scholarly journals Comparative Gene Expression between Two Yeast Species

2014 ◽  
pp. 341-368
Keyword(s):  
Gene Expression ◽  
Yeast Species

scholarly journals Divergent MLS1 promoters lie on a fitness plateau for gene expression

2015 ◽  
Author(s):  
Andrew C Bergen ◽  
Gerilyn M Olsen ◽  
Justin C Fay
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Dynamic Response ◽  
Yeast Species ◽  
Glucose Repression ◽  
Gene Activation ◽  
Malate Synthase ◽  
Expression Divergence ◽  
Fitness Effects ◽  
Single Promoter

Qualitative patterns of gene activation and repression are often conserved despite an abundance of quantitative variation in expression levels within and between species. A major challenge to interpreting patterns of expression divergence is knowing which changes in gene expression affect fitness. To characterize the fitness effects of gene expression divergence we placed orthologous promoters from eight yeast species upstream of malate synthase (MLS1) in Saccharomyces cerevisiae. As expected, we found these promoters varied in their expression level under activated and repressed conditions as well as in their dynamic response following loss of glucose repression. Despite these differences, only a single promoter driving near basal levels of expression caused a detectable loss of fitness. We conclude that the MLS1 promoter lies on a fitness plateau whereby even large changes in gene expression can be tolerated without a substantial loss of fitness.

scholarly journals ModifyingSaccharomyces cerevisiaeAdhesion Properties Regulates Yeast Ecosystem Dynamics

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Debra Rossouw ◽  
Skye P. Meiring ◽  
Florian F. Bauer
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Yeast Species ◽  
Genetic System ◽  
Physical Contact ◽  
Relative Fitness ◽  
Independent Evidence ◽  
Content Type ◽  
Metabolic Interactions ◽  
The Impact

ABSTRACTPhysical contact between yeast species, in addition to better-understood and reported metabolic interactions, has recently been proposed to significantly impact the relative fitness of these species in cocultures. Such data have been generated by using membrane bioreactors, which physically separate two yeast species. However, doubts persist about the degree that the various membrane systems allow for continuous and complete metabolic contact, including the exchange of proteins. Here, we provide independent evidence for the importance of physical contact by using a genetic system to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Such adhesion is controlled by a family of structurally related cell wall proteins encoded by theFLOgene family. As previously shown, the expression of specific members of theFLOgene family inSaccharomyces cerevisiaedramatically changes the coadhesion patterns between this yeast and other yeast species. Here, we use this differential aggregation mediated byFLOgenes as a model to assess the impact of physical contact between different yeast species on the relative fitness of these species in simplified ecosystems. The identity of theFLOgene has a marked effect on the persistence of specific non-Saccharomycesyeasts over the course of extended growth periods in batch cultures. Remarkably,FLO1andFLO5expression often result in opposite outcomes. The data provide clear evidence for the role of physical contact in multispecies yeast ecosystems and suggest thatFLOgene expression may be a major factor in such interactions.IMPORTANCEThe impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard but suffer from numerous limitations. Here, we provide independent evidence for the importance of physical contact by using a genetic system, based on theFLOgene family, to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Our results show that interspecies contact significantly impacts population dynamics and the survival of individual species. Remarkably, different members of theFLOgene family often lead to very different population outcomes, further suggesting thatFLOgene expression may be a major factor in such interactions.

scholarly journals Extracting novel hypotheses and findings from RNA-seq data

2020 ◽  
Vol 20 (2) ◽  
Author(s):  
Tyler Doughty ◽  
Eduard Kerkhoven
Keyword(s):  
Gene Expression ◽  
Yeast Species ◽  
Rna Seq ◽  
High Quality ◽  
New Techniques ◽  
The Past ◽  
Basic Biology ◽  
Extract Information

ABSTRACT Over the past decade, improvements in technology and methods have enabled rapid and relatively inexpensive generation of high-quality RNA-seq datasets. These datasets have been used to characterize gene expression for several yeast species and have provided systems-level insights for basic biology, biotechnology and medicine. Herein, we discuss new techniques that have emerged and existing techniques that enable analysts to extract information from multifactorial yeast RNA-seq datasets. Ultimately, this minireview seeks to inspire readers to query datasets, whether previously published or freshly obtained, with creative and diverse methods to discover and support novel hypotheses.

scholarly journals Inositol and Phosphatidylinositol Mediated Glucose Derepression, Gene Expression and Invertase Secretion in Yeasts

2004 ◽  
Vol 36 (7) ◽  
pp. 443-449 ◽  
Author(s):  
Zhen-Ming Chi ◽  
Jun-Feng Li ◽  
Xiang-Hong Wang ◽  
Shu-Min Yao
Keyword(s):  
Gene Expression ◽  
Cell Growth ◽  
Signaling Pathway ◽  
Filamentous Fungi ◽  
Protein Secretion ◽  
Yeast Species ◽  
Glucose Repression ◽  
Extracellular Proteins ◽  
Yeast Cells ◽  
Regulatory Mechanisms

Abstract Glucose repression occurs in many yeast species and some filamentous fungi, and it represses the expression and secretion of many intracellular and extracellular proteins. In recent years, it has been found that many biochemical reactions in yeast cells are mediated by phosphatidylinositol (PI)-type signaling pathway. However, little is known about the relationships between PI-type signaling and glucose repression, gene expression and invertase secretion in yeasts. Many evidences in our previous studies showed that glucose repression, invertase secretion, gene expression and cell growth were mediated by inositol and PI in Saccharomyces and Schizosaccharomyces. The elucidation of the new regulatory mechanisms of protein secretion, gene expression and glucose repression would be an entirely new aspect of inositol and PI-type signaling regulation in yeasts.

scholarly journals DNA replication timing influences gene expression level

2017 ◽  
Vol 216 (7) ◽  
pp. 1907-1914 ◽  
Author(s):  
Carolin A. Müller ◽  
Conrad A. Nieduszynski
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Temporal Order ◽  
Yeast Species ◽  
Replication Timing ◽  
Histone Genes ◽  
Cell Cycle Genes ◽  
Compensation Mechanisms ◽  
Dna Replication Timing ◽  
Eukaryotic Genomes

Eukaryotic genomes are replicated in a reproducible temporal order; however, the physiological significance is poorly understood. We compared replication timing in divergent yeast species and identified genomic features with conserved replication times. Histone genes were among the earliest replicating loci in all species. We specifically delayed the replication of HTA1-HTB1 and discovered that this halved the expression of these histone genes. Finally, we showed that histone and cell cycle genes in general are exempt from Rtt109-dependent dosage compensation, suggesting the existence of pathways excluding specific loci from dosage compensation mechanisms. Thus, we have uncovered one of the first physiological requirements for regulated replication time and demonstrated a direct link between replication timing and gene expression.

scholarly journals Sequence determinants and evolution of constitutive and alternative splicing in yeast species

2020 ◽  
Author(s):  
Dvir Schirman ◽  
Zohar Yakhini ◽  
Orna Dahan ◽  
Yitzhak Pilpel
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Splice Site ◽  
Rna Splicing ◽  
Yeast Species ◽  
Combinatorial Design ◽  
Splice Sites ◽  
Eukaryotic Gene ◽  
Splicing Efficiency ◽  
Splicing Machinery

RNA splicing is a key process in eukaryotic gene expression. Most Intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Using a combinatorial design of synthetic introns we demonstrate how non-consensus splice site sequences affect splicing efficiency in each of the three splice sites. We then show that S. cerevisiae splicing machinery tends to select alternative 3' splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns' 3' ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism's splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, exposing intronic features that control and facilitate alternative splicing. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome.

scholarly journals Comparative gene expression between two yeast species

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 33 ◽  
Author(s):  
Yuanfang Guan ◽  
Maitreya J Dunham ◽  
Olga G Troyanskaya ◽  
Amy A Caudy
Keyword(s):  
Gene Expression ◽  
Yeast Species

scholarly journals Moonlighting Proteins in Yeasts

2008 ◽  
Vol 72 (1) ◽  
pp. 197-210 ◽  
Author(s):  
Carlos Gancedo ◽  
Carmen-Lisset Flores
Keyword(s):  
Gene Expression ◽  
Phylogenetic Relationships ◽  
Metabolic Pathways ◽  
Regulatory Networks ◽  
Yeast Species ◽  
Biological Processes ◽  
Control Of Gene Expression ◽  
Organelle Assembly ◽  
Moonlighting Proteins ◽  
Experimental Approaches

SUMMARY Proteins able to participate in unrelated biological processes have been grouped under the generic name of moonlighting proteins. Work with different yeast species has uncovered a great number of moonlighting proteins and shown their importance for adequate functioning of the yeast cell. Moonlighting activities in yeasts include such diverse functions as control of gene expression, organelle assembly, and modification of the activity of metabolic pathways. In this review, we consider several well-studied moonlighting proteins in different yeast species, paying attention to the experimental approaches used to identify them and the evidence that supports their participation in the unexpected function. Usually, moonlighting activities have been uncovered unexpectedly, and up to now, no satisfactory way to predict moonlighting activities has been found. Among the well-characterized moonlighting proteins in yeasts, enzymes from the glycolytic pathway appear to be prominent. For some cases, it is shown that despite close phylogenetic relationships, moonlighting activities are not necessarily conserved among yeast species. Organisms may utilize moonlighting to add a new layer of regulation to conventional regulatory networks. The existence of this type of proteins in yeasts should be taken into account when designing mutant screens or in attempts to model or modify yeast metabolism.

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