Surviving in the cold: yeast mutants with extended hibernating lifespan are oxidant sensitive

Metabolic activity generates oxidizing molecules throughout life, but it is still debated if the resulting damage of macromolecules is a causality, or consequence, of the aging process. This problem demands for studying growth- and longevity phenotypes separately. Here, we assayed a complete collection of haploid Saccharomyces cerevisiae knock-out strains for their capacity to endure long periods at low metabolic rates. Deletion of 93 genes, predominantly factors of primary metabolism, allowed yeast to survive for more than 58 months in the cold. The majority of these deletion strains were not resistant against oxidants or reductants, but many were hypersensitive. Hence, survival at low metabolic rates has limiting genetic components, and correlates with stress resistance inversely. Indeed, maintaining the energy consuming anti-oxidative machinery seems to be disadvantageous under coldroom conditions

Trends Biochem Sci

The metabolic network has a modular architecture, is robust to perturbations, and responds to biological stimuli and environmental conditions. Through monitoring by metabolite responsive macromolecules, metabolic pathways interact with the transcriptome and proteome. Whereas pathway interconnecting cofactors and substrates report on the overall state of the network, specialised intermediates measure the activity of individual functional units. Transitions in the network affect many of these regulatory metabolites, facilitating the parallel regulation of the timing and control of diverse biological processes. The metabolic network controls its own balance, chromatin structure and the biosynthesis of molecular cofactors; moreover, metabolic shifts are crucial in the response to oxidative stress and play a regulatory role in cancer

Reductive stress on life span extension in C. elegans

Recently, Schulz and colleagues have contributed to the ongoing controversy on the unproven role of oxidative stress in the aging process in their well-performed study 'Glucose restriction extends Caenorhabditis elegans life span by inducing mitochondrial respiration and increasing oxidative stress' (Cell Metab 2007, 6: 280–293). Here, we suggest an alternative hypothesis that reductive stress can prevent calorie-restriction induced life span extension. We draw attention to this condition as an explanation for some contradictory observations including the deleterious effects from antioxidants

The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions.

Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease-age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network.Work in the Ralser lab is funded from the Wellcome Trust (RG 093735/Z/10/Z), the ERC (Starting grant 260809). Markus A. Keller is supported by the Austrian Science Funds by an Erwin Schrödinger postdoctoral fellowship (FWF, J 3341). Markus Ralser is a Wellcome Trust Research Career Development and Wellcome-Beit Prize fellow.This is the final version of the article. It first appeared from MDPI via http://dx.doi.org/10.3390/biom503210

High-Throughput, High-Precision Colony Phenotyping with Pyphe

Colony fitness screens are powerful approaches for functional genomics and genetics. This protocol describes experimental and computational procedures for assaying the fitness of thousands of microbial strains in numerous conditions in parallel. Data analysis is based on pyphe, an all-in-one bioinformatics toolbox for scanning, image analysis, data normalization, and interpretation. We describe a standard protocol where endpoint colony areas are used as fitness proxy and two variations on this, one using colony growth curves and one using colony viability staining with phloxine B. Different strategies for experimental design, normalization and quality control are discussed. Using these approaches, it is possible to collect hundreds of thousands of data points, with low technical noise levels around 5%, in an experiment typically lasting 2 weeks or less

Cell-to-cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community.

Cells that grow together respond heterogeneously to stress even when they are genetically similar. Metabolism, a key determinant of cellular stress tolerance, may be one source of this phenotypic heterogeneity, however, this relationship is largely unclear. We used self-establishing metabolically cooperating (SeMeCo) yeast communities, in which metabolic cooperation can be followed on the basis of genotype, as a model to dissect the role of metabolic cooperation in single-cell heterogeneity. Cells within SeMeCo communities showed to be highly heterogeneous in their stress tolerance, while the survival of each cell under heat or oxidative stress, was strongly determined by its metabolic specialization. This heterogeneity emerged for all metabolite exchange interactions studied (histidine, leucine, uracil, and methionine) as well as oxidant (H2 O2 , diamide) and heat stress treatments. In contrast, the SeMeCo community collectively showed to be similarly tolerant to stress as wild-type populations. Moreover, stress heterogeneity did not establish as sole consequence of metabolic genotype (auxotrophic background) of the single cell, but was observed only for cells that cooperated according to their metabolic capacity. We therefore conclude that phenotypic heterogeneity and cell to cell differences in stress tolerance are emergent properties when cells cooperate in metabolism.Wellcome Trust (Grant ID: RG 093735/Z/10/Z) and the European Research Council (Starting grant 260809)This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/biot.20150030

The widespread role of non-enzymatic reactions in cellular metabolism.

Enzymes shape cellular metabolism, are regulated, fast, and for most cases specific. Enzymes do not however prevent the parallel occurrence of non-enzymatic reactions. Non-enzymatic reactions were important for the evolution of metabolic pathways, but are retained as part of the modern metabolic network. They divide into unspecific chemical reactivity and specific reactions that occur either exclusively non-enzymatically as part of the metabolic network, or in parallel to existing enzyme functions. Non-enzymatic reactions resemble catalytic mechanisms as found in all major enzyme classes and occur spontaneously, small molecule (e.g. metal-) catalyzed or light-induced. The frequent occurrence of non-enzymatic reactions impacts on stability and metabolic network structure, and has thus to be considered in the context of metabolic disease, network modeling, biotechnology and drug design.We acknowledge funding from the Wellcome Trust (RG 093735/Z/10/Z), the ERC (starting Grant 260809). Markus A Keller is supported by the Austrian Science Funds by an Erwin Schroeder postdoctoral fellowship (FWF, J 3341). Markus Ralser is a Wellcome Trust Research Career Development and Wellcome-Beit Prize fellow.This paper was originally published in Current Opinion in Biotechnology (Keller MA, Piedrafita G, Ralser M, Current Opinion in Biotechnology 2015, 34, 153–161, doi:10.1016/j.copbio.2014.12.020)

Psychiatrised Childhood – Expansive Cultures of Disease: Powerful alliances between psychiatry and corrective training

By the end of the 19th century, the discipline of psychiatry which, at that time, was gaining academic standing, developed an interest in children and childhood. With the establishment of psychiatric university hospitals, its power to provide interpretations accepted by society significantly extended. This paper uses the patient files of the Psychiatric Hospital Hall in Tirol, Austria, (established in 1830) and of Neurological/Psychiatric Hospital Innsbruck, Austria, (established in 1891) to demonstrate how at around 1900 and as the result of new diagnosis schemes (related to the concepts of degeneration, social- and racial hygiene), the medicalisation and psychiatrisation of childhood came into being and the prospering discipline of psychiatry advanced into the role of an educational adviser. Mainly children of working class and peasant farmer backgrounds were the targets of the defectological view of psychiatric and, as the result, special education insights based on the clinical concepts of “social deviance” und “psychopathological inferiority”. The psychiatric prerogative of interpretation with, by then, also psychoeductional claim seized the field of early social pedagogics: Psychiatry developed into the guiding science for corrective training and residential care. The start of regional child psychiatry in 1945 was characterised by an almost seamless continuity with the Nazi era, including continuity of personnel. The files of the later Innsbruck Child Observation Ward (Innsbrucker Kinderbeobachtungsstation, 1954–1979) headed by the hereditary biology and social background theory-guided psychiatrist and curative pedagogue Nowak-Vogl reveal the efficient symbiosis of child psychiatry, corrective training and youth welfare authorities, with serious consequences for the children and adolescents admitted to these institutions.By the end of the 19th century, the discipline of psychiatry which, at that time, was gaining academic standing, developed an interest in children and childhood. With the establishment of psychiatric university hospitals, its power to provide interpretations accepted by society significantly extended. This paper uses the patient files of the Psychiatric Hospital Hall in Tirol, Austria, (established in 1830) and of Neurological/Psychiatric Hospital Innsbruck, Austria, (established in 1891) to demonstrate how at around 1900 and as the result of new diagnosis schemes (related to the concepts of degeneration, social- and racial hygiene), the medicalisation and psychiatrisation of childhood came into being and the prospering discipline of psychiatry advanced into the role of an educational adviser. Mainly children of working class and peasant farmer backgrounds were the targets of the defectological view of psychiatric and, as the result, special education insights based on the clinical concepts of “social deviance” und “psychopathological inferiority”. The psychiatric prerogative of interpretation with, by then, also psychoeductional claim seized the field of early social pedagogics: Psychiatry developed into the guiding science for corrective training and residential care. The start of regional child psychiatry in 1945 was characterised by an almost seamless continuity with the Nazi era, including continuity of personnel. The files of the later Innsbruck Child Observation Ward (Innsbrucker Kinderbeobachtungsstation, 1954–1979) headed by the hereditary biology and social background theory-guided psychiatrist and curative pedagogue Nowak-Vogl reveal the efficient symbiosis of child psychiatry, corrective training and youth welfare authorities, with serious consequences for the children and adolescents admitted to these institutions