Expression profiling of Grosmannia clavigera (Gc) under various conditions
ABSTRACT: Gc, a Mountain pine beetle associated pathogen, can survive from highly abundant pine chemicals ( e.g terpenes) and use some unflavored compound’s as carbon source. using RNA_Seq, we analyzed the transcriptome of Gc when it grew on limonene, mannose oliver-oil, oleic acid as carbon source, as well as when it survived from high concentration of limonene or heptane. We profiled the expression of some interesting genes ( ABC transporters, P450s) potentially involved in the tree-pathogen interaction. An ABC-G group transporter gene (GcABC-G1) was one of the most highly induced genes and characterized as a mono-terpene specific efflux transporter with genetic and molecular tools. RNA- seq also indicated Gc utilize limonene and oleic acid through the same beta-oxidation pathway. However the degradation of limonene is more complex and multiple pathways contributed to the survival/utilization. mRNA was extracted from Gc mycelium under various conditions and cDNA libraries were generated for pair-end sequencing. The 70-100bp illumina sequence read was mapping to reference genome and RNA-Seq was carried out in CLC genomic work bench.
Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes. Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
Project description:ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks. Transcriptional phenotyping during development of abc transporter mutants in Dictyostelium discoideum
Project description:To determine the pleiotropic effect of the ABC transporter gene (Atpdr2) mutation, we performed the microarray analyses on the root tissues of Arabidopsis thaliana wild type (Col-0) and Atpdr2 mutant.
Project description:We used gel electrophoresis coupled with LC-MS based proteomics to identify key transport proteins in the plasma membrane (PM) and tonoplast fractions of Avicennia officinalis leaves. This was part of our attempts to understand salt tolerance and secretion in mangrove plant species. PM and tonoplast proteins were purified using two-aqueous phase partitioning and density gradient centrifugation, respectively. Thirty of the 154 PM proteins and 31 of the 118 tonoplast proteins identified were predicted to have transmembrane domains. About 90% of the identified proteins could be classified based on their functions. The major classes of proteins were predicted to be involved in transport, metabolic processes, signal transduction and defense /stress response, while a few of the proteins were predicted to be involved in membrane trafficking. The main classes of transporter proteins identified included H+-ATPases, ATP-binding cassette transporters (ABC) and aquaporins, all of which could play a role in salt secretion. These data will serve as the baseline membrane proteomic dataset for Avicennia species. Further, this information can contribute to future studies on understanding the mechanism of salt tolerance in halophytes in addition to salt secretion in mangroves.
Project description:The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. Somatic mutations reinforce these physiological effects through enhanced silencing of EZH2 targets in B-cells, and in human B-cell lymphomas. Conditional expression of mutant EZH2 in mice induces GC hyperplasia and accelerated lymphomagenesis in cooperation with BCL2. GCB-type DLBCLs are mostly addicted to EZH2, regardless of mutation status, but not the more differentiated ABC-type DLBCLs, thus clarifying the therapeutic scope of EZH2 targeting. RNA sequencing and H3K27me3 ChIP sequencing of human DLBCL cell lines and murine BCL1 cell line. RNA sequencing, H3K27me3 and H3K4me3 ChIP sequencing of B cells from de-identified human tonsills.
Project description:Krohn2011 - Cerebral amyloid-β
proteostasis regulated by membrane transport protein ABCC1
This model is described in the article:
proteostasis is regulated by the membrane transport protein
ABCC1 in mice.
Krohn M, Lange C, Hofrichter J,
Scheffler K, Stenzel J, Steffen J, Schumacher T, Brüning T,
Plath AS, Alfen F, Schmidt A, Winter F, Rateitschak K, Wree A,
Gsponer J, Walker LC, Pahnke J.
J. Clin. Invest. 2011 Oct; 121(10):
In Alzheimer disease (AD), the intracerebral accumulation of
amyloid-β (Aβ) peptides is a critical yet poorly understood
process. Aβ clearance via the blood-brain barrier is reduced by
approximately 30% in AD patients, but the underlying mechanisms
remain elusive. ABC transporters have been implicated in the
regulation of Aβ levels in the brain. Using a mouse model of AD
in which the animals were further genetically modified to lack
specific ABC transporters, here we have shown that the
transporter ABCC1 has an important role in cerebral Aβ
clearance and accumulation. Deficiency of ABCC1 substantially
increased cerebral Aβ levels without altering the expression of
most enzymes that would favor the production of Aβ from the Aβ
precursor protein. In contrast, activation of ABCC1 using
thiethylperazine (a drug approved by the FDA to relieve nausea
and vomiting) markedly reduced Aβ load in a mouse model of AD
expressing ABCC1 but not in such mice lacking ABCC1. Thus, by
altering the temporal aggregation profile of Aβ,
pharmacological activation of ABC transporters could impede the
neurodegenerative cascade that culminates in the dementia of
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Project description:We performed Illumina sequencing to acquire the differentially expressed genes induced by arsenate and sulfur treatments. We found that sulfur (S) application reduced As concentration of rice grains harvested at 20 days after anthesis (DAA). By contrast with the control, the expression of 1001 genes were found to be significantly changed, 46 genes up-regulated and 954 genes down-regulated in the 20As grains. 1169 genes expressed significantly differently between the samples of control and 20As+120S, with 16 genes up-regulated and 1153 genes down-regulated. Among the differentially expressed genes (DEGs) regulated by As and S treatment, there were 10 DEGs encoding phosphate transporter, and 24 DEGs encoding aquaporin transporter. Some genes involved in As detoxification, such as ABC transporter, glutathione S-transferase and phytochelatin synthase were up-regulated by sulfur treatment. The results provide an insight into the molecular basis of how sulfur application regulates As accumulation in rice grains. Arsenic (As) was artificially added to soil with 20 mg/kg As (Na2AsO4.12H2O, 20As), another treatment was 20As+120S, sulfur (S) were supplied artificially with 120 mg/kg (Na2S2O3•5H2O) to the As-added soil (20As+120S).
Project description:Since, ABC transporters do perform various physiological roles.To get better insight about possible involvement of putative ABC transporter orf19.4531 in different functions transcriptional profiling have been peformed and compared between WT(SC5314) Candida albicans cells vs putative orf19.4531 knockout cells after 6hrs growth of culture.The assay as peformed in biological duplicate sample. Overall design: Agilent one-color experiment,Organism: Candida albicans ,Custom Agilent Candida albicans 8x15k Microarray Gene expression (AMADID: 026377) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
Project description:Recent reports have been suggested involvement of ABC transporters in various physiological roles.To get better insight about possible involvement of vacuolar ABC transporter MLT1/orf19.5100 in different physiological roles transcriptional profiling have been peformed and compared between WT(SC5314) Candida albicans cells vs putative orf19.5100 knockout cells after 6hrs growth of culture.The assay as peformed in biological duplicate sample. Agilent one-color experiment,Organism: Candida albicans ,Custom Agilent Candida albicans 8x15k Microarray Gene expression (AMADID: 026377) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth. 10-day seedlings grown on Pi-sufficient medium or followed by 1-day or 3-day Pi starvation, shoot RNA and root RNA were extracted separately