ATP, RNA, and Phase Separation: The Beginning

Today’s article is the first of a series, and is based on content reported in the ground-breaking peer-reviewed article “Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders” by Doris Loh and Russel J. Reiter published at Antioxidants on September 17, 2021 [1].

[Source: Loh, Doris, and Russel J. Reiter 2021. “Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders” Antioxidants 10, no. 9: 1483. https://doi.org/10.3390/antiox10091483]

There has been extensive research on the pleiotropic properties of melatonin in many different, important areas. A search at the NIH/PubMed archives revealed a total of 28,851 reports (as of October 1, 2021) published on melatonin since 1958, with 1,825 published in 2020 alone. Melatonin may be best described as an antioxidant; but when compared to another major endogenous antioxidant glutathione (GSH), melatonin articles comprise only ~17% of what has been published on GSH. 

Even though it is possible that many of the mechanisms of action by glutathione are better understood while those for melatonin are less clearly elucidated, it is quite clear that the scope of influence by melatonin is as extensive, if not more, than glutathione and other endogenous antioxidants. 

The fact that melatonin has been referred to in literature as a ‘smart’ molecule, with the ability to perform opposite functions in the same pathway such as autophagy where it has been reported to be protective in normal cells but cytotoxic in cancerous cells [2] truly captures the imagination as to how melatonin can exert such different properties in the same pathway under different contexts.

The in-depth, novel review  “Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders” may finally shed light on why and how melatonin can be a ‘smart’ molecule under different contexts. 

The novel review by Loh and Reiter revealed for the first time in literature that melatonin is capable of influencing and regulating phase separation of biomolecular condensates that could result in different outcomes in health and disease. The extensive discussions on biomolecular condensate regulation by melatonin provides a deeper understanding of the fundamental relationships between melatonin, ATP, and RNA shaping the regulation of biomolecular condensates with the implication that this unique relationship between the three elements could have existed since the beginning of life on earth billions of years ago. 

ATP & RNA in the RNA World

Most of you are familiar with adenosine triphosphate, commonly referred to as ATP or the energy currency produced by mitochondria in eukaryotes. However, did you know ATP existed before there was any mitochondrion? 

In a time long before the existence of deoxyribonucleic acid (DNA), the earth was probably dominated by ribonucleic acid (RNA). This “RNA World” is believed to have existed more than 4 billion years ago. It is highly likely that DNA- and protein-based life forms were preceded by life forms based primarily on RNA. In the era known as the “RNA World”, genetic information was stored in RNA molecules instead of DNA sequences [3-6]. However, the synthesis of RNA requires ATP.

Adenosine triphosphate (ATP) is one of the four nucleotide monomers used during RNA synthesis 7. During the “RNA World ”,  ATP existed as an important cofactor of a metabolic system composed of nucleic acid enzymes prior to the evolution of ribosomal protein synthesis. Coenzymes such as ATP, coenzyme A (CoA), s-adenosylmethionine (SAM), and nicotinamide adenine dinucleotide (NADH) supported the catalytic functions of RNA in addition to information processing 8,9. That is probably the reason why RNA has been observed to bind to ATP with high affinity and specificity 10. 

ATP, RNA, and Biomolecular Condensates

The ability to form different compartments or complexes as rapid, organized responses to changing environmental stimuli was probably one of the most important drivers behind the first successful evolutionary steps of life on earth, long before the appearance of the first single-celled organism encapsulated within membranes [6-11]. To this date, these dynamic, self-assembling, liquid-like membraneless organelles (MLOs) or biomolecular condensates that contain protein, RNA, and other nucleic acids remain ubiquitous and essential in all cells of all life forms on earth [12-14].

Liquid-Liquid Phase Separation (LLPS) Drives Biomolecular Condensates

LLPS is the physicochemical process [15] that is now believed to be the fundamental principle that is the basis of cellular processes such as gene regulation [16], metabolism [17], and stress response [18] in all living organisms. 

Brangwynne et al. first discovered condensate droplets known as P-bodies that contained RNA and proteins in 2009 [19]. Since then, science has discovered different features and functions of condensates formed by LLPS. One of these important areas of studies is the difference between membraneless organelles (MLOs) or biomolecular condensates which form as a result of external/endogenous stimuli into reversible, physiological droplets, and those that progress into irreversible pathological aggregates such as amyloids or prionoid-like fibrils associated with many diseases including neurodegeneration [20] and cancer [21]. 

Reversible, Physiological MLOs versus Irreversible, Pathological MLOs

[Source:Babinchak, W. M.; Surewicz, W. K. Liquid-Liquid Phase Separation and Its Mechanistic Role in Pathological Protein Aggregation. J. Mol. Biol. 2020, 432 (7), 1910–1925. https://doi.org/10.1016/j.jmb.2020.03.004]

What is Phase Separation?

Imagine a well-mixed salad dressing containing oil and vinegar to mirror the soluble state of intracellular biomolecules with different chemical characteristics. Phase separation allows the distinct separation of oil from vinegar, or a single phase of mutually soluble components, to ‘demix’ into two or more distinct phases to form dynamic, coherent droplet-like structures without any membranes. These droplets may act as effective biological compartments that can be regarded as bioreaction centers and filters in cells [22]. 

The ability to organize biomolecules such as RNA during early life may have conferred essential survival advantages to rapidly changing environments. If one extends this concept even further, then it becomes much easier to appreciate how cells use phase separation to sense and regulate intracellular and extracellular changes during the last ~3.5 billion years of evolution. 

When external conditions become stressful and/or dangerous, organisms must first be able to sense and then rapidly adapt in order to survive and thrive during dramatic fluctuations in some of the potential primordial environmental stressors such as changes in temperature, oxygen concentration, and nutrient supply [23,24]. 

This ability to sense and respond rapidly to changes in environmental stressors is universally conserved, and the subsequent formation of MLOs in cells may also be universally conserved not only in eukaryotes [25,26], but also in prokaryotes as well [27]. 

Phase separation offers unique advantages to abrupt environmental/cellular changes as fast, on-off switching type responses to small changes that may be both temporally and energetically favorable because these rearrangements of existing cellular molecules can be achieved without the necessity for energetically costly creation or destruction processes [22]. However, these rearrangements would become necessary on a longer time-scale as responses to continued stress inputs, resulting in changes in transcription, translation and protein turnover [28]. 

Phase Separation of a Single-phase Solution into Dense (droplet) and Dilute (surrounding medium) Phases

[Source: Yoo, H.; Triandafillou, C.; Drummond, D. A. Cellular Sensing by Phase Separation: Using the Process, Not Just the Products. J. Biol. Chem. 2019, 294 (18), 7151–7159.  https://doi.org/10.1074/jbc.TM118.001191 ]

In yeast, the increase of a few degrees centigrade in heat can elevate heat-shock gene expressions by a 1000-fold [29]. Heat-shock proteins (HSPs) have recently been associated with stress granules which are reversible MLOs that form under various cellular stress conditions [30]. Stress granules are the “stress-coping” mechanisms used by cells to reprogram protein translation and modulate signaling pathways in order to ensure survival [31]. Whether an organism can form and dissolve MLOs in a timely manner is probably key to solving unanswered questions in health and disease [32]. 

Formation and Dissolution of MLOs are ATP- and RNA-Dependent

Phase separation at its core is a thermodynamic process driven by the reduction or a negative change in global free energy [12,13]. The chemical process of LLPS is entropically unfavorable; therefore energetically supportive reactions are required to offset the energetic cost involved in successful LLPS [33]. 

ATP is the most favored molecule used by living organisms to capture and transfer free energy in order to drive LLPS. During hydrolysis, ATP is transformed into adenosine diphosphate (ADP) and inorganic phosphate (Pi) by ATPases. Cells use the associated release of −7.3 kcal/mol free energy during hydrolysis to fuel energetically favorable reactions that can control the nucleation, composition, and growth of MLOs [34,35]. 

It is believed that most proteins in the human proteome can undergo LLPS, and this constant exchange of substrates and information in the formation and dissolution of dynamic, reversible droplets are mediated not only by ATP-dependent processes, but also by ribonucleic acid (RNA).

RNA are considered critical architectural components in MLOs that can fine-tune biophysical properties and regulate the formation, distribution, and disassembly of MLOs [36] such as stress granules. Stress granules (SGs) can be induced under stress conditions or different diseases such as viral infections, cancer and neurodegeneration. RNA itself can phase separate and nucleate into RNA granules in the absence of proteins. In the presence of proteins, RNA can act as efficient scaffolds to help assemble MLOs like SGs. That is why RNA is often the major component of SGs [37]. 

The presence and the amount of RNA usually can dictate whether MLOs are formed or dissolved. For example, Henninger and colleagues (2021) [38] showed the world how a low amount of RNA under constant protein concentration can induce the formation of MLOs, while increasing RNA levels actually dissolves those MLOs. Why?

 

[Source: Henninger, J. E.; Oksuz, O.; Shrinivas, K.; Sagi, I.; LeRoy, G.; Zheng, M. M.; Andrews, J. O.; Zamudio, A. V.; Lazaris, C.; Hannett, N. M.; Lee, T. I.; Sharp, P. A.; Cissé, I. I.; Chakraborty, A. K.; Young, R. A. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 2021, 184 (1), 207–225.e24. https://doi.org/10.1016/j.cell.2020.11.030 ]

It’s All About Charge!

Cells depend upon RNA to regulate MLOs because RNA molecules contain powerful electrostatic forces of the high negative charge densities buried in RNA phosphate backbones [39,40]. Therefore, when there is a low level of RNA with negative charge present, those RNA will interact with positively charged proteins to induce phase separation and form biomolecular condensates. On the other hand, if there is a lot of negatively charged RNA present, they would end up repelling proteins with positive charge and thus dissolve condensates [38]. It is really just a simple story of opposites attract, but that attraction can result in the assembly of MLOs, which usually, is beneficial, except when the assembled complex is not subsequently dissolved and proceeds into the next stage of becoming irreversible aggregates often associated with diseases such as neurodegeneration and cancer. 

How does melatonin affect phase separation and the formation and dissolution of biomolecular condensates in health and disease? The next article will take us deeper into the magical realm of melatonin and biomolecular condensates. Stay tuned….

If you can’t wait for the next article, you can get a jumpstart and find out all about how melatonin can regulate biomolecular condensates at this link: https://www.mdpi.com/2076-3921/10/9/1483/htm. 

In the meantime, have you had your MEL and AA today? 

 

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