How do proteins shape our lifespan? Exploring aging at the molecular level

Proteins are biomolecules that are essential for every aspect of life. Proteins function as building blocks for structural support to build up organisms. They also perform vital biochemical reactions by acting as enzymes, hormones, defence molecules, and signaling molecules. Proteins are made up of linear chains of amino acids (polypeptides), which are folded at three levels to give a shape or structure to the proteins. The order or arrangement of amino acids in a polypeptide chair is referred to as “primary structure”. The sequence of amino acids is unique to each protein that determines its final structure. These polypeptide chains tend to fold locally by molecular interactions leading to secondary structures. The polypeptide chains continue to fold further, resulting in a final 3D structure known as tertiary structure. Many proteins consist of a single polypeptide chain that folds at three levels to get its final structure. Some proteins are composed of multiple polypeptide chain (subunits). These proteins become functional when all tertiary subunits join together to get quaternary structure. All proteins must be folded properly to attain their 3D structure or conformation to be able to perform their biological functions. This conformation is known as a folded or native state, and the process through which the amino acid chains achieve their final functional structure is known as "protein folding". Each protein has a unique structure that enable and specify their function. If proteins change their defined structures in response to stress or during aging, they misfold and clamp together to form aggregates, eventually losing their function.

Genes carry information to make proteins. Gene expression is a process of transferring this information from DNA to proteins. This takes place in two steps: transcription and translation. During transcription, information in the DNA (genes) is passed to mRNA (messenger RNA or transcript). During translation (proteins synthesis), ribosomes read the mRNA sequence and assemble amino acids in the correct order to form a polypeptide chain, which folds into a functional protein. The entire set of proteins present in a cell or organism at a particular time and under specific conditions is defined as a proteome. While the proteome changes with time, the genome (DNA sequence) remains unchanged, suggesting that the proteome is responsible for phenotypes. For example, a caterpillar and adult butterfly look completely different, despite having the same DNA. Similarly, a strawberry leaf, flower, and fruit look completely different but have the same DNA. Likewise, during aging, our DNA also do not change (except with respect to epigenetic markers); however, proteomes do change as required (Figure 1A). Organisms or cells responds to any external or internal cues by activating or repressing signaling pathways that function to alter gene expression, which in turn remodel the proteome resulting in desired or undesired phenotypes (Figure 1B). Transcription factors are the key effector proteins that operate downstream of the signaling pathways to control the expression of target genes. The expressed proteins (or proteome) must be properly maintained for their coordinated function. This state of functional balance of the proteome is termed as “protein homeostasis” or “proteostasis”. It involves balancing protein production, folding, and degradation.

Proteostasis is balanced by a network of protein quality control factors that regulate protein synthesis, folding, and degradation collectively termed as “proteostasis network”. Since proteins are essential for almost all cellular processes, the life of proteins is highly regulated. The PN ensures that the proteins are synthesized at the right time, location, in right amount, maintain their folded state and degrade or recycle them once their function is over (Figure 2). In the PN, molecular chaperones assist in protein folding and prevent aggregation, whereas degradation systems recognize misfolded proteins and eliminate them.

Protein production is the first step that affect proteostasis balance; therefore, translation rate, fidelity, and protein amounts must be tightly regulated. Molecular chaperones (also known as heat shock proteins) provide assistance in folding and their maintenance. Failure to fold or maintenance results in misfolding and consequent aggregation of the proteins. Protein misfolding can be triggered by mutations, stress, and aging. Damaged, unnecessary, or misfolded proteins are recognized and removed through degradation by the proteasome or autophagy. These protein degradation systems ensure that cells maintain proper protein levels and quality, as well as recycling of amino acids.

Cells possess surveillance systems to protect the proteome under stress conditions. When misfolded proteins are detected, the cells can activate stress responses, such as the heat shock response (HSR) or unfolded protein response (UPR), which in turn regulate gene expression to remodel cellular proteome that ultimately restore proteostasis. Overall, the PN together with stress response pathways function as protein quality control systems to monitor and protect the proteome by preventing protein misfolding and aggregation.

However, the PN capacity tends to decline with age, leading to an increase in protein misfolding and their aggregation resulting in a range of diseases collectively known as proteinopathies. Indeed, protein aggregation is a common feature of many age-related diseases, such as Alzheimer’s, diabetes, cancers, and cardiovascular diseases. Therefore, proteostasis imbalance is considered as one of the primary hallmarks of aging. However, is aging a cause or consequence of proteostasis decline remains an unsolved puzzle. Despite advances in aging research, there are still many unanswered questions, such as what are the primary causes and driver of aging? Does aging in one type of tissue affect other tissues? Do proteostasis changes in one tissue contribute to aging in different tissues? Is improving proteostasis in some tissues sufficient for extending lifespan? Let us look at the aging pathways and how they influence proteostasis.

Aging, the process of growing old, is an inevitable biological phenomenon. It is a complex biological process characterized by the accumulation of molecular and cellular damage over time that results in gradual decline of physiological functions, increased susceptibility to diseases and ultimately death. As the global population ages, understanding the mechanisms behind aging and finding ways to enhance both lifespan (the total years lived) and healthspan (the years lived in good health) has become increasingly critical. Proteins, fundamental to nearly every biological process, play a pivotal role in these aspects of aging.

The regulation of aging is governed by intricate networks of molecular pathways that respond to both genetic and environmental factors. These pathways control key cellular processes, such as metabolism, stress response, proteostasis, and DNA repair, which collectively determine the rate of aging and lifespan. As organisms age, they experience a range of molecular and cellular changes (hallmarks of aging), including DNA damage, telomere shortening, epigenetic changes, loss of proteostasis, mitochondrial dysfunction, impaired cellular communication, etc. Cumulative changes in these processes contribute to the deterioration of tissues and organs over time. Several key pathways and interventions have been identified that regulate aging, often referred to as “aging pathways” These pathways respond to stress, nutrient or energy levels and include: Insulin/Insulin growth factor1 (IGF-1) signaling (IIS), mechanistic target of rapamycin (mTOR), AMP-activated protein kinase (AMPK), Sirtuins, and caloric restriction, to name a few.

IIS pathway controls transcription factors such as FOXO, HSF1, and SKN1/Nrf, which are considered as master regulators of proteostasis. Reduced insulin signaling increases lifespan by promoting expression of stress resistant and longevity genes including molecular chaperones, thereby improving proteostasis. mTOR suppresses autophagy and promotes protein synthesis, leading to an imbalance in proteostasis. Inhibition of the mTOR leads to activation of autophagy and suppression of protein synthesis. This results in clearing of damaged proteins and minimizing production of error-prone proteins, thereby reducing the burden on the proteostasis network. Inhibition of the mTOR pathway has been linked to lifespan extension in multiple model organisms. AMPK is a low energy status sensor, which promotes protein degradation by autophagy and reduce protein synthesis through inhibiting mTOR. Sirtuin protein activation increases lifespan in several organisms by inducing expression of genes required for oxidative stress resistance, mitochondrial function, and autophagy. All these pathways are interconnected and influence each other, creating a complex network that govern the aging process by enhancing proteostasis. However, as organisms age, these mechanisms become less efficient, leading to an accumulation of damaged or misfolded proteins, which can result in cellular stress and contribute to diseases.

Balanced proteostasis is central to cellular health and is essential for healthy aging and longevity. However, proteostasis capacity tend to decline with aging, leading to increase in protein misfolding and aggregation, causing a group of diseases known as proteinopathies. Indeed, protein aggregation is a common feature of many age-related neurological diseases such as Alzheimer’s, Parkinson’s, and Huntington’s as well as non-neuronal diseases such as cataract, diabetes, muscle dystrophy, and cardiovascular diseases (Figure 3). Thus, maintaining proteostasis is crucial not only for longevity but also for quality of life in older age.

With age, the following changes dysregulate the PN:

Changes in protein synthesis with age: As organisms age, the efficiency and fidelity of the protein synthesis declines, leading to an increase in the production of faulty proteins. While some proteins overproduced, others underproduced resulting in imbalances of protein complexes and increase burden on the PN. Interestingly, translation attenuation has been shown to prolong lifespan.

Changes in protein degradation with age: Capacity of the proteasome and autophagy systems declines with age, resulting in the accumulation of misfolded or damaged proteins. The resulting aggregates can impair normal cellular functions and contribute to the aging process and proteinopathies.

Changes in protein folding with age: Proteins fail to maintain their native states, become misfolded, and lose their structure and function. These misfolded proteins also sequester other normal proteins resulting in impaired cellular functions and subsequent cellular death.

The balance between protein synthesis and degradation is crucial for preventing protein misfolding and maintaining a healthy proteome, an essential factor in promoting lifespan and healthspan. Interventions targeting protein synthesis and degradation hold promise for extending lifespan and improving healthspan.

The quest for longevity involves the pursuit of extending human lifespan and improving the quality of life as people age. Boosting proteostasis is a critical target for interventions aimed at extending healthy lifespan. Studies on model organisms promised various antiaging and lifespan extension strategies to boost proteostasis and improve healthspan. These strategies focus on lifestyle interventions, dietary modifications, and therapeutic approaches. A few small molecules identified for their potential to enhance proteostasis and, consequently, promote longevity. Therefore, strategies that enhance proteostasis may not only mitigate the effects of aging but also promote longevity (Figure 4). A few strategies to enhance proteostasis include:

Caloric restriction (CR): Diet or caloric restriction without malnutrition is one of the most studied interventions for lifespan extension. CR intervenes with aging pathways to enhances autophagy and longevity genes expression. CR can decrease the overall load on the PN by reducing accumulation of damaged proteins and improving cellular repair mechanisms.

Pharmacological agents: Chemicals that act as chaperone modulators or chemical chaperones can promote correct folding of proteins and reduce the formation of toxic aggregates. Chemicals that activate proteasome or autophagy help in clearance of toxic misfolded and aggregated proteins.

Therapeutic agents: Compounds such as rapamycin and metformin have been investigated for their ability to enhance proteostasis and promote longevity. Rapamycin, an antifungal agent, functions as an inhibitor of the mTOR, and extends lifespan in various model organisms. In mice, it can extend lifespan by approximately 25%, making it one of the most promising compounds for lifespan extension. Metformin, a medication for type 2 diabetes, has potential to extend lifespan through mechanisms that improve proteostasis. Metformin targets AMPK and mTOR pathways to reduce protein synthesis and enhance autophagy, contributing to improved protein degradation and turnover. Metformin has been shown to increase lifespan and reduce incidence of age-related diseases, making it a promising antiaging candidate for promoting healthspan.

Plant products: Several natural compounds have shown promise in the treatment of proteinopathies and promoting longevity. Resveratrol, a polyphenolic compound found in red wine and various berries, has been extensively studied for its potential antiaging effects. Resveratrol activates sirtuins, and mimic some effects of CR to promote proteostasis, making it a promising longevity-promoting compound. Curcumin, the active compound in turmeric, quercetin a flavonoid found in many fruits, and epigallocatechin gallate (EGCG) found in green tea enhance proteostasis through several mechanisms, improve cellular stress resistance, and mitigate age-related proteinopathies. Association of these compounds with lifespan extension make them as promising antiaging candidates. By integrating all these strategies to boost proteostasis, we can not only improve healthspan but also potentially extend lifespan, leading to a healthier, more vibrant life in our later years.

Aging research has made significant progress in recent years, focusing on understanding the biological mechanisms of aging especially on proteostasis and identifying potential interventions to extend healthy lifespan. While targeting proteostasis and aging pathways holds a great promise as discussed above, it remains to be determined whether similar strategies can be applied safely and effectively to humans. However, ongoing research and emerging technologies in aging biology, artificial intelligence, and drug delivery systems are accelerating progress, and we may see meaningful interventions emerge in the coming decades.

• Kenyon C. (2011). The first long-lived mutants: discovery of the insulin/IGF-1 pathway for ageing. Philos Trans R Soc Lond B Biol Sci. 366(1561):9-16. doi: 10.1098/rstb.2010.0276.

• Labbadia J, Morimoto RI. (2015). The biology of proteostasis in aging and disease. Annu Rev Biochem. 84:435-64. doi: 10.1146/annurev-biochem-060614-033955.

• Reynaud, E. (2010) Protein Misfolding and Degenerative Diseases. Nature Education 3(9):28

• Taylor RC, Dillin A. (2011). Aging as an event of proteostasis collapse. Cold Spring Harb Perspect Biol. 3(5):a004440. doi: 10.1101/cshperspect.a004440.

• Hou Y, Dan X, Babbar M, Wei Y, Hasselbalch SG, Croteau DL, Bohr VA. (2019). Ageing as a risk factor for neurodegenerative disease. Nat Rev Neurol. 15(10):565-581. doi: 10.1038/s41582-019-0244-7.

• Hipp MS, Kasturi P, Hartl FU. (2019). The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol. 20(7):421-435. doi: 10.1038/s41580-019-0101-y

• López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. (2013). The hallmarks of aging. Cell. 153(6):1194-217. doi: 10.1016/j.cell.2013.05.039.

• Tartiere AG, Freije JMP, López-Otín C. (2024). The hallmarks of aging as a conceptual framework for health and longevity research. Front Aging. 5:1334261. doi: 10.3389/fragi.2024.1334261.

• Thompson MA, De-Souza EA. (2023). A Year at the Forefront of Proteostasis and Aging. Biol Open. 12(2):bio059750. doi: 10.1242/bio.059750.

• Tang JX, Xiao FH. (2023). Editorial: The regulation of proteostasis in aging. Front Cell Dev Biol. 11:1221510. doi: 10.3389/fcell.2023.1221510.

• Fontana L, Partridge L. (2015). Promoting health and longevity through diet: from model organisms to humans. Cell. 161(1):106-118. doi: 10.1016/j.cell.2015.02.020.

• Raffin J, de Souto Barreto P, Le Traon AP, Vellas B, Aubertin-Leheudre M, Rolland Y. (2023). Sedentary behavior and the biological hallmarks of aging. Ageing Res Rev. 83:101807. doi: 10.1016/j.arr.2022.101807.

• Shannon OM, Ashor AW, Scialo F, Saretzki G, Martin-Ruiz C, Lara J, Matu J, Griffiths A, Robinson N, Lillà L, Stevenson E, Stephan BCM, Minihane AM, Siervo M, Mathers JC. (2021). Mediterranean diet and the hallmarks of ageing. Eur J Clin Nutr. 75(8):1176-1192. doi: 10.1038/s41430-020-00841-x.

• Bird L (2024) 1999: A vaccine raises hopes of treatment for Alzheimer’s disease. Nature Milestone: Alzheimer’s disease. (https://www.nature.com/articles/d41586-024-02946-w).

Dr. Prasad Kasturi is an assistant professor at the School of Biosciences and Bioengineering, Indian Institute of Technology Mandi (IIT Mandi), Himachal Pradesh, India. He completed a MSc in Biotechnology from Madurai Kamaraj University, Tamil Nadu, India, and a PhD in cell and developmental biology from University of Fribourg, Switzerland, followed by a postdoctoral fellowship at max-Planck Institute for Biochemistry, Munich, Germany. His research focuses on protein quality control during aging using C. elegans model organism. Email: [email protected].