conundrum. Just recently, their results have been published in Nature Communications.

@Claude et al., 2021; Nature Communications

The human body consists of around 40 trillion individual cells and each of them is a structurally distinct, independent and self-sustaining system. Cells are the ‘building blocks of life’. They are able to take up nutrients and to make use of the bound energy, they can react to different environmental stimuli, e.g. temperature, and they safely store our hereditary information, our DNA, inside their nucleus. The full functionality and the correct number of cells are critical for the organismal health.

To maintain a constant number, all cells divide regularly into two fully functional daughter cells. The series of events that take place in order to prepare all cellular organelles for cell division and occur during cell division are part of the cellular process, known as ‘cell cycle’. During one cell cycle, a cell is extremely busy with duplicating the DNA content, transcription, protein synthesis, assembling of the subcellular organelles, import/export of signal molecules, and many more. On top of that, for all these processes to work correctly and efficiently, the cell needs to take care of accurate protein homeostasis despite cell growth and variability of cell volume.

How is histone homeostasis regulated during the cell cycle?

For most proteins, the synthesis rate increases in direct proportion to the cell volume. This means that more proteins are produced while the cell grows bigger and thereby, the correct protein concentration is maintained. However, for proteins such as the basic histone proteins, which bind to the DNA to pack it into the tiny nucleus, machinery-limited regulation might not be the best way to maintain their accurate concentrations. If too many histone proteins are produced but the DNA amount stays the same, the DNA gets more compacted and highly compacted DNA forms an obstacle for many cellular processes. In contrast, too few histones would lead to a loosely packed DNA that can be processed without any control. Both scenarios would harm the integrity and survival of the cell. It is already known in much detail that to maintain the right amount of histones to pack the DNA, cells couple histone production temporally to DNA duplication, so that they are only produced when they are needed. However, given that large cells overall produce more proteins, it was so far unclear how cells could then produce the right amount of histones independent of whether they are small or big at the time of DNA replication. 

Since the cell needs to maintain a constant histone-to-DNA ratio, we proposed that the regulation of the histone concentration is coupled to the amount of DNA in the nucleus (ploidy).”, explained Kora-Lee, a PhD student at the Institute of Functional Epigenetics and the first author of the paper. The team of researcher traced the amount of histone proteins in single cells and population-wide throughout the cell cycle, so from the birth of a cell to its first division, using budding yeast as model organism. “We identified that the histone concentrations decrease with respect to the cell volume, but increased with ploidy. Specifically, cells that enter the cell cycle at a bigger volume still do not produce more histones during S-phase than smaller cells. When the DNA duplicated, the concentration of the histones is therefore doubled as well.”, said Dr. Kurt Schmoller, the corresponding author.

Coordination of histone protein amounts is regulated already on the transcript level

The next step of the researchers was to understand how the observed cell volume-dependent decrease of histone proteins is regulated and on which level. Therefore, they measured how histone mRNA concentrations depend on the cell volume, assessed how histone promoters affect the expression of a reporter gene when the cell volume increases, and verified their results counting single mRNA molecules driven by histone promoters. Their remarkable experimental effort has paid off. The research team could reveal that while most protein concentrations increase proportionally to the cell volume, histone production is coupled to the amount of DNA and that this is regulated already on the transcript level by their promoters.

However, one question had still remained. “To identify the mechanisms that coordinate histone homeostasis to the genome content, we analyzed how the transcription rate of one specific promoter depends on cell volume and ploidy context.”, said Kora-Lee. Using a simplified mathematical model for transcription and histone promoter truncation assays, they could identify that histone concentrations are regulated through template-limited transcription. This means that histone mRNA synthesis is coupled to the gene-copy number but not to the cell volume. 

Altogether, the remarkably elegant combination of experimental procedures enabled the research team to reveal a simple and generalizable mechanism that allows a cell to cope with a fundamental challenge – how to maintain a correct histone-DNA-ratio throughout the cell cycle even though protein biosynthesis is coupled to cell volume.

Further information:

Claude, KL, Bureik, D, Chatzitheodoridou, D, Adarska, P, Singh, A, Schmoller KM. (2021). Transcription coordinates histone amounts and genome content. Nat Commun. DOI: 10.1038/s41467-021-24451-8.