Role of calcium in membrane interactions by PI(4,5)P2-binding proteins

2014 ◽  
Vol 42 (5) ◽  
pp. 1441-1446 ◽  
Author(s):  
Marina E. Monteiro ◽  
Maria J. Sarmento ◽  
Fábio Fernandes
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Fine Tuning ◽  
Protein Activity ◽  
Calcium Dependent ◽  
Spatial Regulation ◽  
Target Membrane ◽  
Temporal And Spatial ◽  
Lateral Organization

Ca2+ and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] are key agents in membrane-associated signalling events. Their temporal and spatial regulation is crucial for activation or recruitment of proteins in the plasma membrane. In fact, the interaction of several signalling proteins with PI(4,5)P2 has been shown to be tightly regulated and dependent on the presence of Ca2+, with co-operative binding in some cases. In these proteins, PI(4,5)P2 and Ca2+ binding typically occurs at different binding sites. In addition, several PI(4,5)P2-binding proteins are known targets of calmodulin (CaM), which, depending on the presence of calcium, can compete with PI(4,5)P2 for protein interaction, translating Ca2+ transient microdomains into variations of PI(4,5)P2 lateral organization in time and space. The present review highlights different examples of calcium-dependent PI(4,5)P2-binding proteins and discusses the possible impact of this dual regulation on fine-tuning of protein activity by triggering target membrane binding in the presence of subtle changes in the levels of calcium or PI(4,5)P2.

scholarly journals The tandem C2 domains of synaptotagmin contain redundant Ca2+ binding sites that cooperate to engage t-SNAREs and trigger exocytosis

2001 ◽  
Vol 154 (6) ◽  
pp. 1117-1124 ◽  
Author(s):  
Cynthia A. Earles ◽  
Jihong Bai ◽  
Ping Wang ◽  
Edwin R. Chapman
Keyword(s):  
Membrane Fusion ◽  
Real Time ◽  
Pc12 Cells ◽  
Binding Sites ◽  
C2 Domain ◽  
C2 Domains ◽  
Synaptotagmin I ◽  
Target Membrane ◽  
Complete Disruption

Real-time voltammetry measurements from cracked PC12 cells were used to analyze the role of synaptotagmin–SNARE interactions during Ca2+-triggered exocytosis. The isolated C2A domain of synaptotagmin I neither binds SNAREs nor inhibits norepinephrine secretion. In contrast, two C2 domains in tandem (either C2A-C2B or C2A-C2A) bind strongly to SNAREs, displace native synaptotagmin from SNARE complexes, and rapidly inhibit exocytosis. The tandem C2 domains of synaptotagmin cooperate via a novel mechanism in which the disruptive effects of Ca2+ ligand mutations in one C2 domain can be partially alleviated by the presence of an adjacent C2 domain. Complete disruption of Ca2+-triggered membrane and target membrane SNARE interactions required simultaneous neutralization of Ca2+ ligands in both C2 domains of the protein. We conclude that synaptotagmin–SNARE interactions regulate membrane fusion and that cooperation between synaptotagmin's C2 domains is crucial to its function.

Temporal and spatial regulation of cAMP signaling in disease: role of cyclic nucleotide phosphodiesterases

2014 ◽  
Vol 28 (6) ◽  
pp. 593-607 ◽  
Author(s):  
Carolina Otero ◽  
Juan P. Peñaloza ◽  
Paula I. Rodas ◽  
Ricardo Fernández-Ramires ◽  
Luis Velasquez ◽  
...  
Keyword(s):  
Cyclic Nucleotide ◽  
Camp Signaling ◽  
Cyclic Nucleotide Phosphodiesterases ◽  
Spatial Regulation ◽  
Temporal And Spatial ◽  
Nucleotide Phosphodiesterases

scholarly journals RsmV, a Small Noncoding Regulatory RNA in Pseudomonas aeruginosa That Sequesters RsmA and RsmF from Target mRNAs

2018 ◽  
Vol 200 (16) ◽  
Author(s):  
Kayley H. Janssen ◽  
Manisha R. Diaz ◽  
Cindy J. Gode ◽  
Matthew C. Wolfgang ◽  
Timothy L. Yahr
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Binding Sites ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Secretion System ◽  
Fine Tuning ◽  
Content Type ◽  
Target Mrnas

ABSTRACT The Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm posttranscriptional regulatory system plays important roles in the inverse control of phenotypes associated with acute and chronic virulence. RsmA and RsmF are RNA-binding proteins that interact with target mRNAs to control gene expression at the posttranscriptional level. Previous work found that RsmA activity is controlled by at least three small, noncoding regulatory RNAs (RsmW, RsmY, and RsmZ). In this study, we took an in silico approach to identify additional small RNAs (sRNAs) that might function in the sequestration of RsmA and/or RsmF (RsmA/RsmF) and identified RsmV, a 192-nucleotide (nt) transcript with four predicted RsmA/RsmF consensus binding sites. RsmV is capable of sequestering RsmA and RsmF in vivo to activate translation of tssA1, a component of the T6SS, and to inhibit T3SS gene expression. Each of the predicted RsmA/RsmF consensus binding sites contributes to RsmV activity. Electrophoretic mobility shifts assays show that RsmF binds RsmV with >10-fold higher affinity than RsmY and RsmZ. Gene expression studies revealed that the temporal expression pattern of RsmV differs from those of RsmW, RsmY, and RsmZ. These findings suggest that each sRNA may play a distinct role in controlling RsmA and RsmF activity. IMPORTANCE The members of the CsrA/RsmA family of RNA-binding proteins play important roles in posttranscriptional control of gene expression. The activity of CsrA/RsmA proteins is controlled by small noncoding RNAs that function as decoys to sequester CsrA/RsmA from target mRNAs. Pseudomonas aeruginosa has two CsrA family proteins (RsmA and RsmF) and at least four sequestering sRNAs (RsmV [identified in this study], RsmW, RsmY, and RsmZ) that control RsmA/RsmF activity. RsmY and RsmZ are the primary sRNAs that sequester RsmA/RsmF, and RsmV and RsmW appear to play smaller roles. Differences in the temporal and absolute expression levels of the sRNAs and in their binding affinities for RsmA/RsmF may provide a mechanism of fine-tuning the output of the Rsm system in response to environmental cues.

scholarly journals Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples

2021 ◽  
Vol 1 ◽  
Author(s):  
Wei Zhou ◽  
Wei Chi ◽  
Wanting Shen ◽  
Wanying Dou ◽  
Junyi Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Gas Sensing ◽  
Fine Tuning ◽  
Computational Tools ◽  
Spatial Regulation ◽  
Search Results ◽  
Biological Interpretation ◽  
Computational Identification ◽  
Temporal And Spatial ◽  
Public Repositories

In proteins, functional centers consist of the key amino acids required to perform molecular functions such as catalysis, ligand-binding, hormone- and gas-sensing. These centers are often embedded within complex multi-domain proteins and can perform important cellular signaling functions that enable fine-tuning of temporal and spatial regulation of signaling molecules and networks. To discover hidden functional centers, we have developed a protocol that consists of the following sequential steps. The first is the assembly of a search motif based on the key amino acids in the functional center followed by querying proteomes of interest with the assembled motif. The second consists of a structural assessment of proteins that harbor the motif. This approach, that relies on the application of computational tools for the analysis of data in public repositories and the biological interpretation of the search results, has to-date uncovered several novel functional centers in complex proteins. Here, we use recent examples to describe a step-by-step guide that details the workflow of this approach and supplement with notes, recommendations and cautions to make this protocol robust and widely applicable for the discovery of hidden functional centers.

scholarly journals RAD51 May Regulate the Expression of Genes Involved in Autophagy Through Interaction with E-box Binding Proteins in Cancer Cell Lines

2020 ◽  
Author(s):  
Keunsoo Kang ◽  
Yoonjung Choi ◽  
Hyeonjin Moon ◽  
Minjin Seo ◽  
Jahyun Yoon ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Cell Lines ◽  
Binding Sites ◽  
Binding Proteins ◽  
Binding Motif ◽  
Expression Of Genes ◽  
Genome Wide ◽  
E Box ◽  
Autophagy Pathway

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found in silico evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway through interaction with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51 binding sites in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-binding sites in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway were significantly occupied by RAD51 in all four cell lines. Taken together, these results predicted a novel role of RAD51 that had not been addressed previously, and provided evidence that RAD51 could possibly be involved in regulating genes associated with the autophagy pathway, through interaction with E-box binding proteins.

Giscience in the Mountain Geography

2010 ◽  
Vol 27 (1-2) ◽  
pp. 81-90
Author(s):  
Krishna Poudel
Keyword(s):  
Spatial Data ◽  
Environmental Data ◽  
Temporal Data ◽  
Observation Systems ◽  
Research Findings ◽  
Temporal And Spatial ◽  
Temporal And Spatial Characteristics ◽  
Mountain Geography ◽  
Different Sources

Mountains have distinct geography and are dynamic in nature compared to the plains. 'Verticality' and 'variation' are two fundamental specificities of the mountain geography. They possess distinct temporal and spatial characteristics in a unique socio-cultural setting. There is an ever increasing need for spatial and temporal data for planning and management activities; and Geo Information (GI) Science (including Geographic Information and Earth Observation Systems). This is being recognized more and more as a common platform for integrating spatial data with social, economic and environmental data and information from different sources. This paper investigates the applicability and challenges of GISscience in the context of mountain geography with ample evidences and observations from the mountain specific publications, empirical research findings and reports. The contextual explanation of mountain geography, mountain specific problems, scientific concerns about the mountain geography, advances in GIScience, the role of GIScience for sustainable development, challenges on application of GIScience in the contexts of mountains are the points of discussion. Finally, conclusion has been made with some specific action oriented recommendations.

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