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1.
GigaByte ; 2023: gigabyte94, 2023.
Article in English | MEDLINE | ID: mdl-37829656

ABSTRACT

Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess antioxidant, anti-inflammatory and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04-Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.

2.
J Nat Prod ; 86(2): 246-255, 2023 02 24.
Article in English | MEDLINE | ID: mdl-36745695

ABSTRACT

Microbial secondary metabolites continue to provide a valuable source of both chemical matter and inspiration for drug discovery in a broad range of therapeutic areas. Beyond this, the corresponding microorganisms represent a sustainable modality for biotechnological production of structurally complex molecules at the quantities required for drug development or even commercial manufacturing. Chromobacterium vaccinii, which has recently been reported as a producer of the pharmacologically highly important Gq inhibitor FR900359 (FR), represents such an example. The characterization of an orphan biosynthetic gene cluster (BGC) located directly downstream of the frs BCG led to the discovery of eight new lipopeptides, valhidepsins A-H (1-8), produced by C. vaccinii. Their chemical structures were elucidated through analysis of 1D and 2D NMR data and high-resolution MS/MS fragmentation methods. The valhidepsins did not display significant antibiotic nor cytotoxic activities but showed surfactant properties. The cluster-compound correlation was demonstrated by generation of a knockout mutant, which abolished production of valhidepsins. This knockout mutant yielded a significantly increased isolated yield of FR.


Subject(s)
Depsipeptides , Lipopeptides , Lipopeptides/chemistry , Tandem Mass Spectrometry , Depsipeptides/chemistry , Multigene Family
3.
Chimia (Aarau) ; 75(7): 620-633, 2021 Aug 25.
Article in English | MEDLINE | ID: mdl-34523403

ABSTRACT

Natural Products (NPs) are molecular' special equipment ' that impart survival benefits on their producers in nature. Due to their evolved functions to modulate biology these privileged metabolites are substantially represented in the drug market and are continuing to contribute to the discovery of innovative medicines such as the recently approved semi-synthetic derivative of the bacterial alkaloid staurosporin in oncology indications. The innovation of low molecular weight compounds in modern drug discovery is built on rapid progress in chemical, molecular biological, pharmacological and data sciences, which together provide a rich understanding of disease-driving molecular interactions and how to modulate them. NPs investigated in these pharmaceutical research areas create new perspectives on their chemical and biological features and thereby new chances to advance medical research. New methods in analytical chemistry linked with searchable NP-databases solved the issue of reisolation and enabled targeted and efficient access to novel molecules from nature. Cheminformatics delivers high resolution descriptions of NPs and explores the substructures that systematically map NP-chemical space by sp³-enriched fragments. Whole genome sequencing has revealed the existence of collocated gene clusters that form larger functional entities together with proximate resistance factors thus avoiding self-inhibition of the encoded metabolites. The analysis of bacterial and fungal genes provides tantalizing glimpses of new compound-target pairs of therapeutic value. Furthermore, a dedicated investigation of structurally unique, selectively active NPs in chemical biology demonstrates their extraordinary power as shuttles between new biological target spaces of pharmaceutical relevance.


Subject(s)
Biological Products , Databases, Factual , Drug Discovery , Drug Industry
4.
Sci Rep ; 10(1): 9670, 2020 06 15.
Article in English | MEDLINE | ID: mdl-32541899

ABSTRACT

Multiplexed gene-signature-based phenotypic assays are increasingly used for the identification and profiling of small molecule-tool compounds and drugs. Here we introduce a method (provided as R-package) for the quantification of the dose-response potency of a gene-signature as EC50 and IC50 values. Two signaling pathways were used as models to validate our methods: beta-adrenergic agonistic activity on cAMP generation (dedicated dataset generated for this study) and EGFR inhibitory effect on cancer cell viability. In both cases, potencies derived from multi-gene expression data were highly correlated with orthogonal potencies derived from cAMP and cell growth readouts, and superior to potencies derived from single individual genes. Based on our results we propose gene-signature potencies as a novel valid alternative for the quantitative prioritization, optimization and development of novel drugs.


Subject(s)
Adrenergic beta-Agonists/pharmacology , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic/drug effects , Neoplasms/genetics , Adrenergic beta-Agonists/therapeutic use , Cell Line, Tumor , Cell Proliferation/drug effects , Cyclic AMP/metabolism , Dose-Response Relationship, Drug , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , Humans , Inhibitory Concentration 50 , Neoplasms/drug therapy , Neoplasms/metabolism , Phenotype , Signal Transduction/drug effects , THP-1 Cells
6.
Nat Microbiol ; 4(3): 470-479, 2019 03.
Article in English | MEDLINE | ID: mdl-30559407

ABSTRACT

The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.


Subject(s)
Adaptation, Physiological , Gastrointestinal Microbiome/genetics , Genetic Variation , Genome, Bacterial , Age Factors , Bacteriophages/genetics , Bacteroides/genetics , Bacteroides/virology , Bifidobacterium bifidum/genetics , Bifidobacterium longum/genetics , Child Development , Child, Preschool , Estonia , Feces/microbiology , Female , Finland , Humans , Infant , Longitudinal Studies , Male , Metabolic Networks and Pathways , Metagenomics , Polymorphism, Single Nucleotide , Probiotics , Russia
7.
Biotechnol Bioeng ; 115(10): 2530-2540, 2018 10.
Article in English | MEDLINE | ID: mdl-29777593

ABSTRACT

An increasing number of nonantibody format proteins are entering clinical development. However, one of the major hurdles for the production of nonantibody glycoproteins is host cell-related proteolytic degradation, which can drastically impact developability and timelines of pipeline projects. Chinese hamster ovary (CHO) cells are the preferred production host for recombinant therapeutic proteins. Using protease inhibitors, transcriptomics, and genetic knockdowns, we have identified, out of the >700 known proteases in rodents, matriptase-1 as the major protease involved in the degradation of recombinant proteins expressed in CHO-K1 cells. Subsequently, matriptase-1 was deleted in CHO-K1 cells using "transcription activator-like effector nucleases" (TALENs) as well as zinc-finger nucleases (ZFNs). This resulted in a superior CHO-K1 matriptase (KO) cell line with strongly reduced or no proteolytic degradation activity toward a panel of recombinantly expressed proteins. The matriptase KO cell line was evaluated in spike-in experiments and showed little or no degradation of proteins incubated in culture supernatant derived from the KO cells. This effect was confirmed when the same proteins were recombinantly expressed in the KO cell line. In summary, the combination of novel cell line engineering tools, next-generation sequencing screening methods, and the recently published Chinese hamster genome has enabled the development of this novel matriptase KO CHO cell line capable of improving expression yields of intact therapeutic proteins.


Subject(s)
Cell Engineering/methods , Gene Knockdown Techniques/methods , Proteolysis , Serine Endopeptidases/genetics , Animals , CHO Cells , Cricetinae , Cricetulus , Humans , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Serine Endopeptidases/metabolism
8.
Am J Hum Genet ; 100(5): 737-750, 2017 May 04.
Article in English | MEDLINE | ID: mdl-28457472

ABSTRACT

Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis. Included in the 2.62 kb overlapping region of these duplications is an enhancer element that is active in epidermal keratinocytes. The activity of this enhancer correlated with CTSB expression in normal differentiating keratinocytes and other cell lines, but not with FDFT1 or NEIL2 expression. Gene expression (qPCR) analysis and immunohistochemistry of the palmar epidermis demonstrated significantly increased expression of CTSB, as well as stronger staining of cathepsin B in the stratum granulosum of affected individuals than in that of control individuals. Analysis of higher-order chromatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote effects of the enhancer. In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals.


Subject(s)
Cathepsin B/metabolism , Enhancer Elements, Genetic , Erythema/genetics , Gene Duplication , Gene Expression Regulation , Keratosis/genetics , Skin Diseases, Genetic/genetics , Case-Control Studies , Cathepsin B/genetics , Chromosome Mapping , Chromosomes, Human, Pair 8/genetics , DNA Copy Number Variations , DNA Glycosylases/genetics , DNA Glycosylases/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Epidermis/metabolism , Epigenomics , Erythema/epidemiology , Female , Genetic Markers , Humans , Keratinocytes/metabolism , Keratosis/epidemiology , MCF-7 Cells , Male , Norway/epidemiology , Pedigree , Skin Diseases, Genetic/epidemiology , South Africa/epidemiology
10.
Am J Hum Genet ; 100(2): 323-333, 2017 02 02.
Article in English | MEDLINE | ID: mdl-28089251

ABSTRACT

Nephronophthisis (NPH), an autosomal-recessive tubulointerstitial nephritis, is the most common cause of hereditary end-stage renal disease in the first three decades of life. Since most NPH gene products (NPHP) function at the primary cilium, NPH is classified as a ciliopathy. We identified mutations in a candidate gene in eight individuals from five families presenting late-onset NPH with massive renal fibrosis. This gene encodes MAPKBP1, a poorly characterized scaffolding protein for JNK signaling. Immunofluorescence analyses showed that MAPKBP1 is not present at the primary cilium and that fibroblasts from affected individuals did not display ciliogenesis defects, indicating that MAPKBP1 may represent a new family of NPHP not involved in cilia-associated functions. Instead, MAPKBP1 is recruited to mitotic spindle poles (MSPs) during the early phases of mitosis where it colocalizes with its paralog WDR62, which plays a key role at MSP. Detected mutations compromise recruitment of MAPKBP1 to the MSP and/or its interaction with JNK2 or WDR62. Additionally, we show increased DNA damage response signaling in fibroblasts from affected individuals and upon knockdown of Mapkbp1 in murine cell lines, a phenotype previously associated with NPH. In conclusion, we identified mutations in MAPKBP1 as a genetic cause of juvenile or late-onset and cilia-independent NPH.


Subject(s)
Intracellular Signaling Peptides and Proteins/genetics , Kidney Diseases, Cystic/congenital , Adolescent , Alleles , Animals , Cell Cycle Proteins , Child , Cilia/genetics , DNA Damage/genetics , Disease Models, Animal , Fibroblasts/cytology , Fibroblasts/metabolism , Fibrosis , Gene Expression Regulation , Humans , Kidney/cytology , Kidney/metabolism , Kidney Diseases, Cystic/diagnosis , Kidney Diseases, Cystic/genetics , Kidney Failure, Chronic/diagnosis , Kidney Failure, Chronic/genetics , Mice , Mice, Knockout , Mitosis , Mutation , NIH 3T3 Cells , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Pedigree , Phenotype , Signal Transduction , Spindle Poles/metabolism , Young Adult , Zebrafish
11.
Front Immunol ; 8: 1824, 2017.
Article in English | MEDLINE | ID: mdl-29375547

ABSTRACT

Heterozygous mutations in the cytotoxic T lymphocyte antigen-4 (CTLA-4) are associated with lymphadenopathy, autoimmunity, immune dysregulation, and hypogammaglobulinemia in about 70% of the carriers. So far, the incomplete penetrance of CTLA-4 haploinsufficiency has been attributed to unknown genetic modifiers, epigenetic changes, or environmental effects. We sought to identify potential genetic modifiers in a family with differential clinical penetrance of CTLA-4 haploinsufficiency. Here, we report on a rare heterozygous gain-of-function mutation in Janus kinase-3 (JAK3) (p.R840C), which is associated with the clinical manifestation of CTLA-4 haploinsufficiency in a patient carrying a novel loss-of-function mutation in CTLA-4 (p.Y139C). While the asymptomatic parents carry either the CTLA-4 mutation or the JAK3 variant, their son has inherited both heterozygous mutations and suffers from hypogammaglobulinemia combined with autoimmunity and lymphoid hyperplasia. Although the patient's lymph node and spleen contained many hyperplastic germinal centers with follicular helper T (TFH) cells and immunoglobulin (Ig) G-positive B cells, plasma cell, and memory B cell development was impaired. CXCR5+PD-1+TIGIT+ TFH cells contributed to a large part of circulating T cells, but they produced only very low amounts of interleukin (IL)-4, IL-10, and IL-21 required for the development of memory B cells and plasma cells. We, therefore, suggest that the combination of the loss-of-function mutation in CTLA-4 with the gain-of-function mutation in JAK3 directs the differentiation of CD4 T cells into dysfunctional TFH cells supporting the development of lymphadenopathy, hypogammaglobulinemia, and immunodeficiency. Thus, the combination of rare genetic heterozygous variants that remain clinically unnoticed individually may lead to T cell hyperactivity, impaired memory B cell, and plasma cell development resulting finally in combined immunodeficiency.

12.
Stem Cell Reports ; 7(6): 1059-1071, 2016 12 13.
Article in English | MEDLINE | ID: mdl-27840045

ABSTRACT

In fragile X syndrome (FXS), CGG repeat expansion greater than 200 triplets is believed to trigger FMR1 gene silencing and disease etiology. However, FXS siblings have been identified with more than 200 CGGs, termed unmethylated full mutation (UFM) carriers, without gene silencing and disease symptoms. Here, we show that hypomethylation of the FMR1 promoter is maintained in induced pluripotent stem cells (iPSCs) derived from two UFM individuals. However, a subset of iPSC clones with large CGG expansions carries silenced FMR1. Furthermore, we demonstrate de novo silencing upon expansion of the CGG repeat size. FMR1 does not undergo silencing during neuronal differentiation of UFM iPSCs, and expression of large unmethylated CGG repeats has phenotypic consequences resulting in neurodegenerative features. Our data suggest that UFM individuals do not lack the cell-intrinsic ability to silence FMR1 and that inter-individual variability in the CGG repeat size required for silencing exists in the FXS population.


Subject(s)
DNA Methylation/genetics , Fragile X Mental Retardation Protein/genetics , Gene Silencing , Induced Pluripotent Stem Cells/metabolism , Mutation/genetics , Neurons/metabolism , Trinucleotide Repeat Expansion/genetics , Cell Differentiation/genetics , Clone Cells , Epigenesis, Genetic , Female , Fragile X Syndrome/genetics , Genetic Loci , Humans , Induced Pluripotent Stem Cells/cytology , Male , Pedigree
13.
PLoS One ; 11(9): e0163129, 2016.
Article in English | MEDLINE | ID: mdl-27649498

ABSTRACT

High throughput random mutagenesis is a powerful tool to identify which residues are important for the function of a protein, and gain insight into its structure-function relation. The human muscle nicotinic acetylcholine receptor was used to test whether this technique previously used for monomeric receptors can be applied to a pentameric ligand-gated ion channel. A mutant library for the α1 subunit of the channel was generated by error-prone PCR, and full length sequences of all 2816 mutants were retrieved using single molecule real time sequencing. Each α1 mutant was co-transfected with wildtype ß1, δ, and ε subunits, and the channel function characterized by an ion flux assay. To test whether the strategy could map the structure-function relation of this receptor, we attempted to identify mutations that conferred resistance to competitive antagonists. Mutant hits were defined as receptors that responded to the nicotinic agonist epibatidine, but were not inhibited by either α-bungarotoxin or tubocurarine. Eight α1 subunit mutant hits were identified, six of which contained mutations at position Y233 or V275 in the transmembrane domain. Three single point mutations (Y233N, Y233H, and V275M) were studied further, and found to enhance the potencies of five channel agonists tested. This suggests that the mutations made the channel resistant to the antagonists, not by impairing antagonist binding, but rather by producing a gain-of-function phenotype, e.g. increased agonist sensitivity. Our data show that random high throughput mutagenesis is applicable to multimeric proteins to discover novel functional mutants, and outlines the benefits of using single molecule real time sequencing with regards to quality control of the mutant library as well as downstream mutant data interpretation.


Subject(s)
High-Throughput Nucleotide Sequencing/methods , Muscles/metabolism , Mutagenesis , Receptors, Nicotinic/genetics , Amino Acid Sequence , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Bungarotoxins/pharmacology , Calcium/metabolism , HEK293 Cells , Humans , Ion Transport/drug effects , Mutation , Nicotinic Agonists/pharmacology , Nicotinic Antagonists/pharmacology , Pyridines/pharmacology , Receptors, Nicotinic/metabolism , Sequence Homology, Amino Acid , Tubocurarine/pharmacology
14.
Metab Brain Dis ; 31(1): 135-56, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26400817

ABSTRACT

D-cycloserine (DCS) has been shown to be effective in facilitating fear extinction in animal and human studies, however the precise mechanisms whereby the co-administration of DCS and behavioural fear extinction reduce fear are still unclear. This study investigated the molecular mechanisms of intrahippocampally administered D-cycloserine in facilitating fear extinction in a contextual fear conditioning animal model. Male Sprague Dawley rats (n = 120) were grouped into four experimental groups (n = 30) based on fear conditioning and intrahippocampal administration of either DCS or saline. The light/dark avoidance test was used to differentiate maladapted (MA) (anxious) from well-adapted (WA) (not anxious) subgroups. RNA extracted from the left dorsal hippocampus was used for RNA sequencing and gene expression data was compared between six fear-conditioned + saline MA (FEAR + SALINE MA) and six fear-conditioned + DCS WA (FEAR + DCS WA) animals. Of the 424 significantly downregulated and 25 significantly upregulated genes identified in the FEAR + DCS WA group compared to the FEAR + SALINE MA group, 121 downregulated and nine upregulated genes were predicted to be relevant to fear conditioning and anxiety and stress-related disorders. The majority of downregulated genes transcribed immune, proinflammatory and oxidative stress systems molecules. These molecules mediate neuroinflammation and cause neuronal damage. DCS also regulated genes involved in learning and memory processes, and genes associated with anxiety, stress-related disorders and co-occurring diseases (e.g., cardiovascular diseases, digestive system diseases and nervous system diseases). Identifying the molecular underpinnings of DCS-mediated fear extinction brings us closer to understanding the process of fear extinction.


Subject(s)
Cycloserine/pharmacology , Extinction, Psychological/drug effects , Fear/drug effects , RNA/genetics , Adaptation, Psychological/drug effects , Animals , Down-Regulation/genetics , Gene Expression/drug effects , Hippocampus , Male , Microinjections , Rats , Rats, Sprague-Dawley , Sequence Analysis, RNA
15.
Chimia (Aarau) ; 70(12): 883-888, 2016 Dec 21.
Article in English | MEDLINE | ID: mdl-28661362

ABSTRACT

This review describes the innovative technological developments that have brought genomics from its beginnings in the late 1980s to the present day and then discusses the ways in which genomics platforms are deployed across Switzerland to play a key role in supporting basic and applied research in both academia and industry.


Subject(s)
Genomics , Oligonucleotide Array Sequence Analysis , Humans , Sequence Analysis, DNA , Switzerland
16.
Nat Commun ; 6: 8666, 2015 Oct 21.
Article in English | MEDLINE | ID: mdl-26487268

ABSTRACT

Ciliopathies are a large group of clinically and genetically heterogeneous disorders caused by defects in primary cilia. Here we identified mutations in TRAF3IP1 (TNF Receptor-Associated Factor Interacting Protein 1) in eight patients from five families with nephronophthisis (NPH) and retinal degeneration, two of the most common manifestations of ciliopathies. TRAF3IP1 encodes IFT54, a subunit of the IFT-B complex required for ciliogenesis. The identified mutations result in mild ciliary defects in patients but also reveal an unexpected role of IFT54 as a negative regulator of microtubule stability via MAP4 (microtubule-associated protein 4). Microtubule defects are associated with altered epithelialization/polarity in renal cells and with pronephric cysts and microphthalmia in zebrafish embryos. Our findings highlight the regulation of cytoplasmic microtubule dynamics as a role of the IFT54 protein beyond the cilium, contributing to the development of NPH-related ciliopathies.


Subject(s)
Carrier Proteins/genetics , Kidney Diseases, Cystic/genetics , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Microtubules/metabolism , Mutation , Retinal Degeneration/genetics , Zebrafish Proteins/genetics , Animals , Blotting, Western , Carrier Proteins/metabolism , Cell Polarity/genetics , Circular Dichroism , Embryo, Nonmammalian , Female , Fluorescent Antibody Technique , Gene Knockout Techniques , HEK293 Cells , High-Throughput Nucleotide Sequencing , Humans , Immunoprecipitation , Kidney Diseases, Cystic/metabolism , Male , Microphthalmos/genetics , Pedigree , Retinal Degeneration/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Zebrafish , Zebrafish Proteins/metabolism
17.
Proc Natl Acad Sci U S A ; 112(21): 6754-9, 2015 May 26.
Article in English | MEDLINE | ID: mdl-25947154

ABSTRACT

Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling--although crucial for crop improvement--is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.


Subject(s)
Glomeromycota/physiology , Mycorrhizae/physiology , Oryza/genetics , Oryza/microbiology , Transcriptome , Cell Wall/genetics , Cell Wall/metabolism , Gene Expression Regulation, Plant , Genes, Plant , Genetic Variation , Hydroxybenzoates/metabolism , Minerals/metabolism , Oryza/physiology , Plant Growth Regulators/genetics , Plant Growth Regulators/metabolism , Plant Roots/genetics , Plant Roots/microbiology , Plant Roots/physiology , Suppression, Genetic , Symbiosis/genetics , Symbiosis/physiology
18.
J Cell Sci ; 128(6): 1217-29, 2015 Mar 15.
Article in English | MEDLINE | ID: mdl-25616894

ABSTRACT

A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon complex, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (including HUN-7293 and cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p (yeast) or Sec61α1 (mammals) that conferred resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and post-translationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 translocon homolog. We suggest 'decatransin' as the name for this new decadepsipeptide translocation inhibitor.


Subject(s)
Biological Products/pharmacology , Endoplasmic Reticulum/drug effects , Membrane Proteins/metabolism , Protein Transport/drug effects , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Animals , Ascomycota/metabolism , COS Cells , Cells, Cultured , Chlorocebus aethiops , HCT116 Cells , Humans , Membrane Proteins/antagonists & inhibitors , Peptides, Cyclic/pharmacology , Polymorphism, Single Nucleotide/genetics , SEC Translocation Channels , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/growth & development
19.
Microbiol Res ; 169(2-3): 107-20, 2014.
Article in English | MEDLINE | ID: mdl-24360837

ABSTRACT

Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.


Subject(s)
Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/genetics , Antifungal Agents/pharmacology , Biosynthetic Pathways , Drug Resistance, Fungal , Gene Expression Regulation, Fungal , High-Throughput Screening Assays , Molecular Sequence Data , Phylogeny , Saccharomyces cerevisiae/classification , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae Proteins/metabolism
20.
J Biol Chem ; 288(38): 27434-27443, 2013 Sep 20.
Article in English | MEDLINE | ID: mdl-23940034

ABSTRACT

TLQP-21, a peptide derived from VGF (non-acronymic) by proteolytic processing, has been shown to modulate energy metabolism, differentiation, and cellular response to stress. Although extensively investigated, the receptor for this endogenous peptide has not previously been described. This study describes the use of a series of studies that show G protein-coupled receptor-mediated biological activity of TLQP-21 signaling in CHO-K1 cells. Unbiased genome-wide sequencing of the transcriptome from responsive CHO-K1 cells identified a prioritized list of possible G protein-coupled receptors bringing about this activity. Further experiments using a series of defined receptor antagonists and siRNAs led to the identification of complement C3a receptor-1 (C3AR1) as a target for TLQP-21 in rodents. We have not been able to demonstrate so far that this finding is translatable to the human receptor. Our results are in line with a large number of physiological observations in rodent models of food intake and metabolic control, where TLQP-21 shows activity. In addition, the sensitivity of TLQP-21 signaling to pertussis toxin is consistent with the known signaling pathway of C3AR1. The binding of TLQP-21 to C3AR1 not only has effects on signaling but also modulates cellular functions, as TLQP-21 was shown to have a role in directing migration of mouse RAW264.7 cells.


Subject(s)
Cell Movement/drug effects , Peptide Fragments/pharmacology , Receptors, Complement/metabolism , Signal Transduction/drug effects , Animals , Base Sequence , CHO Cells , Cricetinae , Cricetulus , Genome-Wide Association Study , HEK293 Cells , Humans , Mice , Molecular Sequence Data , Nerve Growth Factors/pharmacology , Neuropeptides/pharmacology , Pertussis Toxin/pharmacology , Rats , Receptors, Complement/agonists , Receptors, Complement/genetics , Species Specificity , Transcriptome/drug effects
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