Interaction Partners Research Articles

Phosphorylated FAT10 Is More Efficiently Conjugated to Substrates, Does Not Bind to NUB1L, and Does Not Alter Degradation by the Proteasome

Background: FAT10 is a member of the ubiquitin-like modifier family. Similar to ubiquitin, FAT10 has a distinct enzyme cascade consisting of E1-activating, E2-conjugating, and possibly several E3-ligating enzymes, which will covalently link FAT10 to substrate proteins in order to target them directly for proteasomal degradation. FAT10 was reported to be phosphorylated by IKKβ during infection with influenza A virus. Methods: To assess the difference between the FAT10-dependent degradation of phosphorylated FAT10 and the non-phosphorylated FAT10 wild type (FAT10 WT), a mutated FAT10 that mimicked phosphorylation (FAT10 D) was constructed by replacing several serine residues and one threonine residue with aspartic or glutamic acid. The FAT10 degradation or conjugation was compared between the phospho-mimetic FAT10 and the wild-type FAT10 with respect to the dependence of the E3 ligase TRIM25, the UBL-UBA protein NUB1L, and the proteasomal ubiquitin receptor RPN10. Results: The phospho-mimetic FAT10 was more efficiently conjugated to substrate proteins as compared to the wild-type FAT10, particularly if TRIM25 was co-expressed. Additionally, the phospho-mimetic FAT10 was not bound by NUB1L. However, this did not affect FAT10 D or FAT10 WT degradation. No differences were found in the binding affinity of phospho-mimetic FAT10 to RPN10. Conclusions: In brief, the phospho-mimetic FAT10 shows enhanced conjugation efficiency, but phosphorylation does not alter its degradation by the proteasome. This reveals that phosphorylation may fine-tune FAT10’s interactions with specific interaction partners without disrupting its core function of proteasomal degradation.

Protein-Variant-Phenotype Study of NBAS Using AlphaFold in the Aspect of SOPH Syndrome.

NBAS gene variants cause phenotypically distinct and nonoverlapping conditions, SOPH syndrome and ILFS2. NBAS is a so-called "moonlighting" protein responsible for retrograde membrane trafficking and nonsense-mediated decay. However, its three-dimensional model and the nature of its possible interactions with other proteins have remained elusive. Here, we used AlphaFold to predict protein-protein interaction (PPI) sites and mapped them to NBAS pathogenic variants. We repeated in silico milestone studies of the NBAS protein to explain the multisystem phenotype of its variants, with particular emphasis on the SOPH variant (p.R1914H). We revealed the putative binding sites for the main interaction partners of NBAS and assessed the implications of these binding sites for the subdomain architecture of the NBAS protein. Using AlphaFold, we disclosed the far-reaching impact of NBAS variants on the development of each phenotypic trait in patients with NBAS-related pathologies.

Visual Guidance for User Placement in Avatar-Mediated Telepresence Between Dissimilar Spaces.

Rapid advances in technology gradually realize immersive mixed-reality (MR) telepresence between distant spaces. This paper presents a novel visual guidance system for avatar-mediated telepresence, directing users to optimal placements that facilitate the clear transfer of gaze and pointing contexts through remote avatars in dissimilar spaces, where the spatial relationship between the remote avatar and the interaction targets may differ from that of the local user. Representing the spatial relationship between the user/avatar and interaction targets with angle-based interaction features, we assign recommendation scores of sampled local placements as their maximum feature similarity with remote placements. These scores are visualized as color-coded 2D sectors to inform the users of better placements for interaction with selected targets. In addition, virtual objects of the remote space are overlapped with the local space for the user to better understand the recommendations. We examine whether the proposed score measure agrees with the actual user perception of the partner's interaction context and find a score threshold for recommendation through user experiments in virtual reality (VR). A subsequent user study in VR investigates the effectiveness and perceptual overload of different combinations of visualizations. Finally, we conduct a user study in an MR telepresence scenario to evaluate the effectiveness of our method in real-world applications.

A sensitive red/far-red photoswitch for controllable gene therapy in mouse models of metabolic diseases

Red light optogenetic systems are in high demand for the precise control of gene expression for gene- and cell-based therapies. Here, we report a red/far-red light-inducible photoswitch (REDLIP) system based on the chimeric photosensory protein FnBphP (Fn-REDLIP) or PnBphP (Pn-REDLIP) and their interaction partner LDB3, which enables efficient dynamic regulation of gene expression with a timescale of seconds without exogenous administration of a chromophore in mammals. We use the REDLIP system to establish the REDLIP-mediated CRISPR-dCas9 (REDLIPcas) system, enabling optogenetic activation of endogenous target genes in mammalian cells and mice. The REDLIP system is small enough to support packaging into adeno-associated viruses (AAVs), facilitating its therapeutic application. Demonstrating its capacity to treat metabolic diseases, we show that an AAV-delivered Fn-REDLIP system achieved optogenetic control of insulin expression to effectively lower blood glucose levels in type 1 diabetes model mice and control an anti-obesity therapeutic protein (thymic stromal lymphopoietin, TSLP) to reduce body weight in obesity model mice. REDLIP is a compact and sensitive optogenetic tool for reversible and non-invasive control that can facilitate basic biological and biomedical research.

I can’t feel your face: callous-unemotional traits, social anxiety, and approach-avoidance behaviour in conduct disorder

Background and objectivesConduct disorders are associated with deficits in interpersonal behaviour. Both, callous-unemotional traits and social anxiety are often elevated in patients with conduct disorder and are associated with aggressive approach or disproportional avoidance. Previous studies have focused mainly on questionnaire reports of interpersonal behaviour, whereas direct explicit and implicit interpersonal behaviour in social contexts has not been considered sufficiently. Therefore, explicit and implicit interpersonal behaviour were investigated in children and adolescents with conduct disorder in the current study.MethodsForty male adolescent inpatients with conduct disorder and 30 typically developing controls (Mage = 12.5, SD = 1.39) took part in a virtual reality task in which they approached virtual agemates, displaying different facial expressions under the pretext of a cover story while interpersonal distance and walking speed were assessed (indirect condition). In addition, they were asked to move to a comfortable distance for conversation toward the agent (direct condition). Callous-unemotional traits and social anxiety were assessed via questionnaires.ResultsIn the indirect condition, no differences between the groups emerged. In the direct condition, typically developing children adjusted their interpersonal distance to the respective expression that the virtual classmate displayed. They showed significantly greater interpersonal distances to angry classmates than to happy classmates. In contrast, conduct disorder patients’ interpersonal distance, did not differ between emotions. Interpersonal distance preferences were also associated with social anxiety and callous-unemotional traits.ConclusionThe findings suggest that conduct disorder patients fail to adjust their interpersonal behaviour to the facial expression of social interaction partners and that this is associated with social anxiety and callous-unemotional traits. A lack of adjustment to social cues might contribute to and maintain problems with peers in individuals with conduct disorder.

The fungal effector AaAlta1 inhibits PATHOGENESIS-RELATED PROTEIN10-2-mediated callose deposition and defense responses in apple.

Apple leaf spot, caused by Alternaria alternata f. sp mali (ALT), poses a substantial threat to the global apple (Malus × domestica Borkh.) industry. Fungal effectors promote pathogen infestation and survival by interfering with plant immune responses. In our study, we investigated the secretion of effector proteins by the virulent ALT7 strain. Using mass spectrometry, we identified the effector AaAlta1, which belongs to the Alt a 1 protein family (AA1s). Further analysis confirmed that ALT7 secretes AaAlta1. AaAlta1 knockdown mutants displayed reduced pathogenicity in apple tissue culture seedlings, while overexpression strains exhibited enhanced pathogenicity compared to the wild-type ALT7 strain. Using immunoprecipitation followed by mass spectrometry, we isolated pathogenesis-related protein 10-2 (PR10-2) as an interaction partner of AaAlta1 in apple. Knockdown mutants of AaAlta1 showed increased PR10-2-mediated callose deposition in apple, a critical plant defense response. The enhanced defense responses in apple substantially reduced their susceptibility to infection by these ALT7 mutants. Our findings delineate an infection strategy whereby ALT7 secretes AaAlta1 to suppress PR10-2, thereby circumventing the apple defense system.

The societal impact of meaningful social interactions during online focus groups

Against a backdrop of increasing levels of discontent and division reported in democratic societies, meaningful social interactions (especially between strangers) are clearly important to study. Drawing on observations during previous research projects, this article explores whether and how online focus groups (OFGs) can be leveraged to facilitate meaningful social interactions between unfamiliar interaction partners, and the extent to which these interactions have the potential to create societal impact. Our findings suggest that OFGs can facilitate a combination of “emotional”, “informational”, and “tangible” impacts for participants, helping to make social interactions meaningful. Meanwhile, these “individual impacts” could translate to “societal impacts” by empowering people to better participate (and participate better) in the public sphere. This outcome could be accelerated if individuals share newly acquired knowledge onwards with their community, generating a positive feedback loop of further meaningful social interactions. Our findings imply that researchers should strive to ensure that qualitative social research delivers direct value to the participants who take part, separate from the potential (thematic) value it has for the academic(s) involved. This ambition could be supported by academic funding frameworks that recognize “direct value for participants” as a desirable (and assessed) criterion.

Knowledge and Technology Transfer: Trends and Models in Practice of Leading Russian Universities

The research deals with identification of key trends and models of new practices of the leading Russian universities in the fields of knowledge and technology transfer. Topicality of the research is envisaged by the necessity to adapt the system of higher education in Russia to targets of providing technological sovereignty and leadership, which requires introduction of universities in processes of knowledge and technology transfer, as well as commercialization of innovation. The research used methods of substantial analysis of documents demonstrating the experience of leading Russian universities in the field of knowledge and technology transfer, as well as modeling methods as applied to processes of interaction between universities and industrial partners and assessing university potential in the field of innovation activity. As a result key trends of organizational transformation of universities in the field of knowledge and technology transfer were identified: developing mechanisms of accumulating potential results in intellectual activity; building ecosystem for transfer and commercialization of scientific innovation; extending cooperation with industrial partners in promotion of results of intellectual activity to real sector of economy. Apart from that 4 key models of university and industrial partner interaction were found in the field of knowledge and technology transfer (R&D order, R&D proposals, start-up promotion and joint enterprise setting up); the concept of transfer funnels was presented to describe processes of project selection, researchers and R&D orders; the model of estimating potential of universities in the field of knowledge and technology transfer was worked out, which gives an opportunity to find the current standing of the university and trajectory of development strategy. The article also shows the promising trends in innovation activity of universities with regard to present day’s goals of scientific and technological development of the country.

Novel Interacting Partners of MGP-40, a Chitinase-Like Protein in Buffalo Mammary Epithelial Cells.

Mammary Gland Protein-40 (MGP-40), also known as chitinase-3-like protein 1 (CHI3L1), is involved in critical biological processes such as inflammation, tissue remodeling, and cell proliferation, especially during the involution phase of the mammary gland. This study aimed to explore the molecular mechanisms of MGP-40 by identifying its novel interacting partners in buffalo mammary epithelial cells (BuMECs). Stable overexpression of MGP-40 in BuMECs was achieved through transfection with the pCIneo-MGP-40 vector, followed by G418 selection and confirmation by Western blot analysis. To identify interacting proteins, Co-immunoprecipitation (Co-IP) of BuMEC lysate using an anti-YKL-40 antibody was performed, and the eluted proteins were analyzed using SDS-PAGE and mass spectrometry (MALDI-TOF/TOF). The analysis revealed several interacting proteins, including synaptotagmin-like 3, Ras-related Rab19, RIB34A-like protein with coiled coils, and ATP synthase subunit g. These interacting partners suggest that MGP-40 is involved in crucial cellular processes like vesicle trafficking, cytoskeletal organization, and energy metabolism, extending its known functions in inflammation and tissue remodeling. Notably, the interactions with synaptotagmin-like 3 and Rab proteins emphasize MGP-40's potential role in vesicular transport, essential for milk production in mammary epithelial cells, while the association with ATP synthase subunit g links MGP-40 to energy regulation during lactation. These findings provide preliminary insights into the potential roles of MGP-40 in mammary gland physiology, particularly in cellular processes such as vesicle trafficking and energy metabolism. Further studies, including in vivo validation, are essential to confirm these interactions and clarify their relevance to mammary gland function and pathology.

Arctic plant-fungus interaction networks show major rewiring with environmental variation

Global environmental change may lead to changes in community structure and in species interactions, ultimately changing ecosystem functioning. Focusing on spatial variation in fungus–plant interactions across the rapidly changing Arctic, we quantified variation in the identity of interaction partners. We then related interaction turnover to variation in the bioclimatic environment by combining network analyses with general dissimilarity modelling. Overall, we found species associations to be highly plastic, with major rewiring among interaction partners across variable environmental conditions. Of this turnover, a major part was attributed to specific environmental properties which are likely to change with progressing climate change. Our findings suggest that the current structure of plant-root associated interactions may be severely altered by rapidly advancing global warming. Nonetheless, flexibility in partner choice may contribute to the resilience of the system.

Predicting emotion regulation strategies from aspects of the social context in everyday life

Emotion regulation has traditionally been conceptualized as an intrapersonal phenomenon with a focus on individuals’ personal experiences (e.g., feelings) and behaviors. However, a relational perspective on emotions underscores that emotion regulation occurs predominantly in the context of social interactions. Close relationships play an important role in emotion regulation in social interactions, particularly during emerging adulthood when individuals spend more time outside the family home. However, few studies have examined predictors of the use of different emotion regulation strategies in everyday life. Using Ecological Momentary Assessment, we first examined concurrent associations between social contexts (closeness to interaction partner and pleasantness of interaction) and use of emotion regulation strategies (cognitive reappraisal and expressive suppression). Second, we used lagged models to explore potential bidirectional associations between aspects of the social context and emotion regulation strategy use. We collected EMA data four times per day for two weeks, resulting in 3,158 momentary assessments. Better quality of social interactions was associated with both less suppression and less reappraisal at the same moment, but not at subsequent moments. Interestingly, we found that reappraisal at one moment predicted more pleasant interactions and closeness at the next moment. Our findings underscore the importance of understanding both social contexts and emotion regulation on momentary levels. This study holds implications for understanding social context and emotion regulation in the everyday lives of emerging adults.

Exploring α-synuclein Interaction Partners and their Potential Clinical Implications for Parkinson's Disease.

Alpha-synuclein aggregates are strongly associated with Parkinson's disease (PD), a degenerative neurological disorder characterized by a progressive loss in motor functions. Our study aimed to unravel the potential interaction partners of α-synuclein for exploring the synucleinpathy of PD related to α-synuclein aggregates. α-synuclein was expressed in E.coli and purified by affinity chromatography followed by isolation and identification of its interaction partners using pulldown assay coupled with LC-MS/MS. The impacts of the identified interaction partners on PD were evaluated based on GSE205450 dataset. Consequently, 157 proteins were identified by the criteria of unique peptide = 5. Four proteins including ACO2, ANT1, ATP5F1B and CKB were confirmed using immunostaining coupled with α-synuclein-pulldown assay. Transcriptomics assay showed that the dominant biological processes influenced by α-synuclein interaction partners with differential expression were energy metabolism. Together with GSE205450, Western blot assay showed that α-synuclein interaction partners involved in energy metabolism were down-regulated in PD patients and the MPTP-lesioned mice. ROC curves indicated their clinical implications as diagnostic indices of PD. Using ANT1 as an example, we found that protein aggregates formed by ANT1 and α-synuclein predominantly solely appeared in the cells and mice with PD-like variations. Thereby, low levels of the interaction partners of α-synuclein associated with energy metabolism were associated with PD pathogenesis via forming protein aggregates. This study provides an insight into developing innovative targets on PD based on synucleinpathy.

Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes.

Protein complexes composed of strictly essential subunits are abundant in nature and often arise through the gradual complexification of ancestral precursor proteins. Essentiality can arise through the accumulation of changes that are tolerated in the complex state but would be deleterious for the standalone complex components. While this theoretical framework to explain how essentiality arises has been proposed long ago, it is unclear which factors cause essentiality to persist over evolutionary timescales. In this work we show that the central enzyme of photosynthesis, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), can easily start to depend on a newly recruited interaction partner through multiple, genetically distinct mechanisms that affect stability, solubility, and catalysis. We demonstrate that layering multiple mechanisms of essentiality can lead to its persistence, even if any given mechanism reverts. More broadly, our work highlights that new interaction partners can drastically re-shape which substitutions are tolerated in the proteins they are recruited into. This can lead to the evolution of multilayered essentiality through the exploration of areas of sequence space that are only accessible in the complex state.

Astrocytic NHERF-1 Increases Seizure Susceptibility by Inhibiting Surface Expression of TREK-1.

Mature hippocampal astrocytes exhibit a linear current-to-voltage (I-V) K+ membrane conductance called passive conductance. It is estimated to enable astrocytes to keep potassium homeostasis in the brain. We previously reported that the TWIK-1/TREK-1 heterodimeric channels are crucial for astrocytic passive conductance. However, the regulatory mechanism of these channels by other binding proteins remains elusive. Here, we identified Na+/H+ exchange regulator-1 (NHERF-1), a protein highly expressed in astrocytes, as a novel interaction partner for these channels. NHERF-1 endogenously bound to TWIK-1/TREK-1 in hippocampal cultured astrocytes. When NHERF-1 is overexpressed or silenced, surface expression and activity of TWIK-1/TREK-1 heterodimeric channels are inhibited or enhanced, respectively. Furthermore, we confirmed that reduced astrocytic passive conductance by NHERF-1 overexpressing in the hippocampus increases kainic acid (KA)-induced seizure sensitivity. Taken together, these results suggest that NHERF-1 is a key regulator of TWIK-1/TREK-1 heterodimeric channels in astrocytes and suppression of TREK-1 surface expression by NHERF-1 increases KA-induced seizure susceptibility via reduction of astrocytic passive conductance.

Direct and indirect salt effects on homotypic phase separation

The low-complexity domain of hnRNPA1 (A1-LCD) phase separates in a salt-dependent manner. Unlike many intrinsically disordered proteins (IDPs) whose phase separation is suppressed by increasing salt concentrations, the phase separation of A1-LCD is promoted by >100 mM NaCl. To investigate the atypical salt effect on A1-LCD phase separation, we carried out all-atom molecular dynamics simulations of systems comprising multiple A1-LCD chains at NaCl concentrations from 50 to 1000 mM NaCl. The ions occupy first shell as well as more distant sites around the IDP chains, with Arg sidechains and backbone carbonyls the favored partners of Cl– and Na+, respectively. They play two direct roles in driving A1-LCD condensation. The first is to neutralize the high net charge of the protein (+9) by an excess of bound Cl– over Na+; the second is to bridge between A1-LCD chains, thereby fortifying the intermolecular interaction networks in the dense phase. At high concentrations, NaCl also indirectly strengthens π–π, cation–π, and amino–π interactions, by drawing water away from the interaction partners. Therefore, at low salt, A1-LCD is prevented from phase separation by net charge repulsion; at intermediate concentrations, NaCl neutralizes enough of the net charge while also bridging IDP chains to drive phase separation. This drive becomes even stronger at high salt due to strengthened π-type interactions. Based on this understanding, four classes of salt dependence of IDP phase separation can be predicted from amino-acid composition.

Direct and indirect salt effects on homotypic phase separation.

The low-complexity domain of hnRNPA1 (A1-LCD) phase separates in a salt-dependent manner. Unlike many intrinsically disordered proteins (IDPs) whose phase separation is suppressed by increasing salt concentrations, the phase separation of A1-LCD is promoted by >100 mM NaCl. To investigate the atypical salt effect on A1-LCD phase separation, we carried out all-atom molecular dynamics simulations of systems comprising multiple A1-LCD chains at NaCl concentrations from 50 to 1000 mM NaCl. The ions occupy first shell as well as more distant sites around the IDP chains, with Arg sidechains and backbone carbonyls the favored partners of Cl- and Na+, respectively. They play two direct roles in driving A1-LCD condensation. The first is to neutralize the high net charge of the protein (+9) by an excess of bound Cl- over Na+; the second is to bridge between A1-LCD chains, thereby fortifying the intermolecular interaction networks in the dense phase. At high concentrations, NaCl also indirectly strengthens π-π, cation-π, and amino-π interactions, by drawing water away from the interaction partners. Therefore, at low salt, A1-LCD is prevented from phase separation by net charge repulsion; at intermediate concentrations, NaCl neutralizes enough of the net charge while also bridging IDP chains to drive phase separation. This drive becomes even stronger at high salt due to strengthened π-type interactions. Based on this understanding, four classes of salt dependence of IDP phase separation can be predicted from amino-acid composition.

Integrated multi-omics identifies pathways governing interspecies interaction between A. fumigatus and K. pneumoniae

Polymicrobial co- and superinfections involving bacterial and fungal pathogens pose serious challenges for diagnosis and therapy, and are associated with elevated morbidity and mortality. However, the metabolic dynamics of bacterial–fungal interactions (BFI) and the resulting impact on disease outcome remain largely unknown. The fungus Aspergillus fumigatus and the bacterium Klebsiella pneumoniae are clinically important pathogens sharing common niches in the human body, especially in the lower respiratory tract. We have exploited an integrated multi-omics approach to unravel the complex and multifaceted processes implicated in the interspecies communication involving these pathogens in mixed biofilms. In this setting, A. fumigatus responds to the bacterial challenge by rewiring its metabolism, attenuating the translational machineries, and by connecting secondary with primary metabolism, while K. pneumoniae maintains its central metabolism and translation activity. The flexibility in the metabolism of A. fumigatus and the ability to quickly adapt to the changing microenvironment mediated by the bacteria highlight new possibilities for studying the impact of cross-communication between competing interaction partners. The data underscore the complexity governing the dynamics underlying BFI, such as pronounced metabolic changes mounted in A. fumigatus interacting with K. pneumoniae. Our findings identify candidate biomarkers potentially exploitable for improved clinical management of BFI.

Togetherness in musical interaction

This paper presents a model of musical togetherness (MT), defined as the sense of musical connection that arises during real-time interaction and results in feelings of social connection, pleasure, and trust. The model comprises three layers. The first layer, which provides a backdrop for subsequent layers, comprises players’ knowledge and expectations about what will unfold during an interaction. The second layer comprises five processes that build upon one another: Belief in intentional partners in a shared musical environment, perceived liveness, and perceived responsivity mainly strengthen the social dimension of MT, while perceived embodied alignment and joint agency mainly strengthen the positive valence dimension. The third layer comprises rewarding feelings of social connection, pleasure and trust. These feelings feed back to affect the second layer processes, effectively guiding players’ musical decision-making and behaviour. They also feed back to affect the first layer, creating lasting effects on the way players approach musical interactions and relate to their interaction partners. MT should be seen as a fluid aspect of interaction that fluctuates alongside the aesthetic quality of the music. Players will sometimes sacrifice MT in the short term in order to improve the quality of their playing and strengthen their sense of MT in the long term. The MT model provides structure for a construct that has been used casually in the music psychology literature and has implications for how the performance behaviour of ensemble musicians is understood.

Aspekte des Alter(n)s im Schwankzyklus Till Eulenspiegel

In society and in literature, age is often associated with positive (wisdom, life experience) or negative aspects (stubbornness, impatience). The article examines the extent to which the biological age influences social relationships, experiences and/or behaviour, and the reactions of the archetypal German prankster and his interaction partners.

Adaptive protein coevolution preserves telomere integrity.

Many essential conserved functions depend, paradoxically, on proteins that evolve rapidly under positive selection. How such adaptively evolving proteins promote biological innovation while preserving conserved, essential functions remains unclear. Here, we experimentally test the hypothesis that adaptive protein-protein coevolution within an essential multi-protein complex mitigates the deleterious incidental byproducts of innovation under pressure from selfish genetic elements. We swapped a single, adaptively evolving subunit of a telomere protection complex from Drosophila yakuba into its close relative, D. melanogaster . The heterologous subunit uncovered a catastrophic interspecies incompatibility that caused lethal telomere fusions. Restoring six adaptively evolving sites on the protein-protein interaction surface, or introducing the D. yakuba interaction partner, rescued telomere integrity and viability. Our in vivo , evolution-guided manipulations illuminate how adaptive protein-protein coevolution preserves essential functions threatened by an evolutionary pressure to innovate.