scholarly journals The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 461 ◽  
Author(s):  
Ludmila Trilisenko ◽  
Anton Zvonarev ◽  
Airat Valiakhmetov ◽  
Alexey A. Penin ◽  
Irina A. Eliseeva ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phosphate Transport ◽  
Inorganic Polyphosphate ◽  
Oxidative Stresses ◽  
Manganese Uptake ◽  
Oxidation Reduction ◽  
Whole Transcriptome Sequencing ◽  
Essential Function ◽  
Whole Transcriptome

Inorganic polyphosphate (polyP) is crucial for adaptive reactions and stress response in microorganisms. A convenient model to study the role of polyP in yeast is the Saccharomyces cerevisiae strain CRN/PPN1 that overexpresses polyphosphatase Ppn1 with stably decreased polyphosphate level. In this study, we combined the whole-transcriptome sequencing, fluorescence microscopy, and polyP quantification to characterize the CRN/PPN1 response to manganese and oxidative stresses. CRN/PPN1 exhibits enhanced resistance to manganese and peroxide due to its pre-adaptive state observed in normal conditions. The pre-adaptive state is characterized by up-regulated genes involved in response to an external stimulus, plasma membrane organization, and oxidation/reduction. The transcriptome-wide data allowed the identification of particular genes crucial for overcoming the manganese excess. The key gene responsible for manganese resistance is PHO84 encoding a low-affinity manganese transporter: Strong PHO84 down-regulation in CRN/PPN1 increases manganese resistance by reduced manganese uptake. On the contrary, PHM7, the top up-regulated gene in CRN/PPN1, is also strongly up-regulated in the manganese-adapted parent strain. Phm7 is an unannotated protein, but manganese adaptation is significantly impaired in Δphm7, thus suggesting its essential function in manganese or phosphate transport.

scholarly journals Interaction of a Swi3 homolog with Sth1 provides evidence for a Swi/Snf-related complex with an essential function in Saccharomyces cerevisiae.

1997 ◽  
Vol 17 (4) ◽  
pp. 1768-1775 ◽  
Author(s):  
I Treich ◽  
M Carlson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Hybrid System ◽  
Transcriptional Activation ◽  
Leucine Zipper ◽  
Leucine Zipper Motif ◽  
Cell Extracts ◽  
Essential Function ◽  
Self Association ◽  
Two Hybrid

The Saccharomyces cerevisiae Swi/Snf complex has a role in remodeling chromatin structure to facilitate transcriptional activation. The complex has 11 components, including Swi1/Adr6, Swi2/Snf2, Swi3, Snf5, Snf6, Snf11, Swp73/Snf12, and Tfg3. Mammalian homologs of these proteins have been shown to form multiple Swi/Snf-related complexes. Here we characterize an S. cerevisiae Swi3 homolog (Swh3) and present evidence that it associates in a complex with a Snf2 homolog, Sthl. We identified Swh3 as a protein that interacts with the N terminus of Snf2 in the two-hybrid system. Swh3 and Swi3 are functionally distinct, and overexpression of one does not compensate for loss of the other. Swh3 is essential for viability and does not activate transcription of reporters. The Snf2 sequence that interacts with Swh3 was mapped to a region conserved in Sth1. We show that Swh3 and Sth1 fusion proteins interact in the two-hybrid system and coimmunoprecipitate from yeast cell extracts. We also map interactions between Swh3 and Sth1 and examine the role of a leucine zipper motif in self-association of Swh3. These findings, together with previous analysis of Sth1, indicate that Swh3 and Sth1 are associated in a complex that is functionally distinct from the Swi/Snf complex and essential for viability.

scholarly journals Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11216
Author(s):  
Jianlei Sun ◽  
Yumei Dong ◽  
Chongqi Wang ◽  
Shouhua Xiao ◽  
Zigao Jiao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Regulation Of Gene Expression ◽  
Circular Rnas ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Oxidation Reduction ◽  
Whole Transcriptome Sequencing ◽  
Intergenic Regions ◽  
Whole Transcriptome

Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome’s exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or ‘sponges’ for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.

scholarly journals Phosphate Transport and Sensing in Saccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1491-1499 ◽  
Author(s):  
Dennis D Wykoff ◽  
Erin K O'Shea
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Inorganic Phosphate ◽  
Phosphate Uptake ◽  
Phosphate Starvation ◽  
Phosphate Transport ◽  
Glucose Sensors ◽  
Phosphate Transporters ◽  
Synthetic Lethal ◽  
High Phosphate

Abstract Cellular metabolism depends on the appropriate concentration of intracellular inorganic phosphate; however, little is known about how phosphate concentrations are sensed. The similarity of Pho84p, a high-affinity phosphate transporter in Saccharomyces cerevisiae, to the glucose sensors Snf3p and Rgt2p has led to the hypothesis that Pho84p is an inorganic phosphate sensor. Furthermore, pho84Δ strains have defects in phosphate signaling; they constitutively express PHO5, a phosphate starvation-inducible gene. We began these studies to determine the role of phosphate transporters in signaling phosphate starvation. Previous experiments demonstrated a defect in phosphate uptake in phosphate-starved pho84Δ cells; however, the pho84Δ strain expresses PHO5 constitutively when grown in phosphate-replete media. We determined that pho84Δ cells have a significant defect in phosphate uptake even when grown in high phosphate media. Overexpression of unrelated phosphate transporters or a glycerophosphoinositol transporter in the pho84Δ strain suppresses the PHO5 constitutive phenotype. These data suggest that PHO84 is not required for sensing phosphate. We further characterized putative phosphate transporters, identifying two new phosphate transporters, PHO90 and PHO91. A synthetic lethal phenotype was observed when five phosphate transporters were inactivated, and the contribution of each transporter to uptake in high phosphate conditions was determined. Finally, a PHO84-dependent compensation response was identified; the abundance of Pho84p at the plasma membrane increases in cells that are defective in other phosphate transporters.

scholarly journals Transcriptome dynamics in developing leaves from C3 and C4Flaveria species reveal determinants of Kranz anatomy

2018 ◽  
Author(s):  
Kumari Billakurthi ◽  
Thomas J. Wrobel ◽  
Andrea Bräutigam ◽  
Andreas P.M. Weber ◽  
Peter Westhoff ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Parallel Evolution ◽  
Bundle Sheath ◽  
Evolutionary Mechanisms ◽  
Kranz Anatomy ◽  
Bundle Sheath Cells ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome ◽  
Non Negative Matrix Factorization

AbstractC4 species have evolved more than 60 times independently from C3 ancestors. This multiple and parallel evolution of the complex C4 trait indicates common underlying evolutionary mechanisms that might be identified by comparative analysis of closely related C3 and C4 species. Efficient C4 function depends on a distinctive leaf anatomy that is characterized by enlarged, chloroplast rich bundle sheath cells and a narrow vein spacing. To elucidate molecular mechanisms generating this so called Kranz anatomy, we analyzed a developmental series of leaves from the C4 plant Flaveria bidentis and the closely related C3 species Flaveria robusta using leaf clearing and whole transcriptome sequencing. Applying non-negative matrix factorization on the data identified four different zones with distinct transcriptome patterns in growing leaves of both species. Comparing these transcriptome patterns revealed an important role of auxin metabolism and especially auxin homeostasis for establishing the high vein density typical for C4 leaves.

scholarly journals The essential function of Swc4p - a protein shared by two chromatin-modifying complexes of the yeast Saccharomyces cerevisiae - resides within its N-terminal part.

2008 ◽  
Vol 55 (3) ◽  
pp. 603-612 ◽  
Author(s):  
Arkadiusz Miciałkiewicz ◽  
Anna Chełstowska
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Essential Gene ◽  
Random Mutagenesis ◽  
Growth Conditions ◽  
Histone H2a ◽  
Terminal Part ◽  
Yeast Saccharomyces Cerevisiae ◽  
Chromatin Remodeling Complexes ◽  
Essential Function

The Swc4p protein, encoded by an essential gene, is shared by two chromatin-remodeling complexes in Saccharomyces cerevisiae cells: NuA4 (nucleosome acetyltransferase of H4) and SWR1. The SWR1 complex catalyzes ATP-dependent exchange of the nucleosomal histone H2A for H2AZ (Htz1p). The activity of NuA4 is responsible mainly for the acetylation of the H4 histone but also for the acetylation of H2A and H2AZ. In this work we investigated the role of the Swc4p protein. Using random mutagenesis we isolated a collection of swc4 mutants and showed that the essential function of Swc4p resides in its N-terminal part, within the first 269 amino acids of the 476-amino acid-long protein. We also demonstrated that Swc4p is able to accommodate numerous mutations without losing its functionality under standard growth conditions. However, when swc4 mutants were exposed to methyl methanesulfonate (MMS), hydroxyurea or benomyl, severe growth deficiencies appeared, pointing to an involvement of Swc4p in many chromatin-based processes. The mutants' phenotypes did not result from an impairment of histone acetylation, as in the mutant which bears the shortest isolated variant of truncated Swc4p, the level of overall H4 acetylation was unchanged.

scholarly journals Tissue Microbiome Associated With Human Diseases by Whole Transcriptome Sequencing and 16S Metagenomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Rana Salihoğlu ◽  
Tuğba Önal-Süzek
Keyword(s):  
Transcriptome Analysis ◽  
Neurological Diseases ◽  
Microbial Colonization ◽  
16S Rrna Analysis ◽  
Microbiome Composition ◽  
Whole Transcriptome Sequencing ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
The Brain

In recent years, a substantial number of tissue microbiome studies have been published, mainly due to the recent improvements in the minimization of microbial contamination during whole transcriptome analysis. Another reason for this trend is due to the capability of next-generation sequencing (NGS) to detect microbiome composition even in low biomass samples. Several recent studies demonstrate a significant role for the tissue microbiome in the development and progression of cancer and other diseases. For example, the increase of the abundance of Proteobacteria in tumor tissues of the breast has been revealed by gene expression analysis. The link between human papillomavirus infection and cervical cancer has been known for some time, but the relationship between the microbiome and breast cancer (BC) is more novel. There are also recent attempts to investigate the possible link between the brain microbiome and the cognitive dysfunction caused by neurological diseases. Such studies pointing to the role of the brain microbiome in Huntington’s disease (HD) and Alzheimer’s disease (AD) suggest that microbial colonization is a risk factor. In this review, we aim to summarize the studies that associate the tissue microbiome, rather than gut microbiome, with cancer and other diseases using whole-transcriptome analysis, along with 16S rRNA analysis. After providing several case studies for each relationship, we will discuss the potential role of transcriptome analysis on the broader portrayal of the pathophysiology of the breast, brain, and vaginal microbiome.

scholarly journals Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae

2011 ◽  
Vol 193 (4) ◽  
pp. 755-767 ◽  
Author(s):  
Kai Mao ◽  
Ke Wang ◽  
Mantong Zhao ◽  
Tao Xu ◽  
Daniel J. Klionsky
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signaling Pathways ◽  
Energy Production ◽  
Mapk Signaling ◽  
Selective Degradation ◽  
Mitogen Activated Protein ◽  
Essential Function ◽  
Mapk Signaling Pathways ◽  
Assembly Site

Macroautophagy (hereafter referred to simply as autophagy) is a catabolic pathway that mediates the degradation of long-lived proteins and organelles in eukaryotic cells. The regulation of mitochondrial degradation through autophagy plays an essential role in the maintenance and quality control of this organelle. Compared with our understanding of the essential function of mitochondria in many aspects of cellular metabolism such as energy production and of the role of dysfunctional mitochondria in cell death, little is known regarding their degradation and especially how upstream signaling pathways control this process. Here, we report that two mitogen-activated protein kinases (MAPKs), Slt2 and Hog1, are required for mitophagy in Saccharomyces cerevisiae. Slt2 is required for the degradation of both mitochondria and peroxisomes (via pexophagy), whereas Hog1 functions specifically in mitophagy. Slt2 also affects the recruitment of mitochondria to the phagophore assembly site (PAS), a critical step in the packaging of cargo for selective degradation.

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