scholarly journals FPD: A comprehensive phosphorylation database in fungi

2016 ◽  
Author(s):  
Youhuang Bai ◽  
Bin Chen ◽  
Yincong Zhou ◽  
Silin Ren ◽  
Qin Xu ◽  
...  
Keyword(s):  
Critical Role ◽  
Fungal Species ◽  
Phosphorylation Sites ◽  
Post Translational Modification ◽  
High Confidence ◽  
Cellular Processes ◽  
Phosphorylation Motif ◽  
Cycle Growth ◽  
Available Information

AbstractProtein phosphorylation, one of the most classic post-translational modification, plays a critical role in the diverse cellular processes including cell cycle, growth and signal transduction pathways. However, the available information of phosphorylation in fungi is limited. Here we provided a Fungi Phosphorylation Database (FPD) that comprises high-confidence in vivo phosphosites identified by MS-based proteomics in various fungal species. This comprehensive phosphorylation database contains 62,272 non-redundant phosphorylation sites in 11,222 proteins across eight organisms, including Aspergillus flavus, Aspergillus nidulans, Fusarium graminearum, Magnaporthe oryzae, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Cryptococcus neoformans. A fungi-specific phosphothreonine motif and several conserved phosphorylation motif were discovered by comparatively analyzing the pattern of phosphorylation sites in fungi, plants and animals.Database URL: http://bis.zju.edu.cn/FPD/index.php

Functional analysis of the SUMOylation pathway in Drosophila

2008 ◽  
Vol 36 (5) ◽  
pp. 868-873 ◽  
Author(s):  
Ana Talamillo ◽  
Jonatan Sánchez ◽  
Rosa Barrio
Keyword(s):  
Functional Analysis ◽  
Fine Tuning ◽  
Model Systems ◽  
Post Translational Modification ◽  
Reversible Process ◽  
Cellular Processes ◽  
Tuning Mechanism ◽  
Sumo Conjugation

SUMOylation, a reversible process used as a ‘fine-tuning’ mechanism to regulate the role of multiple proteins, is conserved throughout evolution. This post-translational modification affects several cellular processes by the modulation of subcellular localization, activity or stability of a variety of substrates. A growing number of proteins have been identified as targets for SUMOylation, although, for many of them, the role of SUMO conjugation on their function is unknown. The use of model systems might facilitate the study of SUMOylation implications in vivo. In the present paper, we have compiled what is known about SUMOylation in Drosophila melanogaster, where the use of genetics provides new insights on SUMOylation's biological roles.

scholarly journals Crystal structure of yeast Sis1 peptide-binding fragment and Hsp70 Ssa1 C-terminal complex

2006 ◽  
Vol 398 (3) ◽  
pp. 353-360 ◽  
Author(s):  
Jingzhi Li ◽  
Yunkun Wu ◽  
Xinguo Qian ◽  
Bingdong Sha
Keyword(s):  
Crystal Structure ◽  
Close Contact ◽  
Critical Role ◽  
Peptide Binding ◽  
Structural Basis ◽  
Cellular Processes ◽  
Terminal Form ◽  
Charged Residues ◽  
Domain I

Heat shock protein (Hsp) 40 facilitates the critical role of Hsp70 in a number of cellular processes such as protein folding, assembly, degradation and translocation in vivo. Hsp40 and Hsp70 stay in close contact to achieve these diverse functions. The conserved C-terminal EEVD motif in Hsp70 has been shown to regulate Hsp40–Hsp70 interaction by an unknown mechanism. Here, we provide a structural basis for this regulation by determining the crystal structure of yeast Hsp40 Sis1 peptide-binding fragment complexed with the Hsp70 Ssa1 C-terminal. The Ssa1 extreme C-terminal eight residues, G634PTVEEVD641, form a β-strand with the domain I of Sis1 peptide-binding fragment. Surprisingly, the Ssa1 C-terminal binds Sis1 at the site where Sis1 interacts with the non-native polypeptides. The negatively charged residues within the EEVD motif in Ssa1 C-terminal form extensive charge–charge interactions with the positively charged residues in Sis1. The structure-based mutagenesis data support the structural observations.

scholarly journals TGN/EE SNARE protein SYP61 is ubiquitinated and required for carbon/nitrogen-nutrient responses in Arabidopsis

2020 ◽  
Author(s):  
Yoko Hasegawa ◽  
Thais Huarancca Reyes ◽  
Tomohiro Uemura ◽  
Akari Fujimaki ◽  
Yongming Luo ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Critical Role ◽  
Snare Protein ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Protein Receptor ◽  
Sensitive Factor ◽  
Cargo Proteins ◽  
Golgi Network

AbstractUbiquitination is a post-translational modification with reversible attachment of the small protein ubiquitin, which is involved in numerous cellular processes including membrane trafficking. For example, ubiquitination of cargo proteins is known to regulate their subcellular dynamics, and plays important roles in plant growth and stress adaptation. However, the regulatory mechanism of the trafficking machinery components remains elusive. Here, we report Arabidopsis trans-Golgi network/early endosome (TGN/EE) localized soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein SYP61 as a novel ubiquitination target of a membrane localized ubiquitin ligase ATL31. SYP61 is a key component of membrane trafficking in Arabidopsis. SYP61 was ubiquitinated with K63-linked chain by ATL31 in vitro and in plants. The knockdown mutants of SYP61 were hypersensitive to the disrupted carbon (C)/nitrogen (N)-nutrient stress, suggesting its critical role in plant homeostasis in response to nutrients. We also found the ubiquitination status of SYP61 is affected by C/N-nutrient availability. These results provided possibility that ubiquitination of SNARE protein has important role in plant physiology.

scholarly journals Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast

2019 ◽  
Author(s):  
Liam McCarthy ◽  
Amanda Bentley-DeSousa ◽  
Alix Denoncourt ◽  
Yi-Chieh Tseng ◽  
Matthew Gabriel ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Budding Yeast ◽  
Feedback Regulation ◽  
Screening Strategy ◽  
Fungal Species ◽  
Post Translational Modification ◽  
Lysine Residues ◽  
Target Network ◽  
Inorganic Phosphates

ABSTRACTPolyphosphates (polyP) are long chains of inorganic phosphates that can be attached to lysine residues of target proteins as a non-enzymatic post-translational modification. This modification, termed polyphosphorylation, may be particularly prevalent in bacterial and fungal species that synthesize and store large quantities of polyP. In this study, we applied a proven screening strategy to evaluate the polyphosphorylation status of over 200 candidate targets in the budding yeast S. cerevisiae. We report 8 new polyphosphorylated proteins that interact genetically and physically with a previously identified network of targets implicated in ribosome biogenesis. The expanded target network includes vacuolar proteins Prb1 and Apl5, whose modification with polyP suggests a model for feedback regulation of polyP synthesis, while raising additional questions regarding the location of polyphosphorylation in vivo.

scholarly journals Proteome-wide Prediction of Lysine Methylation Reveals Novel Histone Marks and Outlines the Methyllysine Proteome

2018 ◽  
Author(s):  
Kyle K Biggar ◽  
Francois Charih ◽  
Huadong Liu ◽  
Yasser B Ruiz-Blanco ◽  
Leanne Stalker ◽  
...  
Keyword(s):  
Critical Role ◽  
Stem Cell Differentiation ◽  
Biochemical Properties ◽  
Lysine Methylation ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Validation Rate ◽  
Systematic Exploration ◽  
Proteome Level ◽  
Health And Disease

SUMMARYProtein Lys methylation plays a critical role in numerous cellular processes, yet it has been challenging to identify Lys methylation in a systematic manner. We present here an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We have developed MethylSight, a program that predicts Kme events solely on physicochemical and biochemical properties of putative methylation sites, which can then be validated by targeted MS. Using this approach, we have identified 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts ~50,000 Kme sites in non-histone proteins with high confidence, suggesting that Lys methylation is a prevalent post-translational modification. Our work provides a useful resource for systematic exploration of the role of Lys methylation in human health and disease.

scholarly journals Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport

2020 ◽  
Author(s):  
Krisztina Ötvös ◽  
Marco Marconi ◽  
Andrea Vega ◽  
Jose O’ Brien ◽  
Alexander Johnson ◽  
...  
Keyword(s):  
Root Growth ◽  
Nitrogen Source ◽  
Critical Role ◽  
Primary Root ◽  
Dynamic Environment ◽  
Fine Tuning ◽  
Specific Cell ◽  
Post Translational Modification ◽  
Available Nitrogen

AbstractNitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, live in vivo high- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth, i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.

scholarly journals The High Osmolarity Glycerol (HOG) Pathway Functions in Osmosensing, Trap Morphogenesis and Conidiation of the Nematode-Trapping Fungus Arthrobotrys oligospora

2020 ◽  
Vol 6 (4) ◽  
pp. 191
Author(s):  
Chih-Yen Kuo ◽  
Sheng-An Chen ◽  
Yen-Ping Hsueh
Keyword(s):  
Critical Role ◽  
Fungal Species ◽  
Nutrient Sensing ◽  
Mitogen Activated Protein Kinase ◽  
Hog Pathway ◽  
Arthrobotrys Oligospora ◽  
High Osmolarity ◽  
Cellular Processes ◽  
Predation Efficiency ◽  
Mitogen Activated Protein

Hog1, a mitogen-activated protein kinase (MAPK), has been identified in diverse fungal species, and it regulates various cellular processes, such as osmoadaptation, nutrient-sensing, and pathogenesis. However, the roles that Hog1 plays in nematode-trapping fungi were previously unclear. Here, we characterized orthologs of Saccharomyces cerevisiae Hog1 and membrane mucin Msb2 in the nematode-trapping fungus Arthrobotrys oligospora. We generated gene deletion mutants of HOG1 and MSB2 in A. oligospora, and characterized their roles in osmosensing, growth, and trap morphogenesis. We found that both hog1 and msb2 mutants were highly sensitive to high osmolarity. Predation analyses further revealed that hog1 and msb2 deletion caused a reduction in trap formation and predation efficiency. Furthermore, HOG1 is required for conidiation in A. oligospora, demonstrating its critical role in this developmental pathway. In summary, this study demonstrated that the conserved Hog1 and Msb2 govern physiology, growth and development in the nematode-trapping fungus A. oligospora.

Ca2+-Operated Transcriptional Networks: Molecular Mechanisms and In Vivo Models

2008 ◽  
Vol 88 (2) ◽  
pp. 421-449 ◽  
Author(s):  
Britt Mellström ◽  
Magali Savignac ◽  
Rosa Gomez-Villafuertes ◽  
Jose R. Naranjo
Keyword(s):  
Molecular Mechanisms ◽  
Critical Role ◽  
Transcriptional Networks ◽  
Calcium Signal ◽  
In Vivo Models ◽  
Cellular Processes ◽  
Calcium Sensors ◽  
Genes Encoding ◽  
Living Organisms

Calcium is the most universal signal used by living organisms to convey information to many different cellular processes. In this review we present well-known and recently identified proteins that sense and decode the calcium signal and are key elements in the nucleus to regulate the activity of various transcriptional networks. When possible, the review also presents in vivo models in which the genes encoding these calcium sensors-transducers have been modified, to emphasize the critical role of these Ca2+-operated mechanisms in many physiological functions.

scholarly journals Phosphodiesterase Regulation Is Critical for the Differentiation and Pattern of Gene Expression in Granulosa Cells of the Ovarian Follicle

2003 ◽  
Vol 17 (6) ◽  
pp. 1117-1130 ◽  
Author(s):  
Jy-Young Park ◽  
Francois Richard ◽  
Sang-Young Chun ◽  
Jeong-Hoh Park ◽  
Evelyn Law ◽  
...  
Keyword(s):  
Gene Expression ◽  
Granulosa Cells ◽  
Ovarian Follicle ◽  
Critical Role ◽  
Feedback Regulation ◽  
Camp Signaling ◽  
Morphological Examination ◽  
Cellular Processes ◽  
Chain Cleavage

Abstract Feedback regulations are integral components of the cAMP signaling required for most cellular processes, including gene expression and cell differentiation. Here, we provide evidence that one of these feedback regulations involving the cyclic nucleotide phosphodiesterase PDE4D plays a critical role in cAMP signaling during the differentiation of granulosa cells of the ovarian follicle. Gonadotropins induce PDE4D mRNA and increase the cAMP hydrolyzing activity in granulosa cells, demonstrating that a feedback regulation of cAMP is operating in granulosa cells in vivo. Inactivation of the PDE4D by homologous recombination is associated with an altered pattern of cAMP accumulation induced by the gonadotropin LH/human chorionic gonadotropin (hCG), impaired female fertility, and a markedly decreased ovulation rate. In spite of a disruption of the cAMP response, LH/hCG induced P450 side chain cleavage expression and steroidogenesis in a manner similar to wild-type controls. Morphological examination of the ovary of PDE4D−/− mice indicated luteinization of antral follicles with entrapped oocytes. Consistent with the morphological finding of unruptured follicles, LH/hCG induction of genes involved in ovulation, including cyclooxygenase-2, progesterone receptor, and the downstream genes, is markedly decreased in the PDE4D−/− ovaries. These data demonstrate that PDE4D regulation plays a critical role in gonadotropin mechanism of action and suggest that the intensity and duration of the cAMP signal defines the pattern of gene expression during the differentiation of granulosa cells.

scholarly journals Tau Phosphorylation Sites Work in Concert to Promote Neurotoxicity In Vivo

2007 ◽  
Vol 18 (12) ◽  
pp. 5060-5068 ◽  
Author(s):  
Michelle L. Steinhilb ◽  
Dora Dias-Santagata ◽  
Tudor A. Fulga ◽  
Daniel L. Felch ◽  
Mel B. Feany
Keyword(s):  
Neurodegenerative Disorders ◽  
Dominant Role ◽  
Critical Role ◽  
Tau Phosphorylation ◽  
Human Diseases ◽  
Phosphorylation Sites ◽  
Disease Pathogenesis ◽  
Microtubule Binding ◽  
Drosophila Model

Tau is a microtubule binding protein implicated in a number of human neurodegenerative disorders, including Alzheimer's disease. Phosphorylation of serine-proline/threonine-proline sites, targeted by proline-directed kinases, coincides temporally with neurodegeneration in the human diseases. Recently, we demonstrated that this unique group of serines and threonines has a critical role in controlling tau toxicity in a Drosophila model of tauopathy. Here, we use a combination of genetic and biochemical approaches to examine these sites individually and to determine which of them is primarily responsible for controlling tau neurotoxicity. Despite the importance placed on individual phosphoepitopes and their contributions to disease pathogenesis, our results indicate that no single phosphorylation residue plays a dominant role in controlling tau toxicity. These findings suggest that serine-proline/threonine-proline sites cooperate to mediate neurodegeneration in vivo.

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