scholarly journals Identification of Novel Recognition Motifs and Regulatory Targets for the Yeast Actin-regulating Kinase Prk1p

2003 ◽  
Vol 14 (12) ◽  
pp. 4871-4884 ◽  
Author(s):  
Bo Huang ◽  
Guisheng Zeng ◽  
Alvin Y.J. Ng ◽  
Mingjie Cai
Keyword(s):  
Actin Cytoskeleton ◽  
Phosphorylation Site ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Yeast Genome ◽  
Three Dimensional Model ◽  
Recognition Sequence ◽  
Yeast Saccharomyces Cerevisiae

Prk1p is a serine/threonine kinase involved in the regulation of the actin cytoskeleton organization in the yeast Saccharomyces cerevisiae. Previously, we have identified LxxQxTG as the phosphorylation site of Prk1p. In this report, the recognition sequence for Prk1p is investigated more thoroughly. It is found that the presence of a hydrophobic residue at the position of P-5 is necessary for Prk1p phosphorylation and L, I, V, and M are all able to confer the phosphorylation at various efficiencies. The residue flexibility at P-2 has also been identified to include Q, N, T, and S. A homology-based three-dimensional model of the kinase domain of Prk1p provided some structural interpretations for these substrate specificities. The characterization of the [L/I/V/M]xx[Q/N/T/S]xTG motif led to the identification of a spectrum of potential targets for Prk1p from yeast genome. One of them, Scd5p, which contains three LxxTxTG motifs and is previously known to be important for endocytosis and actin organization, has been chosen to demonstrate its relationship with Prk1p. Phosphorylation of Scd5p by Prk1p at the three LxxTxTG motifs could be detected in vitro and in vivo, and deletion of PRK1 suppressed the defects in actin cytoskeleton and endocytosis in one of the scd5 mutants. These results allowed us to conclude that Scd5p is likely another regulatory target of Prk1p.

scholarly journals Yeast as a Model to Understand Actin-Mediated Cellular Functions in Mammals—Illustrated with Four Actin Cytoskeleton Proteins

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 672 ◽  
Author(s):  
Zain Akram ◽  
Ishtiaq Ahmed ◽  
Heike Mack ◽  
Ramandeep Kaur ◽  
Richard C. Silva ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Molecular Mechanisms ◽  
Budding Yeast ◽  
Animal Cell ◽  
Molecular Genetic ◽  
In Vivo Studies ◽  
Yeast Saccharomyces Cerevisiae ◽  
Higher Eukaryotes

The budding yeast Saccharomyces cerevisiae has an actin cytoskeleton that comprises a set of protein components analogous to those found in the actin cytoskeletons of higher eukaryotes. Furthermore, the actin cytoskeletons of S. cerevisiae and of higher eukaryotes have some similar physiological roles. The genetic tractability of budding yeast and the availability of a stable haploid cell type facilitates the application of molecular genetic approaches to assign functions to the various actin cytoskeleton components. This has provided information that is in general complementary to that provided by studies of the equivalent proteins of higher eukaryotes and hence has enabled a more complete view of the role of these proteins. Several human functional homologues of yeast actin effectors are implicated in diseases. A better understanding of the molecular mechanisms underpinning the functions of these proteins is critical to develop improved therapeutic strategies. In this article we chose as examples four evolutionarily conserved proteins that associate with the actin cytoskeleton: (1) yeast Hof1p/mammalian PSTPIP1, (2) yeast Rvs167p/mammalian BIN1, (3) yeast eEF1A/eEF1A1 and eEF1A2 and (4) yeast Yih1p/mammalian IMPACT. We compare the knowledge on the functions of these actin cytoskeleton-associated proteins that has arisen from studies of their homologues in yeast with information that has been obtained from in vivo studies using live animals or in vitro studies using cultured animal cell lines.

scholarly journals Negative regulation of Raf-1 by phosphorylation of serine 621.

1996 ◽  
Vol 16 (10) ◽  
pp. 5409-5418 ◽  
Author(s):  
H Mischak ◽  
T Seitz ◽  
P Janosch ◽  
M Eulitz ◽  
H Steen ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Kinase Activity ◽  
Phosphorylation Site ◽  
Kinase Domain ◽  
Negative Regulation ◽  
Catalytic Function ◽  
Dependent Protein ◽  
The One

The elevation of cyclic AMP (cAMP) levels in the cell downregulates the activity of the Raf-1 kinase. It has been suggested that this effect is due to the activation of cAMP-dependent protein kinase (PKA), which can directly phosphorylate Raf-1 in vitro. In this study, we confirmed this hypothesis by coexpressing Raf-1 with the constitutively active catalytic subunit of PKA, which could fully reproduce the inhibition previously achieved by cAMP. PKA-phosphorylated Raf-1 exhibits a reduced affinity for GTP-loaded Ras as well as impaired catalytic activity. As the binding to GTP-loaded Ras induces Raf-1 activation in the cell, we examined which mechanism is required for PKA-mediated Raf-1 inhibition in vivo. A Raf-1 point mutant (RafR89L), which is unable to bind Ras, as well as the isolated Raf-1 kinase domain were still fully susceptible to inhibition by PKA, demonstrating that the phosphorylation of the Raf-1 kinase suffices for inhibition. By the use of mass spectroscopy and point mutants, PKA phosphorylation site was mapped to a single site in the Raf-1 kinase domain, serine 621. Replacement of serine 621 by alanine or cysteine or destruction of the PKA consensus motif by changing arginine 618 resulted in the loss of catalytic activity. Notably, a mutation of serine 619 to alanine did not significantly affect kinase activity or regulation by activators or PKA. Changing serine 621 to aspartic acid yielded a Raf-1 protein which, when expressed to high levels in Sf-9 insect cells, retained a very low inducible kinase activity that was resistant to PKA downregulation. The purified Raf-1 kinase domain displayed slow autophosphorylation of serine 621, which correlated with a decrease in catalytic function. The Raf-1 kinase domain activated by tyrosine phosphorylation could be downregulated by PKA. Specific removal of the phosphate residue at serine 621 reactivated the catalytic activity. These results are most consistent with a dual role of serine 621. On the one hand, serine 621 appears essential for catalytic activity; on the other hand, it serves as a phosphorylation site which confers negative regulation.

scholarly journals Mutagenesis and Molecular Modeling Reveal Three Key Extracellular Loops of the Membrane Receptor HasR That Are Involved in Hemophore HasA Binding

2007 ◽  
Vol 189 (14) ◽  
pp. 5379-5382 ◽  
Author(s):  
Clément Barjon ◽  
Karine Wecker ◽  
Nadia Izadi-Pruneyre ◽  
Philippe Delepelaire
Keyword(s):  
Molecular Modeling ◽  
Outer Membrane ◽  
Three Dimensional ◽  
Membrane Receptor ◽  
Dimensional Model ◽  
Outer Membrane Receptor ◽  
Three Dimensional Model ◽  
Extracellular Loops

ABSTRACT On the basis of the three-dimensional model of the heme/hemophore TonB-dependent outer membrane receptor HasR, mutants with six-residue deletions in the 11 putative extracellular loops were generated. Although all mutants continued to be active TonB-dependent heme transporters, mutations in three loops abolished hemophore HasA binding both in vivo and in vitro.

scholarly journals Recent Advances in Three-Dimensional Multicellular Spheroid Culture and Future Development

Micromachines ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 96
Author(s):  
Honglin Shen ◽  
Shuxiang Cai ◽  
Chuanxiang Wu ◽  
Wenguang Yang ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Multicellular Spheroids ◽  
Three Dimensional Model ◽  
Advantages And Disadvantages ◽  
High Throughput Drug Screening ◽  
Tumor Research ◽  
Basic Biology ◽  
And Function

Three-dimensional multicellular spheroids (MCSs) have received extensive attention in the field of biomedicine due to their ability to simulate the structure and function of tissues in vivo more accurately than traditional in vitro two-dimensional models and to simulate cell–cell and cell extracellular matrix (ECM) interactions. It has become an important in vitro three-dimensional model for tumor research, high-throughput drug screening, tissue engineering, and basic biology research. In the review, we first summarize methods for MCSs generation and their respective advantages and disadvantages and highlight the advances of hydrogel and microfluidic systems in the generation of spheroids. Then, we look at the application of MCSs in cancer research and other aspects. Finally, we discuss the development direction and prospects of MCSs

scholarly journals The interleaved partial active shape model (IPASM) search algorithm – towards 3D ultrasound-based bone surface reconstruction

10.29007/rbgl ◽  
2019 ◽  
Author(s):  
Benjamin Hohlmann ◽  
Klaus Radermacher
Keyword(s):  
Search Algorithm ◽  
Three Dimensional ◽  
3D Ultrasound ◽  
Three Dimensional Model ◽  
In Vivo Experiments ◽  
Distal Surface ◽  
Cheap Alternative ◽  
Orthopedic Applications

Several orthopedic applications require a three-dimensional model of the bone. Ultrasound is a radiation-free and cheap alternative to the state-of-the-art imaging modalities if its limitations in terms of image quality and viewing range can be overcome. This work presents in-vitro as well as in-vivo experiments evaluating the IPASM search, a method for combined segmentation, registration as well as extrapolation. The algorithm is capable to reconstruct the distal surface of a phantom femur with an average surface distance error of roughly 1mm in case of in-vitro as well as below 2mm for in-vivo records, even if the shape varies strongly from the initial model.

scholarly journals The Role of Palladin in Podocytes

2018 ◽  
Vol 29 (6) ◽  
pp. 1662-1678 ◽  
Author(s):  
Nadine Artelt ◽  
Tim A. Ludwig ◽  
Henrik Rogge ◽  
Panagiotis Kavvadas ◽  
Florian Siegerist ◽  
...  
Keyword(s):  
Actin Cytoskeleton ◽  
Kidney Biopsy ◽  
Three Dimensional ◽  
Focal Adhesions ◽  
Early Developmental Stage ◽  
Zebrafish Embryos ◽  
Filtration Barrier ◽  
Biopsy Specimens

Background Podocyte loss and effacement of interdigitating podocyte foot processes are the major cause of a leaky filtration barrier and ESRD. Because the complex three-dimensional morphology of podocytes depends on the actin cytoskeleton, we studied the role in podocytes of the actin bundling protein palladin, which is highly expressed therein.Methods We knocked down palladin in cultured podocytes by siRNA transfection or in zebrafish embryos by morpholino injection and studied the effects by immunofluorescence and live imaging. We also investigated kidneys of mice with podocyte-specific knockout of palladin (PodoPalld−/− mice) by immunofluorescence and ultrastructural analysis and kidney biopsy specimens from patients by immunostaining for palladin.Results Compared with control-treated podocytes, palladin-knockdown podocytes had reduced actin filament staining, smaller focal adhesions, and downregulation of the podocyte-specific proteins synaptopodin and α-actinin-4. Furthermore, palladin-knockdown podocytes were more susceptible to disruption of the actin cytoskeleton with cytochalasin D, latrunculin A, or jasplakinolide and showed altered migration dynamics. In zebrafish embryos, palladin knockdown compromised the morphology and dynamics of epithelial cells at an early developmental stage. Compared with PodoPalld+/+ controls, PodoPalld−/− mice developed glomeruli with a disturbed morphology, an enlarged subpodocyte space, mild effacement, and significantly reduced expression of nephrin and vinculin. Furthermore, nephrotoxic serum injection led to significantly higher levels of proteinuria in PodoPalld−/− mice than in controls. Kidney biopsy specimens from patients with diabetic nephropathy and FSGS showed downregulation of palladin in podocytes as well.Conclusions Palladin has an important role in podocyte function in vitro and in vivo.

scholarly journals Numerical Modelling of the Behaviour of the Cervical Spine under the Effect of a Flexion / Extension

2019 ◽  
Vol 01 (02) ◽  
pp. 144-153 ◽  
Author(s):  
Nadir Damba ◽  
Abdellatif OUDRANE ◽  
Benaoumeur AOUR ◽  
Mohammed Salah BENNOUNA ◽  
Nabil BELKAHELLA ◽  
...  
Keyword(s):  
Cervical Spine ◽  
Classical Mechanics ◽  
Three Dimensional ◽  
Individual Variability ◽  
In Vitro Tests ◽  
Three Dimensional Model ◽  
Major Interest ◽  
Flexion Extension

Numerical simulation is today widely used in several fields of engineering, and research undertaken for more than 20 years concerning the geometric and mechanical modeling of the spine gradually leads to clinical applications of major interest. Indeed, the in vivo and in vitro evaluation tools pose a certain number of limitations: non-standardized procedures and inter-specimen variability for in vitro tests, medical, ethical constraints, and inter-individual variability for in vivo. These limitations are actually obstacles to comparison. It is notably within the framework of implant comparisons that the methods of structural calculation, and more particularly finite element modeling, widely used in classical mechanics, find their usefulness. in this context, this present work consists in developing a three-dimensional model of the cervical spine, in order to subsequently optimize the fitting of disc prostheses

scholarly journals Identification of Csk tyrosine phosphorylation sites and a tyrosine residue important for kinase domain structure

1997 ◽  
Vol 322 (3) ◽  
pp. 927-935 ◽  
Author(s):  
Vladimir JOUKOV ◽  
Mauno VIHINEN ◽  
Satu VAINIKKA ◽  
Janusz M. SOWADSKI ◽  
Kari ALITALO ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Tyrosine Phosphorylation ◽  
Protein Tyrosine Kinase ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Sh2 Domain ◽  
Binding Studies ◽  
Inactive Form

The lack of a conserved tyrosine autophosphorylation site is a unique feature of the C-terminal Src-kinase, Csk, although this protein tyrosine kinase can be autophosphorylated on tyrosine residues in vitro and in bacteria. Here we show that human Csk is tyrosine phosphorylated in HeLa cells treated with sodium pervanadate. Phosphorylation in vivo occurs mainly at Tyr-184 and in vitro mainly at Tyr-304. A Y304F mutation strongly decreased Csk phosphorylation in vitro, and a Y184F mutation abolished tyrosine phosphorylation in vivo. A catalytically inactive form of Csk was also phosphorylated on Tyr-184 in vivo, suggesting that this is not a site of autophosphorylation. The kinase activity of the Y184F protein was not changed, while the Y304F protein showed one-third of wild-type activity. Three-dimensional modelling of the Csk kinase domain indicated that the Y304F mutation abolishes one of two conserved hydrogen bonds between the upper and the lower lobes in the open conformation of the kinase domain. Phosphopeptide binding studies suggested that phosphorylation of Tyr-184 creates a binding site for low-molecular-mass proteins. Cellular Csk was associated with several phosphoproteins, some of which were interacting with the Csk SH2 domain. Taken together these results indicate that Csk can be phosphorylated in vivo at Tyr-184 by an as yet unknown tyrosine kinase, and that autophosphorylation of Tyr-304 occurs only at abnormally high Csk concentrations in vitro. Furthermore, Tyr-304 is required for the maintenance of the structure of the Csk kinase domain.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

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