scholarly journals Repertoire of Protein Kinases Encoded in the Genome ofTakifugu rubripes

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
R. Rakshambikai ◽  
S. Yamunadevi ◽  
K. Anamika ◽  
N. Tyagi ◽  
N. Srinivasan
Keyword(s):  
Protein Kinases ◽  
Mapk Pathway ◽  
Model Organism ◽  
Takifugu Rubripes ◽  
Group Level ◽  
Putative Protein ◽  
Signaling Mechanisms ◽  
Fugu Genome ◽  
Number Of Genes ◽  
Unique Domain

Takifugu rubripesis teleost fish widely used in comparative genomics to understand the human system better due to its similarities both in number of genes and structure of genes. In this work we survey the fugu genome, and, using sensitive computational approaches, we identify the repertoire of putative protein kinases and classify them into groups and subfamilies. The fugu genome encodes 519 protein kinase-like sequences and this number of putative protein kinases is comparable closely to that of human. However, in spite of its similarities to human kinases at the group level, there are differences at the subfamily level as noted in the case of KIS and DYRK subfamilies which contribute to differences which are specific to the adaptation of the organism. Also, certain unique domain combination of galectin domain and YkA domain suggests alternate mechanisms for immune response and binding to lipoproteins. Lastly, an overall similarity with the MAPK pathway of humans suggests its importance to understand signaling mechanisms in humans. Overall the fugu serves as a good model organism to understand roles of human kinases as far as kinases such as LRRK and IRAK and their associated pathways are concerned.

Differential effects of putative protein kinase C inhibitors on contraction of rat aortic smooth muscle

1993 ◽  
Vol 264 (4) ◽  
pp. H1300-H1306 ◽  
Author(s):  
Y. Shimamoto ◽  
H. Shimamoto ◽  
C. Y. Kwan ◽  
E. E. Daniel
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Induced Response ◽  
Dependent Manner ◽  
Contractile Responses ◽  
Putative Protein ◽  
Calphostin C ◽  
Kinase C ◽  
Putative Protein Kinase

We investigated effects of three kinds of putative protein kinase C (PKC) inhibitors, calphostin C, 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H-7), and stauro-sporine, on aortic muscle contractions induced by KCl, phenylephrine, 12-O-tetradecanoylphorbol-13-acetate (TPA), and phorbol 12, 13-dibutyrate (PDBu). Calphostin C noncompetitively inhibited TPA-induced contractions in a concentration-dependent manner. At 10(-6) M, calphostin C completely abolished responses to TPA and also effectively inhibited PDBu-induced contractions. Such a concentration of calphostin C had no effect on KCl-induced contractions but decreased the maximal tension of phenylephrine-induced response curve by 35.3 +/- 6.6% H-7 (10(-5) M had little effect on TPA-induced contraction but significantly inhibited contractile responses to phenylephrine and KCl. Staurosporine (10(-8) M, 3 x 10(-8) M) inhibited contractile responses to KCl, phenylephrine, and TPA. We suggest that staurosporine and H-7, which are known to act on the catalytic domain of PKC carrying high degree of sequence homology with other protein kinases, are relatively nonselective for PKC. On the other hand, calphostin C acting on the regulatory domain of PKC, which is distinct from other protein kinases, may serve as a relatively more selective PKC inhibitor.

scholarly journals A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

2017 ◽  
Author(s):  
Mario Baumgart ◽  
Emanuel Barth ◽  
Aurora Savino ◽  
Marco Groth ◽  
Philipp Koch ◽  
...  
Keyword(s):  
Gasterosteus Aculeatus ◽  
Model Organism ◽  
Takifugu Rubripes ◽  
Aging Research ◽  
Control Of Gene Expression ◽  
Non Coding Rna ◽  
Nothobranchius Furzeri ◽  
In Captivity ◽  
Supplementary Material

ABSTRACTBackground: The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age-dependent control of gene expression.Results: Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri as compared to other teleosts was a duplication of the miR-29 cluster.Conclusion: The completeness of the catalogue we provide is comparable to that of zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.Availability: All supplementary material can be found online at http://www.rna.uni-jena.de/en/supplements/nothobranchius-furzeri-mirnome/.

scholarly journals Hierarchical transitions and fractal wrinkling drive bacterial pellicle morphogenesis

2021 ◽  
Vol 118 (20) ◽  
pp. e2023504118
Author(s):  
Boyang Qin ◽  
Chenyi Fei ◽  
Bruce Wang ◽  
Howard A. Stone ◽  
Ned S. Wingreen ◽  
...  
Keyword(s):  
Thin Films ◽  
Model Organism ◽  
Seeding Density ◽  
Fluid Interfaces ◽  
Bacterial Cells ◽  
Group Level ◽  
Mechanical Theory ◽  
Pellicle Formation ◽  
Stereo Microscope ◽  
Film Microstructure

Bacterial cells can self-organize into structured communities at fluid–fluid interfaces. These soft, living materials composed of cells and extracellular matrix are called pellicles. Cells residing in pellicles garner group-level survival advantages such as increased antibiotic resistance. The dynamics of pellicle formation and, more generally, how complex morphologies arise from active biomaterials confined at interfaces are not well understood. Here, using Vibrio cholerae as our model organism, a custom-built adaptive stereo microscope, fluorescence imaging, mechanical theory, and simulations, we report a fractal wrinkling morphogenesis program that differs radically from the well-known coalescence of wrinkles into folds that occurs in passive thin films at fluid–fluid interfaces. Four stages occur: growth of founding colonies, onset of primary wrinkles, development of secondary curved ridge instabilities, and finally the emergence of a cascade of finer structures with fractal-like scaling in wavelength. The time evolution of pellicle formation depends on the initial heterogeneity of the film microstructure. Changing the starting bacterial seeding density produces three variations in the sequence of morphogenic stages, which we term the bypass, crystalline, and incomplete modes. Despite these global architectural transitions, individual microcolonies remain spatially segregated, and thus, the community maintains spatial and genetic heterogeneity. Our results suggest that the memory of the original microstructure is critical in setting the morphogenic dynamics of a pellicle as an active biomaterial.

Overexpression of OsMed16 inhibits rice growth and causes spontaneous cell death

2020 ◽  
Author(s):  
Jie Jiang ◽  
Guangzhe Yang ◽  
Yafeng Xin ◽  
Zhigang Wang ◽  
Wei Yan ◽  
...  
Keyword(s):  
Cell Death ◽  
Rna Polymerase Ii ◽  
Leaf Blade ◽  
Leaf Sheath ◽  
Rice Seedling ◽  
Putative Protein ◽  
Rice Growth ◽  
Number Of Genes ◽  
Growth Development ◽  
Spontaneous Cell Death

Abstract Background The Mediator complex transduces information from the DNA-bound transcription factors to the RNA polymerase II transcriptional machinery. Research on plant Mediator subunits was mainly performed in Arabidopsis, while very few of them have been functionally characterized in rice. Results Here the rice Mediator subunit 16, OsMed16, was studied. OsMed16 encoded a putative protein of 1301 amino acids, which is longer than the reported version. It was expressed in various rice organs, and localized in nucleus. Knockout of OsMed16 caused rice seedling lethality. Its overexpression led to rice growth retardation, low yield, and spontaneous cell death in leaf blade and leaf sheath. RNA sequencing suggested that overexpression of OsMed16 altered the expression of a large number of genes. Among them, the up-regulation of some defense-related genes was verified. Conclusions Our results demonstrated that OsMed16 can regulate the expression of a wealth of genes, and alterations in its expression have profound impact on plant growth, development and defense response in rice.

scholarly journals Involvement of Mitogen-Activated Protein Kinase Pathways in Staphylococcus aureus Invasion of Normal Osteoblasts

2001 ◽  
Vol 69 (9) ◽  
pp. 5235-5242 ◽  
Author(s):  
John K. Ellington ◽  
Adam Elhofy ◽  
Kenneth L. Bost ◽  
Michael C. Hudson
Keyword(s):  
Staphylococcus Aureus ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Time Course ◽  
Mapk Pathway ◽  
Mitogen Activated Protein Kinase ◽  
Bacterial Invasion ◽  
Mitogen Activated Protein ◽  
Factor C ◽  
Human And Mouse

ABSTRACT Staphylococcus aureus invades osteoblasts and can persist in the intracellular environment. The present study examined the role of osteoblast mitogen-activated protein kinase (MAPK) pathways in bacterial invasion. S. aureus infection of normal human and mouse osteoblasts resulted in an increase in the phosphorylation of the extracellular signal-regulated protein kinases (ERK 1 and 2). This stimulation of ERK 1 and 2 correlated with the time course of S. aureus invasion, and bacterial adherence induced the MAPK pathway. ERK 1 and 2 phosphorylation was time and dose dependent and required active S. aureus gene expression for maximal induction. The nonpathogenic Staphylococcus carnosus was also able to induce ERK 1 and 2 phosphorylation, albeit at lower levels than S. aureus. Phosphorylation of the stress-activated protein kinases was increased in both infected human and mouse osteoblasts; however, the p38 MAPK pathway was not activated in response to S. aureus. Finally, the transcription factor c-Jun, but not Elk-1 or ATF-2, was phosphorylated in response to S. aureus infection.

scholarly journals Global profiling of distinct cysteine redox forms reveals wide-ranging redox regulation in C. elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jin Meng ◽  
Ling Fu ◽  
Keke Liu ◽  
Caiping Tian ◽  
Ziyun Wu ◽  
...  
Keyword(s):  
Redox Regulation ◽  
Mapk Pathway ◽  
Model Organism ◽  
Redox Signaling ◽  
P38 Map Kinase ◽  
Redox Biology ◽  
C Elegans ◽  
Protein Functions ◽  
Redox Forms

AbstractPost-translational changes in the redox state of cysteine residues can rapidly and reversibly alter protein functions, thereby modulating biological processes. The nematode C. elegans is an ideal model organism for studying cysteine-mediated redox signaling at a network level. Here we present a comprehensive, quantitative, and site-specific profile of the intrinsic reactivity of the cysteinome in wild-type C. elegans. We also describe a global characterization of the C. elegans redoxome in which we measured changes in three major cysteine redox forms after H2O2 treatment. Our data revealed redox-sensitive events in translation, growth signaling, and stress response pathways, and identified redox-regulated cysteines that are important for signaling through the p38 MAP kinase (MAPK) pathway. Our in-depth proteomic dataset provides a molecular basis for understanding redox signaling in vivo, and will serve as a valuable and rich resource for the field of redox biology.

scholarly journals Structure–function analysis of yeast piD261/Bud32, an atypical protein kinase essential for normal cell life

2002 ◽  
Vol 364 (2) ◽  
pp. 457-463 ◽  
Author(s):  
Sonia FACCHIN ◽  
Raffaele LOPREIATO ◽  
Silvia STOCCHETTO ◽  
Giorgio ARRIGONI ◽  
Luca CESARO ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Mutational Analysis ◽  
Function Analysis ◽  
Sequence Similarity ◽  
Putative Protein ◽  
Cell Life ◽  
Sds Page ◽  
Structural Homologues ◽  
Putative Protein Kinase

The Saccharomyces cerevisiae YGR262c/BUD32 gene, whose disruption causes a severe pleiotropic phenotype, encodes a 261-residue putative protein kinase, piD261, whose structural homologues have been identified in a variety of organisms, including humans, and whose function is unknown. We have demonstrated previously that piD261, expressed in Escherichia coli as a recombinant protein, is a Ser/Thr kinase, as judged by its ability to autophosphorylate and to phosphorylate casein. Here we describe a mutational analysis showing that, despite low sequence similarity, the invariant residues representing the signature of protein kinases are conserved in piD261 and in its structural homologues, but are embedded in an altered context, suggestive of unique mechanistic properties. Especially noteworthy are: (i) three unique inserts of unknown function within the N-terminal lobe, (ii) the lack of a lysyl residue which in all other Ser/Thr kinases participates in the catalytic event by interacting with the transferred ATP γ-phosphate, and which in piD261 is replaced by a threonine, and (iii) an exceedingly short activation loop including two serines, Ser-187 and Ser-189, whose autophosphorylation accounts for the appearance of an upshifted band upon SDS/PAGE. A mutant in which these serines are replaced by alanines was devoid of the upshifted band and displayed reduced catalytic activity. This would include piD261 in the category of protein kinases activated by phosphorylation, although it lacks the RD (Arg-Asp) motif which is typical of these enzymes.

Soma/Germline Interactions In Caenorhabditis Elegans Gonad

1999 ◽  
Vol 5 (S2) ◽  
pp. 1072-1073
Author(s):  
David H. Hall ◽  
Virginia P. Winfrey ◽  
Gareth Blaeuer ◽  
Loren H. Hoffman ◽  
Tokiko Furuta ◽  
...  
Keyword(s):  
Gap Junctions ◽  
Freeze Fracture ◽  
Model Organism ◽  
Mature Oocyte ◽  
Sheath Cell ◽  
C Elegans ◽  
Functional Interactions ◽  
Signaling Mechanisms ◽  
Primary Oocyte ◽  
Development Gap

A combination of microscopical methods (TEM, SEM, freeze fracture, confocal, immunoEM) are utilized to demonstrate functional interactions between somatic cells and the germline in the model organism, C. elegans.A variety of signaling mechanisms are required to coordinate activity of maturing oocytes and the somatic sheath of the gonad. Communication via gap junctions allows direct coordination of sheath cell motility and oocyte development. Gap junctions link adjoining sheath cells, and link the sheath to the most mature oocyte. Yolk protein produced in the intestine passes from the pseudocoelom through the basal lamina of the proximal gonad and then through fenestrations (sheath pores) in the gonad sheath before being endocytosed into the most mature oocytes. Myoepithelial specializations anchored by hemi-adherens junctions in the proximal sheath act to squeeze the primary oocyte out of the gonad to the spermatheca for fertilization.

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