Analysis of the proteins of aging Caenorhabditis elegans by high resolution two-dimensional gel electrophoresis

C. elegans: an invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway

With the availability of its complete genome sequence and unique biological features relevant to human disease, Caenorhabditis elegans has become an invaluable model organism for the studies of proteomics, leading to the elucidation of nematode gene function. A journey from the genome to proteome of C. elegans may begin with preparation of expressed proteins, which enables a large-scale analysis of all possible proteins expressed under specific physiological conditions. Although various techniques have been used for proteomic analysis of C. elegans, systematic high-throughput analysis is still to come in order to accommodate studies of post-translational modification and quantitative analysis. Given that no integrated C. elegans protein expression database is available, it is about time that a global C. elegans proteome project is launched through which datasets of transcriptomes, protein-protein interaction and functional annotation can be integrated. As an initial target of a pilot project of the C. elegans proteome project, the cholesterol-mediated signaling pathway will be an excellent example since, like in other organisms, it is one of the key controlling pathways in cell growth and development in C. elegans. As this field tends to broaden to functional proteomics, there is a high demand to develop the versatile proteome informatics tools that can mange many different data in an integrative manner.

Patterns of metabolic activity during aging of the wild type and longevity mutants of Caenorhabditis elegans

At least three mechanisms determine life span in Caenorhabditis elegans. An insulin-like signaling pathway regulates dauer diapause, reproduction and longevity. Reduction-or loss-of-function mutations in this pathway can extend longevity substantially, suggesting that the wild-type alleles shorten life span. The mutations extend life span by activating components of a dauer longevity assurance program in adult life, resulting in altered metabolism and enhanced stress resistance. The Clock (Clk) genes regulate many temporal processes, including life span. Mutation in the Clk genes clk-1 and gro-1 mildly affect energy production, but repress energy consumption dramatically, thereby reducing the rate of anabolic metabolism and lengthening life span. Dietary restriction, either imposed by mutation or by the culture medium increases longevity and uncovers a third mechanism of life span determination. Dietary restriction likely elicits the longevity assurance program. There is still uncertainty as to whether these pathways converge on daf-16 to activate downstream longevity effector genes such as ctl-1 and sod-3. There is overwhelming evidence that the interplay between reactive oxygen species (ROS) and the capacity to resist oxidative stress controls the aging process and longevity. It is as yet not clear whether metabolic homeostasis collapses with age as a direct result of ROS-derived damage or is selectively repressed by longevity-determining genes. The dramatic decline of protein turnover during senescence results in the accumulation of altered enzymes and in a gradual decline of metabolic performance eventually followed by fatal failure of the system.

Protein metabolism and lifespan in Caenorhabditis elegans

Lifespan of the versatile model system Caenorhabditis elegans can be extended by a decrease of insulin/IGF-1 signaling, TOR signaling, mitochondrial function, protein synthesis and dietary intake. The exact molecular mechanisms by which these modulations confer increased life expectancy are yet to be determined but increased stress resistance and improved protein homeostasis seem to be of major importance. In this chapter, we explore the interactions among several genetic pathways and cellular functions involved in lifespan extension and their relation to protein homeostasis in C. elegans. Several of these processes have been associated, however some relevant data are conflicting and further studies are needed to clarify these interactions. In mammals, protein homeostasis is also implicated in several neurodegenerative diseases, many of which can be modeled in C. elegans.

Public and private mechanisms of life extension in Caenorhabditis elegans

Model organisms have been widely used to study the ageing phenomenon in order to learn about human ageing. Although the phylogenetic diversity between vertebrates and some of the most commonly used model systems could hardly be greater, several mechanisms of life extension are public (common characteristic in divergent species) and likely share a common ancestry. Dietary restriction, reduced IGF-signaling and, seemingly, reduced ROS-induced damage are the best known mechanisms for extending longevity in a variety of organisms. In this review, we summarize the knowledge of ageing in the nematode Caenorhabditis elegans and compare the mechanisms of life extension with knowledge from other model organisms.

Genetic control of longevity in C. elegans

The nematode Caenorhabditis elegans has proven to be a very useful tool for studying the genetics of longevity. Over 70 genes have been found to influence lifespan in this worm. Those related to the Ins/IGF signaling pathway are among the best studied and will be focused on in this review. The master regulator of this pathway, the forkhead transcription factor DAF-16, can activate an enhanced life maintenance program in response to environmental and gonadal inputs. DAF-16 up- and downregulates expression of many genes leading to metabolic alterations and increased stress and microbial resistance. This is generally confirmed by biochemical and physiological data. Longevity mutants are not hypometabolic and probably produce more reactive oxygen species than wild type. However, their high antioxidant capacity may result in lower oxidative damage. Enhanced molecular turnover rates may also play a role in their longevity phenotype.

Protein turnover plays a key role in aging

Although the molecular mechanism of aging is unknown, a progressive increase with age in the concentration of damaged macromolecules, especially proteins, is likely to play a central role in senescent decline. In this paper, we discuss evidence that the progressive decrease in protein synthesis and turnover can be the primary cause of the increase in the concentration of damaged proteins with age. Conversely, protein damage itself is likely to be the cause of the decrease in protein turnover. This could establish a positive feedback loop where the increase in protein damage decreases the protein turnover rate, leading to a further increase in the concentration of damaged proteins. The establishment of such a feedback loop should result in an exponential increase in the amount of protein damage-a protein damage catastrophe-that could be the basis of the general deterioration observed in senescent organisms.

Caloric restriction and lifespan: a role for protein turnover?

Oxidative damage to cellular macromolecules has been postulated to be a major contributor to the ageing of diverse organisms. Oxidative damage can be limited by maintaining high anti-oxidant defenses and by clearing/repairing damage efficiently. Protein turnover is one of the main routes by which functional proteins are maintained and damaged proteins are removed. Protein turnover rates decline with age, which might contribute to the accumulation of damaged proteins in ageing cells. Interestingly, protein turnover rates are maintained at high levels in caloric restricted animals. Whether changes in protein turnover are a cause or a consequence of ageing is not clear, and this question has not been a focal point of modern ageing research. Here we survey work on protein turnover and ageing and suggest that powerful genetic models such as the nematode Caenorhabditis elegans are well suited for a thorough investigation of this long-standing question.

A two-dimensional protein map of Caenorhabditis elegans

A protein map of Caenorhabditis elegans was constructed by using two-dimensional gel electrophoresis followed by peptide mass fingerprinting. A whole worm extract of a mixed population was separated on immobilized pH gradient strips 4-7 L, 3-10 NL, 6-11 L and 12% sodium dodecyl sulfate-polyacrylamide gel eletrophoresis (SDS-PAGE) gels. Gels were stained with colloidal Coomassie blue and 286 spots representing 152 proteins were subsequently identified by matrix-assisted laser desorption/ionization-mass spectrometry after in-gel digestion with trypsin. Most of the identified proteins with known cellular function were enzymes related to carbohydrate and lipid metabolism, or structural proteins with subcellular locations in the cytoplasm, mitochondria or cytoskeleton.

An integrated theory of ageing in the nematode Caenorhabditis elegans

Numerous theories of ageing have been proposed, and many have been tested experimentally, particularly using nematode models such as Caenorhabditis elegans. By combining those theories of ageing that remain plausible with recent findings from studies of C. elegans life span mutants, an integrated theory of ageing has been devised. This is formed from 3 interconnected elements: the evolutionary theory of ageing, the oxidative damage theory of ageing, and a nonadaptive programmed ageing theory. This tripartite theory of ageing gives rise to a number of predictions that may be tested experimentally.

Alterations in the proteome of the Euprymna scolopes light organ in response to symbiotic Vibrio fischeri

During the onset of the cooperative association between the Hawaiian sepiolid squid Euprymna scolopes and the marine luminous bacterium Vibrio fischeri, the anatomy and morphology of the host's symbiotic organ undergo dramatic changes that require interaction with the bacteria. This morphogenetic process involves an array of tissues, including those in direct contact with, as well as those remote from, the symbiotic bacteria. The bacteria induce the developmental program soon after colonization of the organ, although complete morphogenesis requires 96 h. In this study, to determine critical time points, we examined the biochemistry underlying bacterium-induced host development using two-dimensional polyacrylamide gel electrophoresis. Specifically, V. fischeri-induced changes in the soluble proteome of the symbiotic organ during the first 96 h of symbiosis were identified by comparing the protein profiles of symbiont-colonized and uncolonized organs. Both symbiosis-related changes and age-related changes were analyzed to determine what proportion of the differences in the proteomes was the result of specific responses to interaction with bacteria. Although no differences were detected over the first 24 h, numerous symbiosis-related changes became apparent at 48 and 96 h and were more abundant than age-related changes. In addition, many age-related protein changes occurred 48 h sooner in symbiotic animals, suggesting that the interaction of squid tissue with V. fischeri cells accelerates certain developmental processes of the symbiotic organ. These data suggest that V. fischeri-induced modifications in host tissues that occur in the first 24 h of the symbiosis are independent of marked alterations in the patterns of abundant proteins but that the full 4-day morphogenetic program requires significant alteration of the host soluble proteome.

Two-dimensional gel electrophoresis of Caenorhabditis elegans homogenates and identification of protein spots by microsequencing

Employing isoelectric focusing on immobilized pH gradients followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) we have obtained a map of C. elegans proteins, from a mixed culture containing all developmental stages, presenting over 2000 spots within the window of isoelectric points (pI) 3.5-9 and a molecular mass of 10-200 kDa. Edman microsequencing yielded successful results in 12 out of 24 analyzed spots. All but one of the N-terminal sequences retrieved C. elegans sequences in cosmid and/or expressed sequence tag clones. Structurally related protein sequences found in data banks included enzymes in energy metabolism (cytochrome oxydase, ATP synthase, enolase), a fatty acid-binding protein, a translationally controlled tumor protein, an unknown C. elegans protein, an acidic ribosomal protein, a titin-like protein, a G-protein beta chain, cyclophilin, and cathepsin D. Experimental determination of N-termini allowed us to define sites of signal cleavage providing further information on the physiological role of the newly found C. elegans proteins. This report demonstrates the possibility of two-dimensional gel electrophoresis and Edman microsequencing in the elucidation of C. elegans proteome.

Genetic analysis of mechanisms of aging

A wide range of genetic models with postponed aging are now available, from selected mice and Drosophilia to mutant Caenorhabditis elegans and Saccharomyces cerevisiae. These systems allow efficient testing of alternative mechanistic hypotheses for aging. Genetic analysis is forging stronger connections between particular alleles and susceptibility to particular 'diseases of aging'; for example, two different genes for Alzheimer disease have been identified.

Rate of aerobic metabolism and superoxide production rate potential in the nematode Caenorhabditis elegans

We have monitored oxygen consumption as a measure of the rate of aerobic metabolism during the lifetime of Caenorhabditis elegans. We have also developed a chemiluminescent technique which measures exogenous NADPH-stimulated superoxide anion production by freeze-thawed worms. In this assay light production depends on the combined activities of all of the enzymes involved in superoxide production, both directly and indirectly, thus reflecting their activity levels immediately prior to freeze fixation. We have designated this parameter the superoxide production rate potential. The superoxide production rate potential is controlled by the longevity determining gene age-1 and varies in a life cycle-dependent fashion. The metabolic rate generally follows these fluctuations, but additionally shows specific alterations as a response to environmental factors. Metabolic rate and superoxide production rate potential increase by 1.3- and 3-fold, respectively, in reproducing adults. This increase is not due to the contribution of embryonating eggs, however. Culture conditions have a large effect on metabolic rate, but not on the superoxide production rate potential. The energetic cost of movement, measured as consumed oxygen, is low relative to the costs of maintenance and reproduction. Identical superoxide production rate potentials are scored in paralyzed and motile worms, as would be expected.

Analysis of proteins related to conditioning for arrested development and differentiation in Haemonchus contortus by two-dimensional gel electrophoresis

The abundance of the majority of proteins of infectious third-stage larvae (L3) of Haemonchus contortus, conditioned for arrested development, remained unaltered. Only seven proteins showed quantitative differences as observed by two-dimensional gel electrophoresis. These differences were also observed in a laboratory strain which has lost the ability for arrested development. The abundance of two of these proteins increased dramatically during conditioning of larvae for 5-10 weeks. This coincided with the highest percentage of inhibited larvae in experimental infections. Moreover, the abundance of these proteins decreased again after prolonged conditioning (22 weeks). The abundance of the other 5 proteins was not correlated to the percentage of inhibition. We therefore conclude that these proteins are involved in the aging process of larvae. The changes in protein between free-living (L3) and parasitic stages (L4) were large and seem to reflect the large environmental changes experienced by the larvae when entering a mammalian host. Early fourth- (EL4) and late fourth- (LL4) stage larvae differed in 9 proteins. One protein was stage-specific for EL4. These results imply that only minor alterations do occur in these stages notwithstanding the large morphological differences between these larvae.