scholarly journals Synaptic AP2 CCV life cycle regulation by the Eps15, ITSN1, Sgip1/AP2, synaptojanin1 interactome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
R. Mishra ◽  
G. F. Sengül ◽  
E. Candiello ◽  
P. Schu
Keyword(s):  
Life Cycle ◽  
Protein Interactions ◽  
Protein Sorting ◽  
Life Time ◽  
Vesicle Recycling ◽  
Severe Intellectual Disability ◽  
Protein Interactome ◽  
Cargo Proteins ◽  
Cycle Regulation ◽  
Secondary Phenotype

AbstractThe AP1/σ1B knockout causes impaired synaptic vesicle recycling and enhanced protein sorting into endosomes, leading to severe intellectual disability. These disturbances in synaptic protein sorting induce as a secondary phenotype the upregulation of AP2 CCV mediated endocytosis. Synapses contain canonical AP2 CCV and AP2 CCV with a more stable coat and thus extended life time. In AP1/σ1B knockout synapses, pool sizes of both CCV classes are doubled. Additionally, stable CCV of the knockout are more stabilised than stable wt CCV. One mechanism responsible for enhanced CCV stabilisation is the reduction of synaptojanin1 CCV levels, the PI-4,5-P2 phosphatase essential for AP2 membrane dissociation. To identify mechanisms regulating synaptojanin1 recruitment, we compared synaptojanin1 CCV protein interactome levels and CCV protein interactions between both CCV classes from wt and knockout mice. We show that ITSN1 determines synaptojanin1 CCV levels. Sgip1/AP2 excess hinders synaptojanin1 binding to ITSN1, further lowering its levels. ITSN1 levels are determined by Eps15, not Eps15L1. In addition, the data reveal that reduced amounts of pacsin1 can be counter balanced by its enhanced activation. These data exemplify the complexity of CCV life cycle regulation and indicate how cargo proteins determine the life cycle of their CCV.

scholarly journals The Protein Interactome of Glycolysis in Escherichia coli

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 16
Author(s):  
Shomeek Chowdhury ◽  
Stephen Hepper ◽  
Mudassir K. Lodi ◽  
Milton H. Saier ◽  
Peter Uetz
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Allosteric Regulation ◽  
Glycolytic Enzymes ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Interacting Protein ◽  
E Coli ◽  
Protein Interactome ◽  
The Impact

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

scholarly journals ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Wenfu Ma ◽  
Elena Goldberg ◽  
Jonathan Goldberg
Keyword(s):  
Endoplasmic Reticulum ◽  
Retrieval System ◽  
Protein Sorting ◽  
Ldl Receptor ◽  
Retention Mechanism ◽  
Protein Uptake ◽  
Er Retention ◽  
Cargo Proteins ◽  
P24 Protein ◽  
Copii Vesicles

Native cargo proteins exit the endoplasmic reticulum (ER) in COPII-coated vesicles, whereas resident and misfolded proteins are substantially excluded from vesicles by a retention mechanism that remains unresolved. We probed the ER retention process using the proteostasis regulator 4-phenylbutyrate (4-PBA), which we show targets COPII protein to reduce the stringency of retention. 4-PBA competes with p24 proteins to bind COPII. When p24 protein uptake is blocked, COPII vesicles package resident proteins and an ER-trapped mutant LDL receptor. We further show that 4-PBA triggers the secretion of a KDEL-tagged luminal resident, implying that a compromised retention mechanism causes saturation of the KDEL retrieval system. The results indicate that stringent ER retention requires the COPII coat machinery to actively sort biosynthetic cargo from diffusible misfolded and resident ER proteins.

scholarly journals Urbanization extends flight phenology and leads to local adaptation of seasonal plasticity in Lepidoptera

2021 ◽  
Vol 118 (40) ◽  
pp. e2106006118
Author(s):  
Thomas Merckx ◽  
Matthew E. Nielsen ◽  
Janne Heliölä ◽  
Mikko Kuussaari ◽  
Lars B. Pettersson ◽  
...  
Keyword(s):  
Life Cycle ◽  
Urban Areas ◽  
Common Garden ◽  
Reaction Norm ◽  
Island Effect ◽  
Seasonal Plasticity ◽  
Common Garden Experiments ◽  
Flight Phenology ◽  
Cycle Regulation ◽  
Genetic Shift

Urbanization is gaining force globally, which challenges biodiversity, and it has recently also emerged as an agent of evolutionary change. Seasonal phenology and life cycle regulation are essential processes that urbanization is likely to alter through both the urban heat island effect (UHI) and artificial light at night (ALAN). However, how UHI and ALAN affect the evolution of seasonal adaptations has received little attention. Here, we test for the urban evolution of seasonal life-history plasticity, specifically changes in the photoperiodic induction of diapause in two lepidopterans, Pieris napi (Pieridae) and Chiasmia clathrata (Geometridae). We used long-term data from standardized monitoring and citizen science observation schemes to compare yearly phenological flight curves in six cities in Finland and Sweden to those of adjacent rural populations. This analysis showed for both species that flight seasons are longer and end later in most cities, suggesting a difference in the timing of diapause induction. Then, we used common garden experiments to test whether the evolution of the photoperiodic reaction norm for diapause could explain these phenological changes for a subset of these cities. These experiments demonstrated a genetic shift for both species in urban areas toward a lower daylength threshold for direct development, consistent with predictions based on the UHI but not ALAN. The correspondence of this genetic change to the results of our larger-scale observational analysis of in situ flight phenology indicates that it may be widespread. These findings suggest that seasonal life cycle regulation evolves in urban ectotherms and may contribute to ecoevolutionary dynamics in cities.

scholarly journals A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings

2020 ◽  
Vol 17 (5) ◽  
pp. 740-747 ◽  
Author(s):  
Marco Tutone ◽  
Giulia Culletta ◽  
Luca Livecchi ◽  
Anna M. Almerico
Keyword(s):  
Protein Interactions ◽  
Roc Curves ◽  
Md Simulations ◽  
Eukaryotic Cell ◽  
Energy Calculation ◽  
Pharmacophore Modelling ◽  
Cyclin Dependent Kinases ◽  
Long Time ◽  
Cycle Regulation ◽  
Pharmacophore Models

Cyclin Dependent Kinases-2 (CDK2) are members of serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicate that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free energy calculation. Comparison with experimental data (K<sub>i</sub>, K<sub>d</sub> and pIC<sub>50</sub>) revealed that short simulations are exhaustive to examine the crucial ligand-protein interactions within the complexes. Information collected on MD simulations of protein-ligand complexes has been used to perform a molecular modelling approach that incorporates flexibility into structure-based pharmacophore modelling (Common Hits Approach, CHA). The high number of pharmacophore models resulting from the MD simulation was thus reduced to a few representative groups of pharmacophore models. The performance of the models has been assessed by using the ROC curves analysis. This definitive set of validated pharmacophore models could be used to screen in-house and/or commercial datasets for detection of new CDK-2 inhibitors. We provide the models to all the researchers involved in this field.

Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway v1

2022 ◽  
Author(s):  
Javier Manzano-Lopez†* ◽  
Sofia Rodriguez-Gallardo† ◽  
Susana Sabido-Bozo† ◽  
Alejandro Cortes-Gomez ◽  
Ana Maria Perez-Linero ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Secretory Pathway ◽  
Protein Complexes ◽  
Secretory Protein ◽  
Extracellular Proteins ◽  
Transient Nature ◽  
Transport Vesicles ◽  
System P ◽  
Cargo Receptor ◽  
Cargo Proteins

Intracellular trafficking through the secretory organelles depends on transient interactions between cargo proteins and transport machinery. Cytosolic coat protein complexes capture specific luminal cargo proteins for incorporation into transport vesicles by interacting with them indirectly through a transmembrane adaptor or cargo receptor. Due to their transient nature, it is difficult to study these specific ternary protein interactions just using conventional native co-immunoprecipitation. To overcome this technical challenge, we have applied a crosslinking assay to stabilize the transient and/or weak protein interactions. Here, we describe a protocol of protein cross-linking and co-immunoprecipitation, which was employed to prove the indirect interaction in the endoplasmic reticulum of a luminal secretory protein with a selective subunit of the cytosolic COPII coat through a specific transmembrane cargo receptor. This method can be extended to address other transient ternary interactions between cytosolic proteins and luminal or extracellular proteins through a transmembrane receptor within the endomembrane system.

Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway v1

2021 ◽  
Author(s):  
Javier Manzano-Lopez † ◽  
Sofia Rodriguez-Gallardo † ◽  
Susana Sabido-Bozo ◽  
Ana Maria Perez-Linero ◽  
Rafael Lucena ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Secretory Pathway ◽  
Protein Complexes ◽  
Secretory Protein ◽  
Extracellular Proteins ◽  
Transient Nature ◽  
Transport Vesicles ◽  
System P ◽  
Cargo Receptor ◽  
Cargo Proteins

Intracellular trafficking through the secretory organelles depends on transient interactions between cargo proteins and transport machinery. Cytosolic coat protein complexes capture specific luminal cargo proteins for incorporation into transport vesicles by interacting with them indirectly through a transmembrane adaptor or cargo receptor. Due to their transient nature, it is difficult to study these specific ternary protein interactions just using conventional native co-immunoprecipitation. To overcome this technical challenge, we have applied a crosslinking assay to immobilize the transient and/or weak protein interactions. Here, we describe a protocol of protein cross-linking and co-immunoprecipitation, which was employed to prove the indirect interaction in the endoplasmic reticulum of a luminal secretory protein with a selective subunit of the cytosolic COPII coat through a specific transmembrane cargo receptor. This method can be extended to address other transient ternary interactions between cytosolic proteins and luminal or extracellular proteins through a transmembrane receptor within the endomembrane system.

Mining Protein Interactome Networks to Measure Interaction Reliability and Select Hub Proteins

2013 ◽  
pp. 222-238
Author(s):  
Young-Rae Cho ◽  
Aidong Zhang
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Functional Characterization ◽  
Flow Simulation ◽  
Protein Protein Interactions ◽  
Systematic Analysis ◽  
Graph Theoretic ◽  
Interactome Network ◽  
Protein Interactome ◽  
Hub Proteins

High-throughput techniques involve large-scale detection of protein-protein interactions. This interaction data set from the genome-scale perspective is structured into an interactome network. Since the interaction evidence represents functional linkage, various graph-theoretic computational approaches have been applied to the interactome networks for functional characterization. However, this data is generally unreliable, and the typical genome-wide interactome networks have a complex connectivity. In this paper, the authors explore systematic analysis of protein interactome networks, and propose a $k$-round signal flow simulation algorithm to measure interaction reliability from connection patterns of the interactome networks. This algorithm quantitatively characterizes functional links between proteins by simulating the propagation of information signals through complex connections. In this regard, the algorithm efficiently estimates the strength of alternative paths for each interaction. The authors also present an algorithm for mining the complex interactome network structure. The algorithm restructures the network by hierarchical ordering of nodes, and this structure re-formatting process reveals hub proteins in the interactome networks. This paper demonstrates that two rounds of simulation accurately scores interaction reliability in terms of ontological correlation and functional consistency. Finally, the authors validate that the selected structural hubs represent functional core proteins.

scholarly journals A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

2020 ◽  
Vol 117 (21) ◽  
pp. 11836-11842 ◽  
Author(s):  
Shayne D. Wierbowski ◽  
Tommy V. Vo ◽  
Pascal Falter-Braun ◽  
Timothy O. Jobe ◽  
Lars H. Kruse ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Massively Parallel ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Numerous Model ◽  
High Quality Protein ◽  
Protein Interactome ◽  
Wide Range ◽  
Dna Elements ◽  
General Tool

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we developPCR-mediatedLinkage of barcodedAdaptersTo nucleic acidElements forsequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome forOryza sativacovering 2,300 genes and constructing a high-quality protein–protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein–protein interactions in a wide range of organisms.

scholarly journals Temporal Viral Genome-Protein Interactions Define Distinct Stages of Productive Herpesviral Infection

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Jill A. Dembowski ◽  
Neal A. DeLuca
Keyword(s):  
Life Cycle ◽  
Protein Interactions ◽  
Viral Genome ◽  
Isotope Labeling ◽  
De Novo ◽  
Affinity Purification ◽  
Human Pathogens ◽  
Host Proteins ◽  
Viral Dna ◽  
Hsv 1

ABSTRACTHerpesviruses utilize multiple mechanisms to redirect host proteins for use in viral processes and to avoid recognition and repression by the host. To investigate dynamic interactions between herpes simplex virus type 1 (HSV-1) DNA and viral and host proteins throughout infection, we developed an approach to identify proteins that associate with the infecting viral genome from nuclear entry through packaging. To accomplish this, virus stocks were prepared in the presence of ethynyl-modified nucleotides to enable covalent tagging of viral genomes after infection for analysis of viral genome-protein interactions by imaging or affinity purification. Affinity purification was combined with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry to enable the distinction between proteins that were brought into the cell by the virus or expressed within the infected cell before or during infection. We found that input viral DNA progressed within 6 h through four temporal stages where the genomes sequentially (i) interacted with intrinsic antiviral and DNA damage response proteins, (ii) underwent a robust transcriptional switch mediated largely by ICP4, (iii) engaged in replication, repair, and continued transcription, and then (iv) transitioned to a more transcriptionally inert state engagingde novo-synthesized viral structural components while maintaining interactions with replication proteins. Using a combination of genetic, imaging, and proteomic approaches, we provide a new and temporally compressed view of the HSV-1 life cycle based on input genome-proteome dynamics.IMPORTANCEHerpesviruses are highly prevalent and ubiquitous human pathogens. Studies of herpesviruses and other viruses have previously been limited by the ability to directly study events that occur on the viral DNA throughout infection. We present a new powerful approach, which allows for the temporal investigation of viral genome-protein interactions at all phases of infection. This work has integrated many results from previous studies with the discovery of novel factors potentially involved in viral infection that may represent new antiviral targets. In addition, the study provides a new view of the HSV-1 life cycle based on genome-proteome dynamics.

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