scholarly journals Transcriptome profiling to identify genes involved in peroxisome assembly and function

2002 ◽  
Vol 158 (2) ◽  
pp. 259-271 ◽  
Author(s):  
Jennifer J. Smith ◽  
Marcello Marelli ◽  
Rowan H. Christmas ◽  
Franco J. Vizeacoumar ◽  
David J. Dilworth ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Clustering Algorithms ◽  
Transcriptome Profiling ◽  
Gene Profiling ◽  
Yeast Cells ◽  
Peroxisome Biogenesis ◽  
Peroxisomal Membrane ◽  
Genes Encoding ◽  
And Function

Yeast cells were induced to proliferate peroxisomes, and microarray transcriptional profiling was used to identify PEX genes encoding peroxins involved in peroxisome assembly and genes involved in peroxisome function. Clustering algorithms identified 224 genes with expression profiles similar to those of genes encoding peroxisomal proteins and genes involved in peroxisome biogenesis. Several previously uncharacterized genes were identified, two of which, YPL112c and YOR084w, encode proteins of the peroxisomal membrane and matrix, respectively. Ypl112p, renamed Pex25p, is a novel peroxin required for the regulation of peroxisome size and maintenance. These studies demonstrate the utility of comparative gene profiling as an alternative to functional assays to identify genes with roles in peroxisome biogenesis.

scholarly journals Global Molecular and Morphological Effects of 24-Hour Chromium(VI) Exposure on Shewanella oneidensis MR-1

2006 ◽  
Vol 72 (9) ◽  
pp. 6331-6344 ◽  
Author(s):  
Karuna Chourey ◽  
Melissa R. Thompson ◽  
Jennifer Morrell-Falvey ◽  
Nathan C. VerBerkmoes ◽  
Steven D. Brown ◽  
...  
Keyword(s):  
Untreated Control ◽  
Expression Profiles ◽  
Shewanella Oneidensis ◽  
Transcriptome Profiling ◽  
Molecular Response ◽  
Chromium Vi ◽  
Stress Protection ◽  
Gene And Protein Expression ◽  
Genes Encoding ◽  
Protein Expression Profiles

ABSTRACT The biological impact of 24-h (“chronic”) chromium(VI) [Cr(VI) or chromate] exposure on Shewanella oneidensis MR-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. Cells challenged aerobically with an initial chromate concentration of 0.3 mM in complex growth medium were compared to untreated control cells grown in the absence of chromate. At the 24-h time point at which cells were harvested for transcriptome and proteome analyses, no residual Cr(VI) was detected in the culture supernatant, thus suggesting the complete uptake and/or reduction of this metal by cells. In contrast to the untreated control cells, Cr(VI)-exposed cells formed apparently aseptate, nonmotile filaments that tended to aggregate. Transcriptome profiling and mass spectrometry-based proteomic characterization revealed that the principal molecular response to 24-h Cr(VI) exposure was the induction of prophage-related genes and their encoded products as well as a number of functionally undefined hypothetical genes that were located within the integrated phage regions of the MR-1 genome. In addition, genes with annotated functions in DNA metabolism, cell division, biosynthesis and degradation of the murein (peptidoglycan) sacculus, membrane response, and general environmental stress protection were upregulated, while genes encoding chemotaxis, motility, and transport/binding proteins were largely repressed under conditions of 24-h chromate treatment.

Function and Regulation of Yeast Hexose Transporters

1999 ◽  
Vol 63 (3) ◽  
pp. 554-569 ◽  
Author(s):  
Sabire Özcan ◽  
Mark Johnston
Keyword(s):  
Transcriptional Repressor ◽  
Glucose Transporters ◽  
Fungal Species ◽  
Yeast Cells ◽  
Yeast Saccharomyces Cerevisiae ◽  
Regulatory Pathways ◽  
Glucose Levels ◽  
Rate Limiting Step ◽  
Genes Encoding ◽  
And Function

SUMMARY Glucose, the most abundant monosaccharide in nature, is the principal carbon and energy source for nearly all cells. The first, and rate-limiting, step of glucose metabolism is its transport across the plasma membrane. In cells of many organisms glucose ensures its own efficient metabolism by serving as an environmental stimulus that regulates the quantity, types, and activity of glucose transporters, both at the transcriptional and posttranslational levels. This is most apparent in the baker’s yeast Saccharomyces cerevisiae, which has 20 genes encoding known or likely glucose transporters, each of which is known or likely to have a different affinity for glucose. The expression and function of most of these HXT genes is regulated by different levels of glucose. This review focuses on the mechanisms S. cerevisiae and a few other fungal species utilize for sensing the level of glucose and transmitting this information to the nucleus to alter HXT gene expression. One mechanism represses transcription of some HXT genes when glucose levels are high and works through the Mig1 transcriptional repressor, whose function is regulated by the Snf1-Snf4 protein kinase and Reg1-Glc7 protein phosphatase. Another pathway induces HXT expression in response to glucose and employs the Rgt1 transcriptional repressor, a ubiquitin ligase protein complex (SCFGrr1) that regulates Rgt1 function, and two glucose sensors in the membrane (Snf3 and Rgt2) that bind glucose and generate the intracellular signal to which Rgt1 responds. These two regulatory pathways collaborate with other, less well-understood, pathways to ensure that yeast cells express the glucose transporters best suited for the amount of glucose available.

scholarly journals Peroxisome import stress impairs ribosome biogenesis and induces endoplasmic reticulum genes

2020 ◽  
Author(s):  
Kerui Huang ◽  
Jinoh Kim ◽  
Hua Bai
Keyword(s):  
Endoplasmic Reticulum ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Human Cells ◽  
Gene Set Enrichment Analysis ◽  
Cleavage Sites ◽  
Peroxisome Biogenesis ◽  
And Function

AbstractPeroxisome biogenesis diseases (PBDs) are characterized by global defects in peroxisomal function and can result in severe brain, liver, kidney, and bone malfunctions. PBDs are due to mutations in peroxisome biogenesis factors (PEX genes) that are responsible for peroxisome assembly and function. There is increasing evidence suggesting that peroxisome import functions decline during aging. The transcriptome profiling of peroxisome import defects is still lacking. To identify conserved responses, we undertook a bioinformatic transcriptomic analysis on Drosophila oenocyte specific Pex1, Pex12 and Pex5 knockdowns. In addition, we performed analysis on human cells with induced peroxisome import stress. We uncovered that oenocyte-specific Pex1, Pex12 and Pex5 have distinct transcriptional profiles with each other. Using gene set enrichment analysis (GSEA), we identified protein processing in endoplasmic reticulum pathway, specifically ER-associated protein degradation (ERAD) pathway is enriched and induced in all PEX knockdowns in Drosophila. Moreover, we uncovered decreased expression in ribosome biogenesis genes in flies and human cells. Indeed, we identified a stall at the 5’-ETS cleavage sites during the ribosome biogenesis and impaired 40S small ribosomal export in both flies and human. Our data indicates an unexpected link between peroxisome and ribosome biogenesis. Our results suggest that reduced ribosome biogenesis could be conserved cellular response to reduce peroxisome import stress.

scholarly journals Peroxisomes form intralumenal vesicles with roles in fatty acid catabolism and protein compartmentalization in Arabidopsis

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Zachary J. Wright ◽  
Bonnie Bartel
Keyword(s):  
Fatty Acid ◽  
Peroxisome Biogenesis ◽  
Peroxisomal Membrane ◽  
Endosomal Sorting ◽  
Large Size ◽  
Single Membrane ◽  
Core Function ◽  
Metabolic Reactions ◽  
And Function ◽  
Fatty Acid Catabolism

AbstractPeroxisomes are vital organelles that compartmentalize critical metabolic reactions, such as the breakdown of fats, in eukaryotic cells. Although peroxisomes typically are considered to consist of a single membrane enclosing a protein lumen, more complex peroxisomal membrane structure has occasionally been observed in yeast, mammals, and plants. However, technical challenges have limited the recognition and understanding of this complexity. Here we exploit the unusually large size of Arabidopsis peroxisomes to demonstrate that peroxisomes have extensive internal membranes. These internal vesicles accumulate over time, use ESCRT (endosomal sorting complexes required for transport) machinery for formation, and appear to derive from the outer peroxisomal membrane. Moreover, these vesicles can harbor distinct proteins and do not form normally when fatty acid β-oxidation, a core function of peroxisomes, is impaired. Our findings suggest a mechanism for lipid mobilization that circumvents challenges in processing insoluble metabolites. This revision of the classical view of peroxisomes as single-membrane organelles has implications for all aspects of peroxisome biogenesis and function and may help address fundamental questions in peroxisome evolution.

scholarly journals Transcriptome analysis identified genes involved in anthocyanin biosynthesis in Rainbow bamboo (Indosasa hispida MeClure cv. ‘Rainbow’)

Plant Omics ◽  
2018 ◽  
pp. 145-152
Author(s):  
Yi Wang ◽  
YuMing Yang ◽  
Juan Wang ◽  
Yuan XiaoLong
Keyword(s):  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Anthocyanin Synthesis ◽  
Expression Levels ◽  
Dihydroflavonol Reductase ◽  
Qrt Pcr ◽  
Genes Encoding ◽  
And Function

Rainbow bamboo (Indosasa hispida) is an ornamental plant, which contains unique red to purple anthocyanin in its culm. However, the biosynthesis and function of anthocyanin in bamboo remains unclear. In this study, RNA-seq was used to investigate the transcriptome of the species and compare the gene expression profiles of red and white culms. The expression levels of genes involved in the anthocyanin biosynthesis pathway were detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In total, 5.92 billion reads were obtained from the culm of Rainbow bamboo, which were assembled into 60,716 unigenes. qRT-PCR showed that the expression levels of anthocyanin biosynthesis-related genes in the red and white culms were higher than that in green leaves and that their levels in the red culm without sheath were higher than that in the white culm with sheath. Transcriptome analysis and qRT-PCR showed that the differences in the expression of genes encoding chalcone isomerase (CHI), dihydroflavonol reductase (DFR), flavonoid 3'-hydroxylase (F3'H), and anthocyanidin 3-O-glycosyltransferase (A3GT) between the culm and leaf were significant. This implies that CHI, DFR, F3'H, and A3GT play important roles in anthocyanin synthesis and accumulation in the culm of Rainbow bamboo.

scholarly journals Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 884
Author(s):  
Dominique J. Wiener ◽  
Kátia R. Groch ◽  
Magdalena A.T. Brunner ◽  
Tosso Leeb ◽  
Vidhya Jagannathan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Profiling ◽  
Structure And Function ◽  
Hair Follicles ◽  
Cellular Growth ◽  
Genes Encoding ◽  
Interfollicular Epidermis ◽  
Differential Gene ◽  
And Function

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.

scholarly journals A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling

2019 ◽  
Author(s):  
Chuanyu Liu ◽  
Tao Wu ◽  
Fei Fan ◽  
Ya Liu ◽  
Liang Wu ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Transcriptional Profiling ◽  
Transcriptome Profiling ◽  
Cost Effective ◽  
Microfluidic System ◽  
Resource Limited ◽  
Cell Transcriptome ◽  
Species Specific ◽  
And Function

AbstractSingle-cell technologies are becoming increasingly widespread and have been revolutionizing our understanding of cell identity, state, diversity and function. However, current platforms can be slow to apply to large-scale studies and resource-limited clinical arenas due to a variety of reasons including cost, infrastructure, sample quality and requirements. Here we report DNBelab C4 (C4), a negative pressure orchestrated, portable and cost-effective device that enables high-throughput single-cell transcriptional profiling. C4 system can efficiently allow discrimination of species-specific cells at high resolution and dissect tissue heterogeneity in different organs, such as murine lung and cerebral cortex. Finally, we show that the C4 system is comparable to existing platforms but has huge benefits in cost and portability and, as such, it will be of great interest for the wider scientific community.

scholarly journals Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

2020 ◽  
Author(s):  
Fei Wu ◽  
Rinse de Boer ◽  
Arjen M. Krikken ◽  
Arman Akşit ◽  
Nicola Bordin ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Hansenula Polymorpha ◽  
Peroxisome Biogenesis ◽  
Organelle Biogenesis ◽  
Peroxisomal Membrane ◽  
Peroxisomal Protein ◽  
Peroxisomal Membrane Protein ◽  
Contact Formation ◽  
And Function

AbstractWe analyzed all four Pex23 family proteins of the yeast Hansenula polymorpha, which localize to the ER. Of these Pex24 and Pex32, but not Pex23 and Pex29, accumulate at peroxisome-ER contacts, where they are important for normal peroxisome biogenesis and proliferation and contribute to organelle positioning and segregation.Upon deletion of PEX24 and PEX32 - and to a lesser extent of PEX23 and PEX29 - peroxisome-ER contacts are disrupted, concomitant with peroxisomal defects. These defects are suppressed upon introduction of an artificial peroxisome-ER tether.Accumulation of Pex32 at peroxisomes-ER contacts is lost in the absence of the peroxisomal membrane protein Pex11. At the same time peroxisome-ER contacts are disrupted, indicating that Pex11 contributes to Pex32-dependent peroxisome-ER contact formation.Summarizing, our data indicate that H. polymorpha Pex24 and Pex32 are tethers at peroxisome-ER contacts that are important for normal peroxisome biogenesis and dynamics.SummaryTwo Hansenula polymorpha ER proteins, Pex24 and Pex32, are tethers at peroxisome-ER contacts and function together with the peroxisomal protein Pex11. Their absence disturbs these contacts leading to multiple peroxisomal defects, which can be restored by an artificial tether.

scholarly journals Identification and Characterization of the Human Orthologue of Yeast Pex14p

1999 ◽  
Vol 19 (3) ◽  
pp. 2265-2277 ◽  
Author(s):  
Garnet K. Will ◽  
Monika Soukupova ◽  
Xinji Hong ◽  
Kai S. Erdmann ◽  
Jan A. K. W. Kiel ◽  
...  
Keyword(s):  
Protein Import ◽  
Complementation Group ◽  
Yeast Cells ◽  
Central Component ◽  
Peroxisome Biogenesis ◽  
Peroxisomal Membrane ◽  
Significant Similarity ◽  
Peroxisomal Protein ◽  
C Terminus ◽  
Peroxisomal Targeting

ABSTRACT Pex14p is a central component of the peroxisomal protein import machinery, which has been suggested to provide the point of convergence for PTS1- and PTS2-dependent protein import in yeast cells. Here we describe the identification of a human peroxisome-associated protein (HsPex14p) which shows significant similarity to the yeast Pex14p. HsPex14p is a carbonate-resistant peroxisomal membrane protein with its C terminus exposed to the cytosol. The N terminus of the protein is not accessible to exogenously added antibodies or protease and thus might protrude into the peroxisomal lumen. HsPex14p overexpression leads to the decoration of tubular structures and mislocalization of peroxisomal catalase to the cytosol. HsPex14p binds the cytosolic receptor for the peroxisomal targeting signal 1 (PTS1), a result consistent with a function as a membrane receptor in peroxisomal protein import. Homo-oligomerization of HsPex14p or interaction of the protein with the PTS2-receptor or HsPex13p was not observed. This distinguishes the human Pex14p from its counterpart in yeast cells and thus supports recent data suggesting that not all aspects of peroxisomal protein import are conserved between yeasts and humans. The role of HsPex14p in mammalian peroxisome biogenesis makesHsPEX14 a candidate PBD gene for being responsible for an unrecognized complementation group of human peroxisome biogenesis disorders.

scholarly journals Transcriptional Profiling Shows that Gcn4p Is a Master Regulator of Gene Expression during Amino Acid Starvation in Yeast

2001 ◽  
Vol 21 (13) ◽  
pp. 4347-4368 ◽  
Author(s):  
Krishnamurthy Natarajan ◽  
Michael R. Meyer ◽  
Belinda M. Jackson ◽  
David Slade ◽  
Christopher Roberts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Target Genes ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Transcriptional Response ◽  
Analysis Data ◽  
Amino Acid Starvation ◽  
Master Regulator ◽  
Genes Encoding

ABSTRACT Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments using two different strains derived from S288c revealed that more than 1,000 genes were induced, and a similar number were repressed, by a factor of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Δ strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p target genes. Gcn4p also activates genes involved in glycogen homeostasis, and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcription factors were identified as targets, suggesting that Gcn4p is a master regulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS inducedGCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profiling of a gcn4Δ mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.

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