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NeuroImage Dec 2022In primates, faces and bodies activate distinct regions in the inferior temporal (IT) cortex and are typically studied separately. Yet, primates interact with whole...
In primates, faces and bodies activate distinct regions in the inferior temporal (IT) cortex and are typically studied separately. Yet, primates interact with whole agents and not with random concatenations of faces and bodies. Despite its social importance, it is still poorly understood how faces and bodies interact in IT. Here, we addressed this gap by measuring fMRI activations to whole agents and to unnatural face-body configurations in which the head was mislocated with respect to the body, and examined how these relate to the sum of the activations to their corresponding faces and bodies. First, we mapped patches in the IT of awake macaques that were activated more by images of whole monkeys compared to objects and found that these mostly overlapped with body and face patches. In a second fMRI experiment, we obtained no evidence for superadditive responses in these "monkey patches", with the activation to the monkeys being less or equal to the summed face-body activations. However, monkey patches in the anterior IT were activated more by natural compared to unnatural configurations. The stronger activations to natural configurations could not be explained by the summed face-body activations. These univariate results were supported by regression analyses in which we modeled the activations to both configurations as a weighted linear combination of the activations to the faces and bodies, showing higher regression coefficients for the natural compared to the unnatural configurations. Deeper layers of trained convolutional neural networks also contained units that responded more to natural compared to unnatural monkey configurations. Unlike the monkey fMRI patches, these units showed substantial superadditive responses to the natural configurations. Our monkey fMRI data suggest configuration-sensitive face-body interactions in anterior IT, adding to the evidence for an integrated face-body processing in the primate ventral visual stream, and open the way for mechanistic studies using single unit recordings in these patches.
Topics: Animals; Brain Mapping; Pattern Recognition, Visual; Photic Stimulation; Temporal Lobe; Magnetic Resonance Imaging; Macaca
PubMed: 36216293
DOI: 10.1016/j.neuroimage.2022.119676 -
Current Opinion in Cell Biology Jun 2015The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that... (Review)
Review
The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that low complexity/disordered protein motifs and repetitive binding domains drive assembly of droplets of nuclear RNA/protein by promoting nucleoplasmic phase separation. Nucleation and maturation of these structures is regulated by, and may in turn affect, factors including post-translational modifications, protein concentration, transcriptional activity, and chromatin state. Here we present a concise review of these exciting recent advances, and discuss current and future challenges in understanding the assembly, regulation, and function of nuclear RNA/protein bodies.
Topics: Animals; Biophysical Phenomena; Cell Nucleus; Chromatin; Humans; Intranuclear Inclusion Bodies; Nuclear Proteins; Protein Processing, Post-Translational
PubMed: 25942753
DOI: 10.1016/j.ceb.2015.04.003 -
Applied Microbiology and Biotechnology Feb 2019The bacterium Escherichia coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant... (Review)
Review
The bacterium Escherichia coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant protein can be located intracellularly, which often leads to protein aggregates inside of the cytoplasm, forming so the called inclusion bodies (IBs). When compared to other protein expression strategies, inclusion body formation allows high product titers and also the possibility of expressing proteins being toxic for the host. In the past years, the comprehension of inclusion bodies being only inactive protein aggregates changed, and the new term of non-classical inclusion bodies emerged. These inclusion bodies are believed to contain a reasonable amount of active protein within their structure. However, subsequent downstream processing, such as homogenisation of cells, centrifugation or solubilisation of IBs, is prone to variable process performance and is often known to result in low extraction yields. It is hypothesised that variations in IB quality attributes are responsible for those effects and that such attributes can be controlled by upstream process conditions. In this review, we address the impact of process design (process parameters) in the upstream on defined inclusion body quality attributes. The following topics are therefore addressed: (i) an overview of the range of inclusion body applications (including emerging technologies); (ii) analytical methods to determine quality attributes; and (iii) screws in process engineering to achieve the desired quality attributes for different inclusion body-based applications. Process parameters in the upstream can be used to trigger different quality attributes including protein activity, but are not exploited to a satisfying content yet. Design by quality approaches in the upstream are already considered for a multitude of existing processes. Further intensifying this approach may pave the industrial application for new IB-based products and improves IB processing, as discussed within this review.
Topics: Bacterial Physiological Phenomena; Cytoplasm; Escherichia coli; Inclusion Bodies; Protein Engineering; Recombinant Proteins
PubMed: 30569219
DOI: 10.1007/s00253-018-9569-1 -
Frontiers in Cellular Neuroscience 2019Circadian rhythms are biological variables that oscillate with periods close to 24 h that are generated internally by biological clocks. Depending on the tissue/cell...
Circadian rhythms are biological variables that oscillate with periods close to 24 h that are generated internally by biological clocks. Depending on the tissue/cell type, about 5-20% of genes are expressed rhythmically. Unexpectedly, the correlation between the oscillations of messengers and the proteins they encode is low. We hypothesize that these discrepancies could be because in certain phases of the circadian cycle some messengers could be translationally silenced and stored. Processing bodies (PBs) are membraneless organelles formed by ribonucleoprotein aggregates located in the cytoplasm. They contain silenced messengers and factors involved in mRNA processing. A previous work showed that the number of cells containing these mRNA granules varies when comparing two time-points in U2OS cell cultures and that these differences disappear when an essential clock gene is silenced. Here we evaluate whether PBs oscillate in Neuro2A cells. We analyzed in cell cultures synchronized with dexamethasone the variations in the number, the signal intensity of the markers used (GE-1/HEDLS and DDX6), and the area of PBs between 8 and 68 h post-synchronization. All three parameters oscillated with periods compatible with a circadian regulated process. The most robust rhythm was the number of PBs. These rhythms could be generated by oscillations in proteins that have been involved in the nucleation of these foci such as LSM1, TTP, and BRF1. The described phenomenon would allow to explain the differences observed in the temporal profiles of some messengers and their proteins and to understand how circadian clocks can control post-transcriptionally cellular functions.
PubMed: 31736713
DOI: 10.3389/fncel.2019.00487 -
Folia Morphologica 2020Nuclear bodies (NB) are membrane-less subnuclear organelles that perform important functions in the cell, such as transcription, RNA splicing, processing and transport...
BACKGROUND
Nuclear bodies (NB) are membrane-less subnuclear organelles that perform important functions in the cell, such as transcription, RNA splicing, processing and transport of ribosomal pre-RNA, epigenetic regulation, and others. The aim of the work was to analyse the classification of NB in the Terminologia Histologica (TH) and biological and bibliographical databases.
MATERIALS AND METHODS
The semantic structure of the Nucleoplasm section in the TH was analysed and unsystematic bibliographical search was made in the PubMed, SciELO, EMBASE databases and European Bioinformatics Institute (EMBL-EBI) biology database to identify which structures are classified as NB.
RESULTS
It was found that the terms Corpusculum convolutum, Macula interchromatinea and Corpusculum PML are not correctly classified in the TH, since they are subordinated under the term Chromatinum and not under Corpusculum nucleare. The bibliography consulted showed that 100%, 92.6% and 81.5% of articles mentioned Corpusculum convolutum, Macula interchromatinea and Corpusculum PML, respectively as nuclear bodies.
CONCLUSIONS
It is suggested to relocate the terms Corpusculum convolutum, Macula interchromatinea and Corpusculum PML with the name of Corpusculum nucleare and the incorporation of two new entities to the Histological Terminology according to the information collected: paraspeckles and histone locus body.
Topics: Cell Nucleus; Humans; Terminology as Topic
PubMed: 31448403
DOI: 10.5603/FM.a2019.0091 -
Virology Aug 2022In the adenovirus-infected cells, virus mRNAs are selectively exported to the cytoplasm by virus early gene products to facilitate virus replication. We previously...
In the adenovirus-infected cells, virus mRNAs are selectively exported to the cytoplasm by virus early gene products to facilitate virus replication. We previously showed AU-rich elements (AREs) containing mRNAs are exported to the cytoplasm and stabilized in infected cells. Here, we analyzed ribonucleoprotein (RNP) granules in the cytoplasm that are involved in mRNA degradation to elucidate the mechanism of ARE-mRNA stabilization in adenovirus infected cells. Our findings showed that processing bodies (PBs) aggregate, then almost all PBs are translocated to aggresomes formed by adenoviral gene products during the late phase of infection. Furthermore, E4orf3 was required for the PBs translocation, and the same domains of E4orf3-mutants required to change the form of promyelocytic leukemia bodies were also needed for PBs translocation. Luciferase activity showed that these domains were critical for miRNA- and ARE-mediated mRNA decay. These findings suggest that adenovirus changes the behavior of PBs to prevent ARE-mRNA downregulation.
Topics: Adenoviridae; Adenoviridae Infections; Cytoplasm; Humans; Processing Bodies; RNA, Messenger; Viral Proteins; Virus Replication
PubMed: 35779334
DOI: 10.1016/j.virol.2022.06.009 -
Molecular Horticulture Aug 2023The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their...
The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their roles in thermotolerance are scarce. Here, we identified a heat-inducible CCCH gene LlC3H18 from lily. LlC3H18 was localized in the cytoplasm and nucleus under normal conditions, while it translocated in the cytoplasmic foci and co-located with the markers of two messenger ribonucleoprotein (mRNP) granules, processing bodies (PBs) and stress granules (SGs) under heat stress conditions, and it also exhibited RNA-binding ability. In addition, LlC3H18 exhibited transactivation activity in both yeast and plant cells. In lily and Arabidopsis, overexpression of LlC3H18 damaged their thermotolerances, and silencing of LlC3H18 in lily also impaired its thermotolerance. Similarly, Arabidopsis atc3h18 mutant also showed decreased thermotolerance. These results indicated that the appropriate expression of C3H18 was crucial for establishing thermotolerance. Further analysis found that LlC3H18 directly bound to the promoter of LlWRKY33 and activated its expression. Besides, it was found that LlMYB305 acted as an upstream factor of LlC3H18 and activated its expression. In conclusion, we demonstrated that there may be a LlMYB305-LlC3H18-LlWRKY33 regulatory module in lily that is involved in the establishment of thermotolerance and finely regulates heat stress response.
PubMed: 37789438
DOI: 10.1186/s43897-023-00064-1 -
Journal of Molecular Biology Mar 2023Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E...
Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). In this study, we show that Drosophila eIF4E-1 and eIF4E-3 occur in PBs along the DEAD-box RNA helicase Me31B. We show that Me31B interacts with eIF4E-1 and eIF4E-3 by means of yeast two-hybrid system, FRET in D. melanogaster S2 cells and coimmunoprecipitation in testis. Truncation and point mutations of Me31B proteins show two eIF4E-binding sites located in different protein domains. Residues Y401-L407 (at the carboxy-terminus) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminus) are critical for interaction with eIF4E-3. The residue W117 in eIF4E-1 and the homolog position F103 in eIF4E-3 are necessary for Me31B-eIF4E interaction suggesting that the change of tryptophan to phenylalanine provides specificity. Me31B represents a novel type of eIF4E-interacting protein with dual and specific interaction domains that might be recognized by different eIF4E isoforms in different tissues, adding complexity to the control of gene expression in eukaryotes.
Topics: Animals; Male; Drosophila melanogaster; Drosophila Proteins; Eukaryotic Initiation Factor-4E; Protein Binding; Protein Biosynthesis; Protein Isoforms; Protein Interaction Domains and Motifs
PubMed: 36638908
DOI: 10.1016/j.jmb.2023.167949 -
Journal of Virology Sep 2021Several viruses have been proven to inhibit the formation of RNA processing bodies (P-bodies); however, knowledge regarding whether enterovirus blocks P-body formation...
Several viruses have been proven to inhibit the formation of RNA processing bodies (P-bodies); however, knowledge regarding whether enterovirus blocks P-body formation remains unclear, and the detailed molecular mechanisms and functions of picornavirus regulation of P-bodies are limited. Here, we show the crucial role of 2A protease in inhibiting P-bodies to promote viral replication during enterovirus 71 infection. Moreover, we found that the activity of 2A protease is essential to inhibit P-body formation, which was proven by the result that infection with EV71-2A, a 2A protease activity-inactivated recombinant virus, failed to block the formation of P-bodies. Furthermore, we show that DDX6, a scaffolding protein of P-bodies, interacted with viral RNA to facilitate viral replication rather than viral translation, by using a luciferase mRNA reporter system and nascent RNA capture assay. Altogether, our data first demonstrate that the 2A protease of enterovirus inhibits P-body formation to facilitate viral RNA synthesis by recruiting the P-body components to viral RNA. Processing bodies (P-bodies) are constitutively present in eukaryotic cells and play an important role in the mRNA cycle, including regulation of gene expression and mRNA degradation. The P-body is the structure that viruses manipulate to facilitate their survival. Here, we show that the 2A protease alone was efficient to block P-body formation during enterovirus 71 infection, and its activity is essential. When the assembly of P-bodies was blocked by 2A protease, DDX6 and 4E-T, which were required for P-body formation, bound to viral RNA to facilitate viral RNA synthesis. We propose a model revealing that EV71 manipulates P-body formation to generate an environment that is conducive to viral replication by facilitating viral RNA synthesis: 2A protease blocked P-body assembly to make it possible for virus to take advantage of P-body components.
Topics: Cell Line, Tumor; Cytoplasmic Granules; DEAD-box RNA Helicases; Enterovirus A, Human; HeLa Cells; Humans; Nucleocytoplasmic Transport Proteins; Peptide Hydrolases; Proto-Oncogene Proteins; RNA, Viral; Ribonucleoproteins; Virus Replication
PubMed: 34287048
DOI: 10.1128/JVI.00922-21 -
Frontiers in Bioscience (Landmark... Jun 2015Extensive research has been carried out in the past two decades to provide insights into the molecular mechanisms by which the Nucleophosmin-Anaplastic Lymphoma Kinase... (Review)
Review
Extensive research has been carried out in the past two decades to provide insights into the molecular mechanisms by which the Nucleophosmin-Anaplastic Lymphoma Kinase (NPM-ALK) exerts its oncogenic effects. These studies led to the concept that NPM-ALK acts at the transcriptional level through the activation of several transcription factors downstream of many different signaling pathways including JAK3/STAT3, PI3K/AKT and RAS/ERK. Nevertheless, the discovery of several RNA-binding proteins (RBPs) within ALK interactome suggested an additional and complementary role of this oncogenic kinase at the post-transcriptional level. This review gives emerging views in ALK-mediated post-transcriptional regulation with a focus on RBPs that are associated with ALK. We will summarize the capacity of NPM-ALK in modulating the biological properties of RBPs and then discuss the role of cytoplasmic aggregates, called AGs for "ALK granules", which are observed in anaplastic large cell lymphoma (ALCL) expressing the ALK kinase. AGs contain polyadenylated mRNAs and numerous RBPs but are distinct from processing bodies (PBs) and stress granules (SGs), two well-known discrete cytoplasmic sites involved in mRNA fate.
Topics: Anaplastic Lymphoma Kinase; Gene Expression Regulation; Models, Genetic; RNA Processing, Post-Transcriptional; RNA-Binding Proteins; Receptor Protein-Tyrosine Kinases; Ribonucleoproteins
PubMed: 25961555
DOI: 10.2741/4369