Identification of protein-protein interactions of the occlusion-derived virus-associated proteins of Helicoverpa armigera nucleopolyhedrovirus

Recombinant A' protein could be reconstituted into U2 small nuclear ribonucleoprotein particles (snRNPs) upon addition to HeLa cell extracts as determined by coimmunoprecipitation and particle density; however, direct binding to U2 RNA could not be demonstrated except in the presence of the U2 snRNP B" protein. Mutational analysis indicated that a central core region of A' was required for particle reconstitution. This region consists of five tandem repeats of approximately 24 amino acids each that exhibit a periodicity of leucine and asparagine residues that is distinct from the leucine zipper. Similar leucine-rich (Leu-Leu motif) repeats are characteristic of a diverse array of soluble and membrane-associated proteins from yeasts to humans but have not been reported previously to reside in nuclear proteins. Several of these proteins, including Toll, chaoptin, RNase/angiogenin inhibitors, lutropin-choriogonadotropin receptor, carboxypeptidase N, adenylyl cyclase, CD14, and human immunodeficiency virus type 1 Rev, may be involved in protein-protein interactions. Our findings suggest that in cell extracts the Leu-Leu motif of A' is required for reconstitution with U2 snRNPs and perhaps with other components involved in splicing through protein-protein interactions.

Download Full-text

Group I Metabotropic Glutamate Receptors and Interacting Partners: An Update

International Journal of Molecular Sciences ◽

10.3390/ijms23020840 ◽

2022 ◽

Vol 23 (2) ◽

pp. 840

Author(s):

Li-Min Mao ◽

Alaya Bodepudi ◽

Xiang-Ping Chu ◽

John Q. Wang

Keyword(s):

Synaptic Plasticity ◽

Protein Interactions ◽

Metabotropic Glutamate Receptors ◽

Adaptor Proteins ◽

Mammalian Brain ◽

Amino Acid Residues ◽

Protein Protein Interactions ◽

Metabotropic Glutamate ◽

Group I ◽

Associated Proteins

Group I metabotropic glutamate (mGlu) receptors (mGlu1/5 subtypes) are G protein-coupled receptors and are broadly expressed in the mammalian brain. These receptors play key roles in the modulation of normal glutamatergic transmission and synaptic plasticity, and abnormal mGlu1/5 signaling is linked to the pathogenesis and symptomatology of various mental and neurological disorders. Group I mGlu receptors are noticeably regulated via a mechanism involving dynamic protein–protein interactions. Several synaptic protein kinases were recently found to directly bind to the intracellular domains of mGlu1/5 receptors and phosphorylate the receptors at distinct amino acid residues. A variety of scaffolding and adaptor proteins also interact with mGlu1/5. Constitutive or activity-dependent interactions between mGlu1/5 and their interacting partners modulate trafficking, anchoring, and expression of the receptors. The mGlu1/5-associated proteins also finetune the efficacy of mGlu1/5 postreceptor signaling and mGlu1/5-mediated synaptic plasticity. This review analyzes the data from recent studies and provides an update on the biochemical and physiological properties of a set of proteins or molecules that interact with and thus regulate mGlu1/5 receptors.

Download Full-text

H2V, a Database for Human Proteins and Genes in Response to SARS-CoV-2, SARS-CoV, and MERS-CoV Infection

10.21203/rs.3.rs-61338/v1 ◽

2020 ◽

Author(s):

Nan Zhou ◽

Jinku Bao ◽

Yuping Ning

Keyword(s):

Differentially Expressed Genes ◽

Protein Interactions ◽

Viral Infections ◽

Antiviral Agents ◽

Differentially Expressed ◽

Easy Access ◽

Differentially Expressed Proteins ◽

Protein Protein Interactions ◽

Associated Proteins ◽

Human Proteins

Abstract The ongoing COVID-19 pandemic in the world is caused by SARS-CoV-2, a new coronavirus firstly discovered in the end of 2019. It has led to more than 10 million confirmed cases and more than 500,000 confirmed deaths across 216 countries by 1 July 2020, according to WHO statistics. SARS-CoV-2, SARS-CoV, and MERS-CoV are alike, killing people, impairing economy, and inflicting long-term impacts on the society. However, no specific drug or vaccine has been approved as a cure for these viruses. The efforts to develop antiviral measures are hampered by insufficient understanding of molecular responses of human to viral infections. In this study, we collected experimentally validated human proteins that interact with SARS-CoV-2 proteins, human proteins whose expression, translation and phosphorylation levels experience significantly changes after SARS-CoV-2 or SARS-CoV infection, human proteins that correlate with COVID-19 severity, and human genes whose expression levels significantly changed upon SARS-CoV-2 or MERS-CoV infection. A database, H2V, was then developed for easy access to these data. Currently H2V includes: 332 human-SARS-CoV-2 protein-protein interactions; 65 differentially expressed proteins, 232 differentially translated proteins, 1298 differentially phosphorylated proteins, 204 severity associated proteins, and 4012 differentially expressed genes responding to SARS-CoV-2 infection; 66 differentially expressed proteins responding to SARS-CoV infection; and 6981 differentially expressed genes responding to MERS-CoV infection. H2V can help to understand the cellular responses associated with SARS-CoV-2, SARS-CoV and MERS-CoV infection. It is expected to speed up the development of antiviral agents and shed light on the preparation for potential coronavirus emergency in the future.Database url: http://www.zhounan.org/h2v

Download Full-text

A silencer is required for maintenance of transcriptional repression throughout Drosophila development

Development ◽

10.1242/dev.124.21.4343 ◽

1997 ◽

Vol 124 (21) ◽

pp. 4343-4350 ◽

Cited By ~ 4

Author(s):

A. Busturia ◽

C.D. Wightman ◽

S. Sakonju

Keyword(s):

Protein Interactions ◽

Transcriptional Repression ◽

Transcriptional Silencing ◽

Active Role ◽

Polycomb Group ◽

Homeotic Genes ◽

Protein Protein Interactions ◽

Drosophila Development ◽

Larval Stages ◽

Associated Proteins

Transcriptional silencing by the Polycomb Group of genes maintains the position-specific repression of homeotic genes throughout Drosophila development. The Polycomb Group of genes characterized to date encode chromatin-associated proteins that have been suggested to form heterochromatin-like structures. By studying the expression of reporter genes, we have identified a 725 bp fragment, called MCP725, in the homeotic gene Abdominal-B, that accurately maintains position-specific silencing during proliferation of imaginal cells. Silencing by MCP725 requires the Polycomb and the Polycomblike genes, indicating that it contains a Polycomb response element To investigate the mechanisms of transcriptional silencing by MCP725, we have studied its temporal requirements by removing MCP725 from the transgene at various times during development. We have discovered that excision of MCP725 during larval stages leads to loss of silencing. Our findings indicate that the silencer is required for the maintenance of the repressed state throughout cell proliferation. They also suggest that propagation of the silenced state does not occur merely by templating of a heterochromatin structure by virtue of protein-protein interactions. Rather, they suggest that silencers play an active role in the maintenance of the position-specific repression throughout development.

Download Full-text

DCL and Associated Proteins of Arabidopsis thaliana - An Interaction Study

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.61.85 ◽

2017 ◽

Vol 61 ◽

pp. 85-94

Author(s):

Paushali Roy ◽

Abhijit Datta

Keyword(s):

Arabidopsis Thaliana ◽

Protein Interactions ◽

Stress Responses ◽

Interaction Study ◽

Protein Protein Interactions ◽

Protein Expression Level ◽

Double Stranded Rna ◽

Rna Molecules ◽

Associated Proteins

During RNA interference in plants, Dicer-like/DCL proteins process longer double-stranded RNA (dsRNA) precursors into small RNA molecules. In Arabidopsis thaliana there are four DCLs (DCL1, DCL2, DCL3, and DCL4) that interact with various associated proteins to carry out this processing. The lack of complete structural-functional information and characterization of DCLs and their associated proteins leads to this study where we have generated the structures by modelling, analysed the structures and studied the interactions of Arabidopsisthaliana DCLs with their associated proteins with the homology-derived models to screen the interacting residues. Structural analyses indicate existence of significant conserved domains that may play imperative roles during protein-protein interactions. The interaction study shows some key domain-domain (including multi-domains and inter-residue interactions) interfaces and specific residue biases (like arginine and leucine) that may help in augmenting the protein expression level during stress responses. Results point towards plausible stable associations to carry out RNA processing in a synchronised pattern by elucidating the structural properties and protein-protein interactions of DCLs that may hold significance for RNAi researchers.

Download Full-text

Leucine periodicity of U2 small nuclear ribonucleoprotein particle (snRNP) A' protein is implicated in snRNP assembly via protein-protein interactions.

Molecular and Cellular Biology ◽

10.1128/mcb.11.3.1578 ◽

1991 ◽

Vol 11 (3) ◽

pp. 1578-1589 ◽

Cited By ~ 18

Author(s):

L D Fresco ◽

D S Harper ◽

J D Keene

Keyword(s):

Protein Interactions ◽

Leucine Zipper ◽

Tandem Repeats ◽

Mutational Analysis ◽

Particle Density ◽

Protein Protein Interactions ◽

Small Nuclear Ribonucleoprotein ◽

Cell Extracts ◽

Associated Proteins ◽

Nuclear Ribonucleoprotein

Recombinant A' protein could be reconstituted into U2 small nuclear ribonucleoprotein particles (snRNPs) upon addition to HeLa cell extracts as determined by coimmunoprecipitation and particle density; however, direct binding to U2 RNA could not be demonstrated except in the presence of the U2 snRNP B" protein. Mutational analysis indicated that a central core region of A' was required for particle reconstitution. This region consists of five tandem repeats of approximately 24 amino acids each that exhibit a periodicity of leucine and asparagine residues that is distinct from the leucine zipper. Similar leucine-rich (Leu-Leu motif) repeats are characteristic of a diverse array of soluble and membrane-associated proteins from yeasts to humans but have not been reported previously to reside in nuclear proteins. Several of these proteins, including Toll, chaoptin, RNase/angiogenin inhibitors, lutropin-choriogonadotropin receptor, carboxypeptidase N, adenylyl cyclase, CD14, and human immunodeficiency virus type 1 Rev, may be involved in protein-protein interactions. Our findings suggest that in cell extracts the Leu-Leu motif of A' is required for reconstitution with U2 snRNPs and perhaps with other components involved in splicing through protein-protein interactions.

Download Full-text

Proteomics Analysis of Helicoverpa armigera Single Nucleocapsid Nucleopolyhedrovirus Identified Two New Occlusion-Derived Virus-Associated Proteins, HA44 and HA100

Journal of Virology ◽

10.1128/jvi.00632-07 ◽

2007 ◽

Vol 81 (17) ◽

pp. 9377-9385 ◽

Cited By ~ 68

Author(s):

Fei Deng ◽

Ranran Wang ◽

Minggang Fang ◽

Yue Jiang ◽

Xushi Xu ◽

...

Keyword(s):

Helicoverpa Armigera ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

Structural Proteins ◽

Proteomics Analysis ◽

Group I ◽

Associated Proteins ◽

Helicoverpa Armígera ◽

Group Ii ◽

First Time

ABSTRACT Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry were used to analyze the structural proteins of the occlusion-derived virus (ODV) of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus (HearNPV), a group II NPV. Twenty-three structural proteins of HearNPV ODV were identified, 21 of which have been reported previously as structural proteins or ODV-associated proteins in other baculoviruses. These include polyhedrin, P78/83, P49, ODV-E18, ODV-EC27, ODV-E56, P74, LEF-3, HA66 (AC66), DNA polymerase, GP41, VP39, P33, ODV-E25, helicase, P6.9, ODV/BV-C42, VP80, ODV-EC43, ODV-E66, and PIF-1. Two proteins encoded by HearNPV ORF44 (ha44) and ORF100 (ha100) were discovered as ODV-associated proteins for the first time. ha44 encodes a protein of 378 aa with a predicted mass of 42.8 kDa. ha100 encodes a protein of 510 aa with a predicted mass of 58.1 kDa and is a homologue of the gene for poly(ADP-ribose) glycohydrolase (parg). Western blot analysis and immunoelectron microscopy confirmed that HA44 is associated with the nucleocapsid and HA100 is associated with both the nucleocapsid and the envelope of HearNPV ODV. HA44 is conserved in group II NPVs and granuloviruses but does not exist in group I NPVs, while HA100 is conserved only in group II NPVs.

Download Full-text

Subcellular localization of skeletal muscle lipid droplets and PLIN family proteins OXPAT and ADRP at rest and following contraction in rat soleus muscle

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00163.2011 ◽

2012 ◽

Vol 302 (1) ◽

pp. R29-R36 ◽

Cited By ~ 24

Author(s):

Rebecca E. K. MacPherson ◽

Eric A. F. Herbst ◽

Erica J. Reynolds ◽

Rene Vandenboom ◽

Brian D. Roy ◽

...

Keyword(s):

Skeletal Muscle ◽

Lipid Droplet ◽

Protein Interactions ◽

Lipid Droplets ◽

Droplet Surface ◽

Protein Protein Interactions ◽

Muscle Lipid ◽

Droplet Distribution ◽

Associated Proteins ◽

Skeletal Muscle Lipid

Skeletal muscle lipid droplet-associated proteins (PLINs) are thought to regulate lipolysis through protein-protein interactions on the lipid droplet surface. In adipocytes, PLIN2 [adipocyte differentiation-related protein (ADRP)] is found only on lipid droplets, while PLIN5 (OXPAT, expressed only in oxidative tissues) is found both on and off the lipid droplet and may be recruited to lipid droplet membranes when needed. Our purpose was to determine whether PLIN5 is recruited to lipid droplets with contraction and to investigate the myocellular location and colocalization of lipid droplets, PLIN2, and PLIN5. Rat solei were isolated, and following a 30-min equilibration period, they were assigned to one of two groups: 1) 30 min of resting incubation and 2) 30 min of stimulation ( n = 10 each). Immunofluorescence microscopy was used to determine subcellular content, distribution, and colocalization of lipid droplets, PLIN2, and PLIN5. There was a main effect for lower lipid and PLIN2 content in stimulated compared with rested muscles ( P < 0.05). Lipid droplet distribution declined exponentially from the sarcolemma to the fiber center in the rested muscles ( P = 0.001, r2= 0.99) and linearly in stimulated muscles (slope = −0.0023 ± 0.0006, P < 0.001, r2= 0.93). PLIN2 distribution declined exponentially from the sarcolemma to the fiber center in both rested and stimulated muscles ( P < 0.0001, r2= 0.99 rest; P = 0.0004, r2= 0.98 stimulated), while PLIN5 distribution declined linearly (slope = −0.0085 ± 0.0009, P < 0.0001, r2= 0.94 rest; slope=−0.0078 ± 0.0010, P = 0.0003, r2= 0.91 stimulated). PLIN5-lipid droplets colocalized at rest with no difference poststimulation ( P = 0.47; rest r2= 0.55 ± 0.02, stimulated r2= 0.58 ± 0.03). PLIN2-lipid droplets colocalized at rest with no difference poststimulation ( P = 0.48; rest r2= 0.66 ± 0.02, stimulated r2= 0.65 ± 0.02). Contrary to our hypothesis, these results show that PLIN5 is not recruited to lipid droplets with contraction in isolated skeletal muscle.

Download Full-text

Systematic discovery of mutation-directed neo-protein-protein interactions in cancer

10.1101/2021.10.03.462422 ◽

2021 ◽

Author(s):

Xiulei Mo ◽

Qiankun Niu ◽

Andrey A Ivanov ◽

Yiu Huen Tsang ◽

Cong Tang ◽

...

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Braf V600e ◽

Driver Mutations ◽

Live Cells ◽

Protein Protein Interactions ◽

Mutant Variant ◽

Signaling Axis ◽

Tumorigenesis And Progression ◽

Associated Proteins

Comprehensive sequencing of patient tumors reveals numerous genomic mutations across tumor types that enable tumorigenesis and progression. A subset of oncogenic driver mutations results in neomorphic activity where the mutant protein mediates functions not engaged by the parental molecule. Here, we identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI) with a quantitative High Throughput differential Screening (qHT-dS) platform. Coupling of highly sensitive BRET biosensors with miniaturized co-expression in an ultra-HTS format allows large-scale monitoring of interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells. Screening of 13,392 interactions with 1,474,560 data points revealed a landscape of gain-of-interactions encompassing both oncogenic and tumor suppressor mutations. For example, the recurrent BRAF V600E lesion mediates KEAP1 neoPPI, rewiring a BRAFV600E-KEAP1 signaling axis and creating collateral vulnerability to NQO1 substrates, offering a combination therapeutic strategy. Thus, cancer genomic alterations can create neo-interactions, informing variant-directed therapeutic approaches for precision medicine.

Download Full-text

The microtubule-associated histone methyltransferase SET8, facilitated by transcription factor LSF, methylates α-tubulin

Journal of Biological Chemistry ◽

10.1074/jbc.ra119.010951 ◽

2020 ◽

Vol 295 (14) ◽

pp. 4748-4759 ◽

Cited By ~ 2

Author(s):

Hang Gyeong Chin ◽

Pierre-Olivier Esteve ◽

Cristian Ruse ◽

Jiyoung Lee ◽

Scott E. Schaus ◽

...

Keyword(s):

Transcription Factor ◽

Protein Interactions ◽

Posttranslational Modifications ◽

Organelle Transport ◽

Histone H4 ◽

Protein Protein Interactions ◽

Molecule Inhibitor ◽

Associated Proteins ◽

Lysine Methyltransferase

Microtubules are cytoskeletal structures critical for mitosis, cell motility, and protein and organelle transport and are a validated target for anticancer drugs. However, how tubulins are regulated and recruited to support these distinct cellular processes is incompletely understood. Posttranslational modifications of tubulins are proposed to regulate microtubule function and dynamics. Although many of these modifications have been investigated, only one prior study reports tubulin methylation and an enzyme responsible for this methylation. Here we used in vitro radiolabeling, MS, and immunoblotting approaches to monitor protein methylation and immunoprecipitation, immunofluorescence, and pulldown approaches to measure protein–protein interactions. We demonstrate that N-lysine methyltransferase 5A (KMT5A or SET8/PR-Set7), which methylates lysine 20 in histone H4, bound α-tubulin and methylated it at a specific lysine residue, Lys311. Furthermore, late SV40 factor (LSF)/CP2, a known transcription factor, bound both α-tubulin and SET8 and enhanced SET8-mediated α-tubulin methylation in vitro. In addition, we found that the ability of LSF to facilitate this methylation is countered by factor quinolinone inhibitor 1 (FQI1), a specific small-molecule inhibitor of LSF. These findings suggest the general model that microtubule-associated proteins, including transcription factors, recruit or stimulate protein-modifying enzymes to target tubulins. Moreover, our results point to dual functions for SET8 and LSF not only in chromatin regulation but also in cytoskeletal modification.

Download Full-text