The rules of aging: are they universal? Is the yeast model relevant for gerontology?

The success of experimental biology was possible due to the use of model organisms. It is believed that the mechanisms of aging have a universal character and they are conserved in a wide range of organisms. The explanation of these universal mechanisms by tracing survival curves of model organisms clearly suggests that death of individuals is a direct consequence of aging. Furthermore, the use of unicellular organisms like yeast Saccharomyces cerevisiae to explain the aging processes of multicellular organisms runs the risk of oversimplification. Aging is a very complex process and therefore in this paper we present arguments suggesting that some of these fundamental assumptions require a deep rethinking and verification.

Download Full-text

Yil102c-A is a Functional Homologue of the DPMII Subunit of Dolichyl Phosphate Mannose Synthase in Saccharomyces cerevisiae

International Journal of Molecular Sciences ◽

10.3390/ijms21238938 ◽

2020 ◽

Vol 21 (23) ◽

pp. 8938

Author(s):

Sebastian Piłsyk ◽

Urszula Perlinska-Lenart ◽

Anna Janik ◽

Elżbieta Gryz ◽

Marta Ajchler-Adamska ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Functional Analysis ◽

Trichoderma Reesei ◽

Transmembrane Domain ◽

Human Cells ◽

Catalytic Subunit ◽

Yeast Saccharomyces Cerevisiae ◽

Dolichyl Phosphate ◽

Functional Homolog ◽

Wide Range

In a wide range of organisms, dolichyl phosphate mannose (DPM) synthase is a complex of tree proteins Dpm1, Dpm2, and Dpm3. However, in the yeast Saccharomyces cerevisiae, it is believed to be a single Dpm1 protein. The function of Dpm3 is performed in S. cerevisiae by the C-terminal transmembrane domain of the catalytic subunit Dpm1. Until present, the regulatory Dpm2 protein has not been found in S. cerevisiae. In this study, we show that, in fact, the Yil102c-A protein interacts directly with Dpm1 in S. cerevisiae and influences its DPM synthase activity. Deletion of the YIL102c-A gene is lethal, and this phenotype is reversed by the dpm2 gene from Trichoderma reesei. Functional analysis of Yil102c-A revealed that it also interacts with glucosylphosphatidylinositol-N-acetylglucosaminyl transferase (GPI-GnT), similar to DPM2 in human cells. Taken together, these results show that Yil102c-A is a functional homolog of DPMII from T. reesei and DPM2 from humans.

Download Full-text

Signalling functions for sphingolipid long-chain bases in Saccharomyces cerevisiae

Biochemical Society Transactions ◽

10.1042/bst0331170 ◽

2005 ◽

Vol 33 (5) ◽

pp. 1170-1173 ◽

Cited By ~ 15

Author(s):

K. Liu ◽

X. Zhang ◽

C. Sumanasekera ◽

R.L. Lester ◽

R.C. Dickson

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Kinase ◽

Second Messengers ◽

Dependent Protein Kinase ◽

Yeast Saccharomyces Cerevisiae ◽

Signalling Molecules ◽

Cellular Processes ◽

Wide Range ◽

Dependent Protein ◽

Long Chain

Over the past several years, studies of sphingolipid functions in the baker's yeast Saccharomyces cerevisiae have revealed that the sphingoid LCBs (long-chain bases), dihydrosphingosine and PHS (phytosphingosine), are important signalling molecules or second messengers under heat stress and during non-stressed conditions. LCBs are now recognized as regulators of AGC-type protein kinase (where AGC stands for protein kinases A, G and C) Pkh1 and Pkh2, which are homologues of mammalian phosphoinositide-dependent protein kinase 1. LCBs were previously shown to activate Pkh1 and Pkh2, which then activate the downstream protein kinase Pkc1. We have recently demonstrated that PHS stimulates Pkh1 to activate additional downstream kinases including Ypk1, Ypk2 and Sch9. We have also found that PHS acts downstream of Pkh1 and partially activates Ypk1, Ypk2 and Sch9. These kinases control a wide range of cellular processes including growth, cell wall integrity, stress resistance, endocytosis and aging. As we learn more about the cellular processes controlled by Ypk1, Ypk2 and Sch9, we will have a far greater appreciation of LCBs as second messengers.

Download Full-text

Isolation and characterization of omnipotent suppressors in the yeast Saccharomyces cerevisiae.

Genetics ◽

10.1093/genetics/124.3.515 ◽

1990 ◽

Vol 124 (3) ◽

pp. 515-522

Author(s):

L P Wakem ◽

F Sherman

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Analysis ◽

Low Temperatures ◽

Carbon Sources ◽

Yeast Saccharomyces Cerevisiae ◽

Hypertonic Medium ◽

Isolation And Characterization ◽

Wide Range ◽

Chromosome Ii

Abstract Approximately 290 omnipotent suppressors, which enhance translational misreading, were isolated in strains of the yeast Saccharomyces cerevisiae containing the psi+ extrachromosomal determinant. The suppressors could be assigned to 8 classes by their pattern of suppression of five nutritional markers. The suppressors were further distinguished by differences in growth on paromomycin medium, hypertonic medium, low temperatures (10 degrees), nonfermentable carbon sources, alpha-aminoadipic acid medium, and by their dominance and recessiveness. Genetic analysis of 12 representative suppressors resulted in the assignment of these suppressors to 6 different loci, including the three previously described loci SUP35 (chromosome IV), SUP45 (chromosome II) and SUP46 (chromosome II), as well as three new loci SUP42 (chromosome IV), SUP43 (chromosome XV) and SUP44 (chromosome VII). Suppressors belonging to the same locus had a wide range of different phenotypes. Differences between alleles of the same locus and similarities between alleles of different loci suggest that the omnipotent suppressors encode proteins that effect different functions and that altered forms of each of the proteins can effect the same function.

Download Full-text

Yeast as a Tool to Understand the Significance of Human Disease-Associated Gene Variants

Genes ◽

10.3390/genes12091303 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1303

Author(s):

Tiziana Cervelli ◽

Alvaro Galli

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Variability ◽

Human Disease ◽

Human Genetics ◽

Model Organism ◽

Model Organisms ◽

Gene Variants ◽

Yeast Saccharomyces Cerevisiae ◽

Next Generation Dna Sequencing ◽

Sequencing Technologies

At present, the great challenge in human genetics is to provide significance to the growing amount of human disease-associated gene variants identified by next generation DNA sequencing technologies. Increasing evidences suggest that model organisms are of pivotal importance to addressing this issue. Due to its genetic tractability, the yeast Saccharomyces cerevisiae represents a valuable model organism for understanding human genetic variability. In the present review, we show how S. cerevisiae has been used to study variants of genes involved in different diseases and in different pathways, highlighting the versatility of this model organism.

Download Full-text

Phagocytosis: a repertoire of receptors and Ca2+ as a key second messenger

Bioscience Reports ◽

10.1042/bsr20080082 ◽

2008 ◽

Vol 28 (5) ◽

pp. 287-298 ◽

Cited By ~ 21

Author(s):

Alirio J. Melendez ◽

Hwee Kee Tay

Keyword(s):

Phagosome Maturation ◽

Physiological Event ◽

Signalling Molecules ◽

Complex Process ◽

Large Particles ◽

A Cell ◽

Unicellular Organisms ◽

Multicellular Organisms ◽

Innate Defence

Receptor-mediated phagocytosis is a complex process that mediates the internalization, by a cell, of other cells and large particles; this is an important physiological event not only in mammals, but in a wide diversity of organisms. Of simple unicellular organisms that use phagocytosis to extract nutrients, to complex metazoans in which phagocytosis is essential for the innate defence system, as a first line of defence against invading pathogens, as well as for the clearance of damaged, dying or dead cells. Evolution has armed multicellular organisms with a range of receptors expressed on many cells that serve as the molecular basis to bring about phagocytosis, regardless of the organism or the specific physiological event concerned. Key to all phagocytic processes is the finely controlled rearrangement of the actin cytoskeleton, in which Ca2+ signals play a major role. Ca2+ is involved in cytoskeletal changes by affecting the actions of a number of contractile proteins, as well as being a cofactor for the activation of a number of intracellular signalling molecules, which are known to play important roles during the initiation, progression and resolution of the phagocytic process. In mammals, the requirement of Ca2+ for the initial steps in phagocytosis, and the subsequent phagosome maturation, can be quite different depending on the type of cell and on the type of receptor that is driving phagocytosis. In this review we discuss the different receptors that mediate professional and non-professional phagocytosis, and discuss the role of Ca2+ in the different steps of this complex process.

Download Full-text

Sequencing and functional analysis of the yeast genome.

Acta Biochimica Polonica ◽

10.18388/abp.1998_4201 ◽

1998 ◽

Vol 45 (3) ◽

pp. 627-643 ◽

Cited By ~ 5

Author(s):

M Zagulski ◽

C J Herbert ◽

J Rytka

Keyword(s):

Saccharomyces Cerevisiae ◽

Eukaryotic Genome ◽

Model Organisms ◽

Yeast Genome ◽

Entire Genome ◽

Yeast Saccharomyces Cerevisiae ◽

Entire Genome Sequence ◽

Sequencing Project ◽

New Genes ◽

Public Data

The genome of the yeast Saccharomyces cerevisiae was sequenced by an international consortium of laboratories from Europe, Canada, the U.S.A. and Japan. This project is now finished and the complete sequence of the first eukaryotic genome was released to the public data bases in April 1996. An overview and preliminary analysis of the entire genome sequence was presented in a special issue of Nature in May 1997, entitled "The yeast genome directory". At its origin the Yeast Genome Sequencing Project provoked much debate and controversy; however, the final results obtained and the insights this has given us into the organisation and content of a eukaryotic genome have more than justified the expectations of the supporters of the project. The importance of genomic sequencing and analysis, especially of model organisms, is now widely accepted and this has resulted in the birth of the new science of genomics (Botstein & Cherry, 1997, Proc. Natl. Acad. Sci. U.S.A. 94, 5506). The information from gene and protein sequences ultimately lead to functional description of all genes. The main strategies describing possible ways to analyse the function of new genes that have been identified by systematic sequencing of Saccharomyces cerevisiae genome are described.

Download Full-text

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

International Journal of Molecular Sciences ◽

10.3390/ijms222212410 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12410

Author(s):

Daniel P. Brink ◽

Celina Borgström ◽

Viktor C. Persson ◽

Karen Ofuji Osiro ◽

Marie F. Gorwa-Grauslund

Keyword(s):

Saccharomyces Cerevisiae ◽

Signaling Pathways ◽

Raw Materials ◽

Current Status ◽

Chemical Production ◽

Edible Plant ◽

Yeast Saccharomyces Cerevisiae ◽

Glucose Signaling ◽

Glucose Depletion ◽

Wide Range

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker’s yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.

Download Full-text

The Resistance of Yeast Saccharomyces Cerevisiae to Extreme Conditions

UNIVERSITY NEWS. NORTH-CAUCASIAN REGION. NATURAL SCIENCES SERIES ◽

10.18522/1026-2237-2021-2-113-118 ◽

2021 ◽

pp. 113-118

Author(s):

Elvira A. Islammagomedova ◽

Eslanda A. Khalilova ◽

Rasul Z. Gasanov ◽

Aida A. Abakarova ◽

Dinara A. Aliverdieva

Keyword(s):

Saccharomyces Cerevisiae ◽

Extreme Values ◽

Maximum Size ◽

Surface Color ◽

Yeast Saccharomyces Cerevisiae ◽

Wide Range ◽

Extreme Factors ◽

Alkaline Conditions ◽

Biotechnological Processes ◽

Resistant Strains

The resistance of the yeast Saccharomyces cerevisiae DAW-3а and Y-503 to the conditions of extreme values of pH, NaCl, temperature has been studied. Under different cultivation modes, the rounded shape of DAW-3a cells is pre-served and this parameter Y-503 changes. Under conditions of different pH values and 30°C, the maximum sizes of cells and giant colonies of the polyploid Y-503 strain were found in comparison with the haploid DAW-3a; at 37°C, the advantage of Y-503 was not observed and the colony sizes of both strains were practically the same. The reaction of the strains to critical concentrations of NaCl in the medium was identical: a decrease in the size of cells and colonies was found; change in the shape, surface, color and structure of colonies. Under conditions of the simultaneous influence of an elevated temperature of 37°C, a wide range of pH and 5 % NaCl, the cell size decreased slightly; under neutral and alkaline conditions of cultivation, a slightly greater tolerance of yeast to salt stress was established; a decrease in the size of giant colonies was found, while the maximum size of the studied strains was noted at pH 11.0, the minimum at pH 3.0. The study of the tolerance of the yeast S. cerevisiae DAW-3a and Y-503 to extreme factors is of particular interest in connection with the possibility of using stress-resistant strains in biotechnological processes.

Download Full-text

Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight

Journal of Fungi ◽

10.3390/jof7090712 ◽

2021 ◽

Vol 7 (9) ◽

pp. 712

Author(s):

Ticiana Fernandes ◽

Flávia Silva-Sousa ◽

Fábio Pereira ◽

Teresa Rito ◽

Pedro Soares ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Homologous Proteins ◽

Yeast Saccharomyces Cerevisiae ◽

Closely Related Species ◽

Biotechnological Potential ◽

Torulaspora Delbrueckii ◽

Phylogenetic Placement ◽

The Core ◽

Wide Range ◽

Core Proteome

Torulaspora delbrueckii has attracted interest in recent years, especially due to its biotechnological potential, arising from its flavor- and aroma-enhancing properties when used in wine, beer or bread dough fermentation, as well as from its remarkable resistance to osmotic and freezing stresses. In the present review, genomic, biochemical, and phenotypic features of T. delbrueckii are described, comparing them with other species, particularly with the biotechnologically well-established yeast, Saccharomyces cerevisiae. We conclude about the aspects that make this yeast a promising biotechnological model to be exploited in a wide range of industries, particularly in wine and bakery. A phylogenetic analysis was also performed, using the core proteome of T. delbrueckii, to compare the number of homologous proteins relative to the most closely related species, understanding the phylogenetic placement of this species with robust support. Lastly, the genetic tools available for T. delbrueckii improvement are discussed, focusing on adaptive laboratorial evolution and its potential.

Download Full-text

Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists

Comparative and Functional Genomics ◽

10.1155/2012/134839 ◽

2012 ◽

Vol 2012 ◽

pp. 1-21 ◽

Cited By ~ 15

Author(s):

Rosemary Jagus ◽

Tsvetan R. Bachvaroff ◽

Bhavesh Joshi ◽

Allen R. Place

Keyword(s):

Regulation Of Gene Expression ◽

Babesia Bovis ◽

Initiation Factor ◽

Model Organisms ◽

Text Book ◽

Translational Initiation ◽

Functional Studies ◽

Wide Range ◽

Genome Features ◽

Multicellular Organisms

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasiteBabesia bovisto 112,000-220,050 Mb in the dinoflagellateProrocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

Download Full-text