scholarly journals Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

2012 ◽  
Vol 11 (11) ◽  
pp. 1510-1522 ◽  
Author(s):  
Peter Henriksen ◽  
Sebastian A. Wagner ◽  
Brian T. Weinert ◽  
Satyan Sharma ◽  
Giedrė Bačinskaja ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Synthesis ◽  
High Resolution Mass Spectrometry ◽  
Budding Yeast ◽  
Large Fraction ◽  
Model Organism ◽  
Bioinformatic Analysis ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Acetylation Site

Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes.

scholarly journals Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria

2019 ◽  
Vol 20 (19) ◽  
pp. 4792 ◽  
Author(s):  
Mingkun Yang ◽  
Hui Huang ◽  
Feng Ge
Keyword(s):  
Large Fraction ◽  
Bioinformatic Analysis ◽  
High Light ◽  
Site Directed Mutagenesis ◽  
Oxygenic Photosynthesis ◽  
Post Translational Modification ◽  
Functional Studies ◽  
Photosynthetic Organisms ◽  
Model Combining ◽  
And Function

Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.

scholarly journals Leveraging budding yeast Saccharomyces cerevisiae for discovering aging modulation substances for functional food

2019 ◽  
Vol 9 (5) ◽  
pp. 297
Author(s):  
Shaoyu Wang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Bioactive Compounds ◽  
Functional Food ◽  
Budding Yeast ◽  
Model Organism ◽  
Cellular Systems ◽  
Cell Factory ◽  
Compression Of Morbidity ◽  
Bioactive Substances ◽  
Yeast Saccharomyces Cerevisiae

Background: Discovery of bioactive substances contained in functional food and the mechanism of their aging modulation are imperative steps in developing better, potent and safer functional food for promoting health and compression of morbidity in the aging population.  Budding yeast (Saccharomyces cerevisiae) is invaluable model organism for aging modulation and bioactive compounds discovery. In this paper we have conceptualised a framework for achieving such aim. This framework consists of four components: discovering targets for aging modulation, discovering and validating caloric restriction mimetics, acting as cellular systems for screening natural products or compounds for aging modulation and being a biological factory for producing bioactive compounds according to the roles the yeast systems play. It have been argued that the component of being a biological factory for producing bioactive compounds has much underexplored which also present an opportunity for new active substance discovery and validation for health promotion in functional food industry.Keywords: Aging modulation, budding yeast, functional food, bioactive substances, cell factory

scholarly journals Profiling of lysine-acetylated proteins in human urine

2017 ◽  
Author(s):  
Weiwei Qin ◽  
Zhenhuan Du ◽  
He Huang ◽  
Youhe Gao
Keyword(s):  
Human Urine ◽  
High Resolution Mass Spectrometry ◽  
The Body ◽  
Lysine Acetylation ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Normal Human ◽  
Measurable Change

AbstractBiomarker is the measurable change associated with a physiological or pathophysiological process, its nature is change. Contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of the lysine acetylated proteins as biomarker in urine.

scholarly journals In vivo characterisation of fluorescent proteins in budding yeast

2018 ◽  
Author(s):  
Dennis Botman ◽  
Daan Hugo de Groot ◽  
Phillipp Schmidt ◽  
Joachim Goedhart ◽  
Bas Teusink
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Fluorescent Proteins ◽  
Codon Optimization ◽  
Budding Yeast ◽  
Model Organism ◽  
Ph Sensitivity ◽  
Future Studies ◽  
Signal Readout

AbstractFluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins.

scholarly journals Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e28228 ◽  
Author(s):  
Zhike Lu ◽  
Zhongyi Cheng ◽  
Yingming Zhao ◽  
Samuel L. Volchenboum
Keyword(s):  
Bioinformatic Analysis ◽  
Lysine Acetylation ◽  
Post Translational Modification

scholarly journals Tracking Diacylglycerol and Phosphatidic Acid Pools in Budding Yeast

2015 ◽  
Vol 8s1 ◽  
pp. LPI.S31781 ◽  
Author(s):  
Suriakarthiga Ganesan ◽  
Brittney N. Shabits ◽  
Vanina Zaremberg
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phosphatidic Acid ◽  
Physical Properties ◽  
Negative Curvature ◽  
Fluorescent Proteins ◽  
Budding Yeast ◽  
Model Organism ◽  
Current Evidence ◽  
C1 Domain

Phosphatidic acid (PA) and diacylglycerol (DAG) are key signaling molecules and important precursors for the biosynthesis of all glycerolipids found in eukaryotes. Research conducted in the model organism Saccharomyces cerevisiae has been at the forefront of the identification of the enzymes involved in the metabolism and transport of PA and DAG. Both these lipids can alter the local physical properties of membranes by introducing negative curvature, but the anionic nature of the phosphomonoester headgroup in PA sets it apart from DAG. As a result, the mechanisms underlying PA and DAG interaction with other lipids and proteins are notoriously different. This is apparent from the analysis of the protein domains responsible for recognition and binding to each of these lipids. We review the current evidence obtained using the PA-binding proteins and domains fused to fluorescent proteins for in vivo tracking of PA pools in yeast. In addition, we present original results for visualization of DAG pools in yeast using the C1 domain from mammalian PKCδ. An emerging first cellular map of the distribution of PA and DAG pools in actively growing yeast is discussed.

scholarly journals LAIPT: Lysine Acetylation Site Identification with Polynomial Tree

2018 ◽  
Vol 20 (1) ◽  
pp. 113 ◽  
Author(s):  
Wenzheng Bao ◽  
Bin Yang ◽  
Zhengwei Li ◽  
Yong Zhou
Keyword(s):  
Amino Acid ◽  
Chemical Properties ◽  
Classification Model ◽  
Lysine Acetylation ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Acetylation Site ◽  
Site Identification ◽  
Physical And Chemical ◽  
Peptide Segments

Post-translational modification plays a key role in the field of biology. Experimental identification methods are time-consuming and expensive. Therefore, computational methods to deal with such issues overcome these shortcomings and limitations. In this article, we propose a lysine acetylation site identification with polynomial tree method (LAIPT), making use of the polynomial style to demonstrate amino-acid residue relationships in peptide segments. This polynomial style was enriched by the physical and chemical properties of amino-acid residues. Then, these reconstructed features were input into the employed classification model, named the flexible neural tree. Finally, some effect evaluation measurements were employed to test the model’s performance.

scholarly journals Dependence of the yeast Saccharomyces cerevisiae post-reproductive lifespan on the reproductive potential.

2013 ◽  
Vol 60 (1) ◽  
Author(s):  
Renata Zadrag-Tecza ◽  
Mateusz Molon ◽  
Jan Mamczur ◽  
Tomasz Bilinski
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Inverse Relationship ◽  
Budding Yeast ◽  
Reproductive Potential ◽  
Model Organism ◽  
Reproductive Stage ◽  
Yeast Cells ◽  
Yeast Saccharomyces Cerevisiae ◽  
Two Stages

The lifespan of budding yeast cells is divided into two stages: reproductive and post-reproductive. The post-reproductive stage of the yeast's lifespan has never been characterized before. We have analyzed the influence of various mutations on the post-reproductive (PRLS) and replicative (RLS) lifespans. The results indicate that PRLS demonstrates an inverse relationship with RLS. The observed lack of differences in the total lifespan (TLS) (expressed in units of time) of strains differing up to five times in RLS (expressed in the number of daughters formed) suggests the necessity of revision of opinions concerning the use of yeast as a model organism of gerontology.

scholarly journals The Budding Yeast Saccharomyces cerevisiae as a Valuable Model Organism for Investigating Anti-Aging Compounds

2021 ◽  
Author(s):  
Yanni Sudiyani ◽  
Muhammad Eka Prastya ◽  
Roni Maryana ◽  
Eka Triwahyuni ◽  
Muryanto
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Life Span ◽  
Budding Yeast ◽  
Model Organism ◽  
Nutrient Sensing ◽  
Serine Threonine Kinase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Ethanol Acetic Acid ◽  
Chronological Life Span ◽  
Screening Platform

Saccharomyces cerevisiae, the budding yeast was long history as industrial baker’s yeast due to its ability to produce numerous product such as ethanol, acetate, industrial bakers etc. Interestingly, this yeast was also important tools for studying biological mechanism in eukaryotic cells including aging, autophagy, mitochondrial response etc. S. cerevisiae has arisen as a powerful chemical and genetic screening platform, due to a rapid workflow with experimental amenability and the availability of a wide range of genetic mutant libraries. Calorie restriction (CR) as the reduction of nutrients intake could promote yeast longevity through some pathways such as inhibition of nutrient sensing target of rapamycin (TOR), serine–threonine kinase (SCH9), protein adenylate cyclase (AC), protein kinase A (PKA) and ras, reduced ethanol, acetic acid and apoptotic process. In addition, CR also induces the expression of antioxidative proteins, sirtuin2 (Sir2), autophagy and induction of mitochondrial yeast adaptive response. Three methods, spotting test; chronological life span (CLS) and replicative life span (RLS) assays, have been developed to study aging in S. cerevisiae. Here, we present strategies for pharmacological anti-aging screens in yeast, discuss common pitfalls and summarize studies that have used yeast for drug discovery.

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