Introduction to the Book

Why is it important to understand long-lived proteins (LLPs) and long-lived cells (LLCs) and their breakdown? This question forms the theme of this book.

Long-Lived Proteins Are Ubiquitous

A major finding in the past decade has been that LLPs and LLCs are found throughout the human body. Initially, this discovery was surprising because a common conception in biochemistry, reinforced by undergraduate teaching, was that proteins turnover. This is indeed true for the majority of cellular polypeptides.

Most proteins are created, perform their function, and then are destroyed. Indeed, this aspect of a protein's existence forms a plank of proteostasis, the realm of biochemistry that investigates the many regulatory processes that work together to maintain a relatively constant environment within the cell. Proteostasis also allows a cell to regulate the levels of certain proteins in response to external stresses. One example is the increased concentration of heat-shock proteins in cells, which are synthesized in response to elevated temperatures. Without the ability to degrade old proteins and synthesize new proteins, proteostasis would not be possible.

Clearly, LLPs are a subset of proteins that do not fall within this proteostatic framework because they are, by definition, long lived. One of the aims of this book is to demonstrate that these long-lived components are not simply inert bystanders but that they decompose and their breakdown in the body has a number of major outcomes.

Aging

One area where LLPs will assume much greater significance is in the field of human aging. At present, most research into the mechanism of aging uses short-lived animals, e.g. fruit flies, nematodes, and rodents. It is obvious that LLP breakdown will have little, or no, significant role in the aging of species whose lifetime is measured in days or weeks. Therefore, to some extent, experiments that can be readily undertaken within the time frame of typical grants have shaped the direction of the overall field of aging research. A key question then is to what degree do short-lived animal studies reproduce biochemical events that are responsible for human aging.

As will become clear after reading the chapters in this tome, there are many organs and tissues where cells are long lived and where proteins are LLPs. Furthermore, some of these LLPs are present for years, decades, or even, in some cases, our whole lives. All LLPs decompose. In many instances, this breakdown is due to spontaneous chemical processes that are mediated by the properties of the amino acid side chains. In other cases, reactive metabolites such as sugars and their metabolites bind to the LLPs or the proteins are modified enzymatically. In every instance, the structure of the LLP will be altered.

Although it is possible to analyze the deterioration of these LLPs over time, it is much harder to measure the physiological impact of the gradual deterioration of such LLPs. This is particularly so because aging is accompanied by several factors that may each contribute to the observed loss of function. One major difficulty is that such studies must be performed in long-lived species: ideally, in humans or in other primates. In the case of humans, the number of experiments that are possible is restricted, and it is very difficult to have replicates. Researchers must also accept a diverse genetic background. Despite these restrictions, it will become increasingly important to examine aging in long-lived animals with particular reference to the age-dependent degradation of LLPs. This in no way diminishes the need to complement such studies with parallel experiments on DNA degradation. These two pillars are not separate. One can demonstrate their interrelationship using two examples: the longevity of some histones and the deterioration of some LLP components of the nuclear pore. If long-lived histones deteriorate, it may affect gene transcription. Breakdown of the structure of the nuclear pore in postmitotic cells could influence the transport of molecules into the realm of the chromosome as well as the transport of molecules, such as mRNA, out of the nucleus.

Absent from this book is a discussion of another macromolecular group: lipids. This field is of interest because lens membrane phospholipids change significantly in humans as a function of age. Polysaccharides are also not covered, and data on the age-dependent alterations to glycoproteins is scant.

Autoimmunity

Another area of LLPs that, at the time of writing, is almost an empty page is that of LLP breakdown and autoimmunity. In Chapter 6, it is hypothesized that the age-related decomposition of human LLPs is responsible for many, if not most, cases of autoimmune disease. The fact that LLPs and LLCs are ubiquitous and that they decompose over time to form new structures that were not present at the time of birth effectively means that the body of an adult human contains many "foreign" antigens. In this case, "foreign" does not refer to extraneous antigens but simply to a normal human LLP that has, over time, become significantly altered. Very little is known about the immunogenicity of the suite of novel post-translational modifications that accompany aging of LLPs. One exception is where it has been shown that replacement of one L-Asp by an isoAsp residue increases the immune response greatly, which suggests that the introduction of other novel structures into LLPs is likely to act as a trigger for an autoimmune response. This is amplified by the recognition that most LLPs will accumulate a number of different modifications that may act synergistically as immune stimulants. In some cases, this response to an altered self may lead to the development of an autoimmune disease.

Age-Related Diseases

Sadly, little headway has been made in efforts to combat major age-related diseases, particularly neurological ones, such as Parkinson's, multiple sclerosis, motor neurone disease (Amyotrophic lateral sclerosis) and Alzheimer's disease. Their incidence increases as we live longer lives, with the result that there is already a huge impact on the health care budgets of all nations, particularly those of developed countries.

It is noteworthy that many of the age-related diseases listed above involve proteinopathies, where protein aggregates accumulate inside the cells. The reason for this accumulation is poorly understood. It is my contention that the age-related decomposition of proteins that is documented in this book will be found to play a role in the formation of such protein aggregates. Once this factor is recognized, the focus of research should necessarily alter.

One important implication of this perspective is that the thrust of age-related disease research will necessarily change to humans because short-lived animals cannot recapitulate the sorts of changes that are observed as a result of long-lived macromolecular breakdown.

To illustrate this point, a number of age-related PTMs, including racemization and covalent cross-linking, cannot be readily processed by the protein recycling machinery of the cell. An inevitable consequence is that such modified LLPs accumulate in the lysozyme and cytoplasm. This aspect is covered in Chapter 7.

Once the eyes of scientists are opened to the ubiquitous phenomenon of age-related protein degradation, greater progress should be made in understanding these neurological diseases.

Our Lenses in the Vanguard

It will become apparent from the chapters in this book that much of our current understanding of the consequences of LLPs on the cells and proteins contained within them has been derived from investigations of the human lens. Although this is a well-studied tissue, there are still fundamental aspects that remain to be understood. It is likely that some of these will have relevance for other tissues of the body. As just one example, it appears that once the levels of chaperones, such as a-crystallin, within fiber cells drop significantly with age, that protein aggregates bind tightly to the interior of cell membranes. This attachment impedes cell-to-cell transport within the lens with dire consequences for the concentration of glutathione in the lens nucleus because this antioxidant is synthesized and reduced exclusively in the outer part of the lens. Is this observation lens specific or could a similar phenomenon occur in other aged postmitotic cells such as neurons? Neurons are dependent on a supply of cysteine from astrocytes for glutathione synthesis because they lack the capacity to import glutathione directly. It is not known if aging affects this requisite transport process. It will be important to determine the extent to which lens data can be applied more generally.

It is my hope, and I am sure that of the other authors in this book, that by illustrating the many and varied aspects of LLPs and LLCs, that readers will come to appreciate the importance of this newly recognized family of cells and macromolecules. At the moment, this is a nascent field, but I am confident that in the near future, it will blossom exponentially.

Brain and Memory

I will finish with a musing on memory, the molecular basis of which still remains largely a scientific enigma. I have long thought that LLPs could play a part in, or...