Canonical Function Research Articles

A mitochondrial unfolded protein response-independent role of DVE-1 in longevity regulation

The special AT-rich sequence-binding (SATB) protein DVE-1 is widely recognized for its pivotal involvement in orchestrating the retrograde mitochondrial unfolded protein response (mitoUPR) in C. elegans. In our study of downstream factors contributing to lifespan extension in sensory ciliary mutants, we find that DVE-1 is crucial for this longevity effect independent of its canonical mitoUPR function. Additionally, DVE-1 also influences lifespan under conditions of dietary restriction and germline loss, again distinct from its role in mitoUPR. Mechanistically, while mitochondrial stress typically prompts nuclear accumulation of DVE-1 to initiate the transcriptional mitoUPR program, these long-lived mutants reduce DVE-1 nuclear accumulation, likely by enhancing its cytosolic translocation. This observation suggests a cytosolic role for DVE-1 in lifespan extension. Overall, our study implies that, in contrast to the more narrowly defined role of the mitoUPR-related transcription factor ATFS-1, DVE-1 may possess broader functions than previously recognized in modulating longevity and defending against stress.

PCNA-binding activity separates RNF168 functions in DNA replication and DNA double-stranded break signaling.

RNF168 orchestrates a ubiquitin-dependent DNA damage response to regulate the recruitment of repair factors, such as 53BP1 to DNA double-strand breaks (DSBs). In addition to its canonical functions in DSB signaling, RNF168 may facilitate DNA replication fork progression. However, the precise role of RNF168 in DNA replication remains unclear. Here, we demonstrate that RNF168 is recruited to DNA replication factories in a manner that is independent of the canonical DSB response pathway regulated by Ataxia-Telangiectasia Mutated (ATM) and RNF8. We identify a degenerate Proliferating Cell Nuclear Antigen (PCNA)-interacting peptide (DPIP) motif in the C-terminus of RNF168, which together with its Motif Interacting with Ubiquitin (MIU) domain mediates binding to mono-ubiquitylatedPCNA at replication factories. An RNF168 mutant harboring inactivating substitutions in its DPIP box and MIU1 domain (termed RNF168 ΔDPIP/ΔMIU1) is not recruited to sites of DNA synthesis and fails to support ongoing DNA replication. Notably, the PCNA interaction-deficient RNF168 ΔDPIP/ΔMIU1 mutant fully rescues the ability of RNF168-/- cells to form 53BP1 foci in response to DNA DSBs. Therefore, RNF168 functions in DNA replication and DSB signaling are fully separable. Our results define a new mechanism by which RNF168 promotes DNA replication independently of its canonical functions in DSB signaling.

Different cropping systems impact soil health by improving soil biological activities and total organic carbon content

ABSTRACT This study assesses the impact of different cropping systems on changes in total organic carbon (TOC), its fractions and biological activities to evaluate the changes in soil health. The rice-wheat cropping system (RWCS) had significantly higher total organic carbon (TOC) (38.8%) and soil organic carbon (SOC, 43.6%) compared to the pearl millet-mustard cropping system (PMCS). Active C pools were significantly higher in soils under cotton-wheat (CW) and pearl millet-wheat cropping systems (PWCS) than RWCS, whereas passive C pools (63% of TOC), the microbial biomass carbon (MBC) and dehydrogenase activity (DHA) were highest under RWCS than other systems. Soils under these cropping systems exhibited a significant polynomial relationship of TOC with SOC and dissolved organic carbon (DOC). Two significant canonical discriminant functions involving TOC, SOC, DOC, very labile carbon (CVL), labile carbon (CL), less labile carbon (CLL), recalcitrant carbon (CR), MBC and DHA could distinguish the different cropping systems and contributed 94.7%. The principal component analysis identified that TOC, SOC, pH and EC were the most reliable and contributing variables for assessing soil health under different cropping systems. Three PCs explained the 79.2% variability of the total variance of the original data set.

Comment on: “Analytical solutions to the Schrödinger equation for a generalized Cornell potential and its applications to diatomic molecules and heavy mesons”

We analyze a recent calculation of the energy levels of some quantum-mechanical models derived from the so-called generalized Cornell potential. We argue that the authors obtained essentially the same spectrum for potentials with considerably different spectra. We show that the authors obtained negative eigenvalues in the case of a positive-definite potential. The reason is due to the approximation used in the solution of the Schrödinger equation. We point out that the omission of the sum over the rotational degrees of freedom in the canonical partition function leads to incomplete expressions for the thermodynamic functions.

From fat storage to immune hubs: the emerging role of adipocytes in coordinating the immune response to infection.

Adipose tissue is a rich source of diverse cell populations, including immune cells, adipocytes and stromal cells. Interactions between these different cell types are now appreciated to be critical for maintaining tissue structure and function, by governing processes such as adipogenesis, lipolysis and differentiation of white to beige adipocytes. Interactions between these cells also drive inflammation in obesity, leading to an expansion of adipose tissue immune cells, and the secretion of proinflammatory cytokines from immune cells and from adipocytes themselves. However, in evolutionary terms, obesity is a recent phenomenon, raising the question of why adipocytes evolved to express factors that influence the immune response. Studies of various pathogens indicate that adipocytes are highly responsive to infection, altering their metabolic profiles in a way that can be used to release nutrients and fuel the immune response. In the case of infection with the extracellular parasite Trypanosoma brucei, attenuating the ability of adipocytes to sense the cytokine IL-17 results in a loss of control of the local immune response and an increased pathogen load. Intriguingly, comparisons of the adipocyte response to infection suggest that the immune responses of these cells occur in a pathogen-dependent manner, further confirming their complexity. Here, with a focus on murine adipose tissue, we discuss the emerging concept that, in addition to their canonical function, adipocytes are immune signalling hubs that integrate and disseminate signals from the immune system to generate a local environment conducive to pathogen clearance.

RETINOBLASTOMA-RELATED Has Both Canonical and Noncanonical Regulatory Functions During Thermo-Morphogenic Responses in Arabidopsis Seedlings.

Warm temperatures accelerate plant growth, but the underlying molecular mechanism is not fully understood. Here, we show that increasing the temperature from 22°C to 28°C rapidly activates proliferation in the apical shoot and root meristems of wild-type Arabidopsis seedlings. We found that one of the central regulators of cell proliferation, the cell cycle inhibitor RETINOBLASTOMA-RELATED (RBR), is suppressed by warm temperatures. RBR became hyper-phosphorylated at a conserved CYCLIN-DEPENDENT KINASE (CDK) site in young seedlings growing at 28°C, in parallel with the stimulation of the expressions of the regulatory CYCLIN D/A subunits of CDK(s). Interestingly, while under warm temperatures ectopic RBR slowed down the acceleration of cell proliferation, it triggered elongation growth of post-mitotic cells in the hypocotyl. In agreement, the central regulatory genes of thermomorphogenic response, including PIF4 and PIF7, as well as their downstream auxin biosynthetic YUCCA genes (YUC1-2 and YUC8-9) were all up-regulated in the ectopic RBR expressing line but down-regulated in a mutant line with reduced RBR level. We suggest that RBR has both canonical and non-canonical functions under warm temperatures to control proliferative and elongation growth, respectively.

Initiation of ERAD by the bifunctional complex of Mnl1 mannosidase and protein disulfide isomerase.

Misfolded glycoproteins in the endoplasmic reticulum (ER) lumen are translocated into the cytosol and degraded by the proteasome, a conserved process called ER-associated protein degradation (ERAD). In S. cerevisiae , the glycan of these proteins is trimmed by the luminal mannosidase Mnl1 (Htm1) to generate a signal that triggers degradation. Curiously, Mnl1 is permanently associated with protein disulfide isomerase (Pdi1). Here, we have used cryo- electron microscopy, biochemical, and in vivo experiments to clarify how this complex initiates ERAD. The Mnl1-Pdi1 complex first de-mannosylates misfolded, globular proteins that are recognized through a C-terminal domain (CTD) of Mnl1; Pdi1 causes the CTD to ignore completely unfolded polypeptides. The disulfides of these globular proteins are then reduced by the Pdi1 component of the complex, generating unfolded polypeptides that can be translocated across the membrane. Mnl1 blocks the canonical oxidative function of Pdi1, but allows it to function as the elusive disulfide reductase in ERAD.

Inflammasome protein scaffolds the DNA damage complex during tumor development.

Inflammasome sensors activate cellular signaling machineries to drive inflammation and cell death processes. Inflammasomes also control the development of certain diseases independently of canonical functions. Here, we show that the inflammasome protein NLR family CARD domain-containing protein 4 (NLRC4) attenuated the development of tumors in the Apcmin/+ mouse model. This response was independent of inflammasome signaling by NLRP3, NLRP6, NLR family apoptosis inhibitory proteins, absent in melanoma 2, apoptosis-associated speck-like protein containing a caspase recruitment domain, caspase-1 and caspase-11. NLRC4 interacted with the DNA-damage-sensing ataxia telangiectasia and Rad3-related (ATR)-ATR-interacting protein (ATRIP)-Ewing tumor-associated antigen 1 (ETAA1) complex to promote the recruitment of the checkpoint adapter protein claspin, licensing the activation of the kinase checkpoint kinase-1 (CHK1). Genotoxicity-induced activation of the NLRC4-ATR-ATRIP-ETAA1 complex drove the tumor-suppressing DNA damage response and CHK1 activation, and further attenuated the accumulation of DNA damage. These findings demonstrate a noninflammatory function of an inflammasome protein in promoting the DNA damage response and mediating protection against cancer.

Physical activity motivations and psychological well-being among university students: a canonical correlation analysis.

With increasing concern about mental health issues and active lifestyles among university students, understanding the interplay between different physical activity motivations and various dimensions of psychological well-being is important. The present study aims to explore the canonical relationship between physical activity motivations based on self-determination theory and psychological well-being according to Ryff's model in university students. Nine hundred and sixty-six Chinese university students participated in this study. A canonical correlation analysis was conducted using six variables of motivations as predictors of six variables of psychological well-being. The canonical correlation analysis yielded two canonical functions. The first canonical function, which was primary, indicated that intrinsic motivation, integrated regulation, identified regulation, and introjected regulation contributed the most to psychological well-being. The second canonical function indicated that a decrease in external motivation and amotivation accounted for an increase in personal growth. This study underscores the importance of elucidating the underlying motivations driving physical activity behaviors in order to enhance psychological well-being in this population.

NF-κB regulated expression of A20 controls IKK dependent repression of RIPK1 induced cell death in activated T cells.

IKK signalling is essential for survival of thymocytes by repressing RIPK1 induced cell death rather than its canonical function of activating NF-κB. The role of IKK signalling in activated T cells is unclear. To investigate this, we analysed activation of IKK2 deficient T cells. While TCR triggering was normal, proliferation and expansion was profoundly impaired. This was not due to defective cell cycle progression, rather dividing T cells became sensitised to TNF induced cell death, since inhibition of RIPK1 kinase activity rescued cell survival. Gene expression analysis of activated IKK2 deficient T cells revealed defective expression of Tnfaip3, that encodes A20, a negative regulator of NF-κB. To test whether A20 expression was required to protect IKK2 deficient T cells from cell death, we generated mice with T cells lacking both A20 and IKK2. Doing this resulted in near complete loss of peripheral T cells, in contrast to mice lacking one or other gene. Strikingly, this phenotype was completely reversed by inactivation of RIPK1 kinase activity in vivo. Together, our data show that IKK signalling in activated T cells protects against RIPK1 dependent death, both by direct phosphorylation of RIPK1 and through NF-κB mediated induction of A20, that we identify for the first time as a key modulator of RIPK1 activity in T cells.

Protein disulfide isomerase A4 binds to Brucella BtpB and mediates intracellular NAD+/NADH metabolism in RAW264.7 cells

The Toll/interleukin-1 receptor (TIR) signaling domain is distributed widely in mammalian Toll-like receptors and adaptors, plant nucleotide-binding leucine-rich repeat receptors, and specific bacterial virulence proteins. Proteins that possess TIR domain exhibit NADase activity which is distinct from the canonical signaling function of these domains. However, the effects of bacterial TIR domain proteins on host metabolic switches and the underlying mechanism of NADase activity in these proteins remain unclear. Here, we utilized Brucella TIR domain-containing type IV secretion system effector protein, BtpB, to explore the mechanism of NADase activity in host cells. We showed that using ectopic expression BtpB not only generates depletion of NAD+ but also loss of NADH and ATP in RAW264.7 macrophage cells. Moreover, immunoprecipitation-mass spectrometry, co-immunoprecipitation, and confocal microscope assays revealed that BtpB interacted with host protein disulfide isomerase A4 (PDIA4). The Brucella mutant strain deleted the gene for BtpB, significantly decreased PDIA4 expression. Furthermore, our data revealed that PDIA4 played an important role in regulating intracellular NAD+/NADH levels in macrophages, and PDIA4 overexpression restored the decline of intracellular NAD+ and NADH levels induced by Brucella BtpB. The results provide new insights into the metabolic regulatory activity of TIR domain proteins in the critical human and animal pathogen Brucella.

Deterministic 3-server on a circle and the limitation of canonical potentials

The deterministic k-server conjecture states that there is a k-competitive deterministic algorithm for the k-server problem for any metric space. We show that the work function algorithm is 3-competitive for the 3-server problem on circle metrics, a case left open by Coester and Koutsoupias (2021). Our analysis follows the existing framework but introduces a new potential function which may be viewed as a relaxation of the counterpart by Coester and Koutsoupias (2021). We further notice that the new potential function and many existing ones can be rewritten in a canonical form. Through a computer-aided verification, however, we find that no such canonical potential function can resolve the deterministic 3-server conjecture for general metric spaces under the current analysis framework.

A non-canonical repressor function of JUN restrains YAP activity and liver cancer growth

Yes-associated protein (YAP) and its homolog, transcriptional coactivator with PDZ-binding motif (TAZ), are the main transcriptional downstream effectors of the Hippo pathway. Decreased Hippo pathway activity leads to nuclear translocation of YAP/TAZ where they interact with TEAD transcription factors to induce target gene expression. Unrestrained YAP/TAZ activity can lead to excessive growth and tumor formation in a short time, underscoring the evolutionary need for tight control of these two transcriptional coactivators. Here, we report that the AP-1 component JUN acts as specific repressor of YAP/TAZ at joint target sites to decrease YAP/TAZ activity. This function of JUN is independent of its heterodimeric AP-1 partner FOS and the canonical AP-1 function. Since expression of JUN is itself induced by YAP/TAZ, our work identifies a JUN-dependent negative feedback loop that buffers YAP/TAZ activity at joint genomic sites. This negative feedback loop gets disrupted in liver cancer to unlock the full oncogenic potential of YAP/TAZ. Our results thus demonstrate an additional layer of control for the interplay of YAP/TAZ and AP-1.

A single septin from a polyextremotolerant yeast recapitulates many canonical functions of septin hetero-oligomers.

Morphological complexity and plasticity are hallmarks of polyextremotolerant fungi. Septins are conserved cytoskeletal proteins and key contributors to cell polarity and morphogenesis. They sense membrane curvature, coordinate cell division, and influence diffusion at the plasma membrane. Four septin homologues are conserved from yeasts to humans, the systems in which septins have been most studied. But there is also a fifth family of opisthokont septins that remain biochemically mysterious. Members of this family, Group 5 septins, appear in the genomes of filamentous fungi, but are understudied due to their absence from ascomycete yeasts. Knufia petricola is an emerging model polyextremotolerant black fungus that can also serve as a model system for Group 5 septins. We have recombinantly expressed and biochemically characterized KpAspE, a Group 5 septin from K. petricola. This septin--by itself in vitro--recapitulates many functions of canonical septin hetero-octamers. KpAspE is an active GTPase that forms diverse homo-oligomers, binds shallow membrane curvatures, and interacts with the terminal subunit of canonical septin hetero-octamers. These findings raise the possibility that Group 5 septins govern the higher-order structures formed by canonical septins, which in K. petricola cells form extended filaments, and provide insight into how septin hetero-oligomers evolved from ancient homomers.

SREBP2 restricts osteoclast differentiation and activity by regulating IRF7 and limits inflammatory bone erosion

Osteoclasts are multinucleated bone-resorbing cells, and their formation is tightly regulated to prevent excessive bone loss. However, the mechanisms by which osteoclast formation is restricted remain incompletely determined. Here, we found that sterol regulatory element binding protein 2 (SREBP2) functions as a negative regulator of osteoclast formation and inflammatory bone loss. Cholesterols and SREBP2, a key transcription factor for cholesterol biosynthesis, increased in the late phase of osteoclastogenesis. The ablation of SREBP2 in myeloid cells resulted in increased in vivo and in vitro osteoclastogenesis, leading to low bone mass. Moreover, deletion of SREBP2 accelerated inflammatory bone destruction in murine inflammatory osteolysis and arthritis models. SREBP2-mediated regulation of osteoclastogenesis is independent of its canonical function in cholesterol biosynthesis but is mediated, in part, by its downstream target, interferon regulatory factor 7 (IRF7). Taken together, our study highlights a previously undescribed role of the SREBP2-IRF7 regulatory circuit as a negative feedback loop in osteoclast differentiation and represents a novel mechanism to restrain pathological bone destruction.

Computation of rate coefficients in solutions based on transition state theory combined with a heuristically corrected polarizable continuum model: intermolecular Diels-Alder reactions as case studies.

Transition state theory (TST) based on activation parameters computed using quantum mechanics calculations combined with the polarizable continuum model (QM/PCM) is a fundamental tool for investigating reaction rates in the liquid phase. In conventional QM/PCM methods, thermodynamic data and partition functions for a solute are often derived from a quasi-ideal gas treatment (IGT) widely implemented in commercially available computation packages. This approach tends to overestimate entropy because calculations of thermodynamic parameters in the liquid phase ignore hindered translational and rotational modes in real solutions. The present work formulated partition functions for more realistic solutes hindered by surrounding solvent molecules in conjunction with the basic QM/PCM concept. In addition, a configuration partition function for solute molecules at a standard concentration of 1 mol dm-3 was incorporated using a simple lattice model. The canonical partition function and thermodynamic functions were derived based on statistical thermodynamics for localized systems. Expressions for rate coefficients within TST were also derived with a consistent formalism based on the standard state selected in partition function calculations. The performance of the proposed method was assessed by predicting rate coefficients for three different Diels-Alder reactions and comparing these with experimental results. QM/PCM calculations at the G4//ωB97X-D/6-311++G(d,p)/IEF-PCM level of theory with corrections for the dispersion and repulsion energies were performed to obtain the electronic structures of stationary points on potential energy surfaces as a means of finding activation enthalpy, entropy and Gibbs energy values based on revised partition functions as well as predicting rate coefficients. The activation Gibbs energies obtained from our proposed method were lower than those obtained from the IGT method due to reasonable entropy computations. The proposed method overestimated the rate coefficients by one to two orders of magnitude compared to the experimental values, whereas the IGT method underestimated them by the same amount. This discrepancy arises because the proposed method calculates the partition function from the viewpoint of a localized system, whereas the IGT method calculates it from the viewpoint of a non-localized system. Given that actual liquids exist in a state between non-localized and localized systems, it is essential to formulate the partition function in a way that more accurately represents the liquid state.

Exploring the role of RNASET2 in the immune response of black soldier fly larvae.

T2 RNases are transferase-type enzymes distributed across phyla, crucial for breaking down single-stranded RNA molecules. In addition to their canonical function, several T2 enzymes exhibit pleiotropic roles, contributing to various biological processes, such as the immune response in invertebrates and vertebrates. This study aims at characterizing RNASET2 in the larvae of black soldier fly (BSF), Hermetia illucens, which are used for organic waste reduction and the production of valuable insect biomolecules for feed formulation and other applications. Given the exposure of BSF larvae to pathogens present in the feeding substrate, it is likely that the mechanisms of their immune response have undergone significant evolution and increased complexity. After in silico characterization of HiRNASET2, demonstrating the high conservation of this T2 homolog, we investigated the expression pattern of the enzyme in the fat body and hemocytes, two districts mainly involved in the insect immune response, in larvae challenged with bacterial infection. While no variation in HiRNASET2 expression was observed in the fat body following infection, a significant upregulation of HiRNASET2 synthesis occurred in hemocytes shortly after the injection of bacteria in the larva. The intracellular localization of HiRNASET2 in lysosomes of plasmatocytes, its extracellular association with bacteria, and the presence of a putative antimicrobial domain in the molecule, suggest its potential role in RNA clean-up and as an alarm molecule promoting phagocytosis activation by hemocytes. These insights contribute to the characterization of the immune response ofHermetia illucens larvae and may facilitate the development of animal feedstuff enriched with highly valuable BSF bioactive compounds.

Parallel superposition of small-amplitude oscillatory shear flow upon steady shear flow from rotarance theory

The power of a macromolecular theory for the transport properties of a polymeric liquid increases with the number of analytical expressions for its most important material functions. In this work, we add another of these canonical function to our recent series of material function derivations for rotarance theory. By rotarance theory, we mean the explanation of the elasticity of polymeric liquids by use of (i) the diffusion equation to get the orientation distribution in Euler coordinates, and (ii) the integration in phase space using this distribution to get the target material function. In this paper, we target parallel superposition of oscillatory shear flow upon steady shear flow. We arrive at analytical expressions for both parts of the complex viscosity in parallel superposition. We find that these explain the classic experimental observations in parallel superposition: (a) the maximum in the real part of the complex viscosity, and (b) the negative values of minus its imaginary part, and (c) the independence of the steady mean shear stress from the superposed oscillation.

ANALISIS POSITIONING COFFEE SHOP LOKAL DI WILAYAH JABODETABEK

This research aims to examine the concept of coffee shop brand positioning in Indonesia, namely Kopi Janji Jiwa, Kopi Kenangan, Point Coffee, Kopi Lain Hati, and Kopi Kulo. The data collection method used was by distributing questionnaires online with samples taken using non-probability sampling techniques with purposive sampling to respondents who enjoy 5 coffee shop brands in Indonesia. Descriptive testing is used to analyze the influence of positioning on the coffee shop brand. The data used in this research is primary data obtained from distributing questionnaires to 41 respondents. This research uses cross sectional research, namely a research method carried out over a relatively short time and in a certain place. The data analysis method used in this research is to analyze the attributes owned using the attribute based approach. In this research, three outputs will be produced, namely canonical discriminant function, preference map, as well as market strategy and marketing mix.

Fibroblast growth factor homologous factors: canonical and non-canonical mechanisms of action.

Since their discovery nearly 30years ago, fibroblast growth factor homologous factors (FHFs) are now known to control the functionality of excitable tissues through a range of mechanisms. Nervous and cardiac system dysfunctions are caused by loss- or gain-of-function mutations in FHF genes. The best understood 'canonical' targets for FHF action are voltage-gated sodium channels, and recent studies have expanded the repertoire of ways that FHFs modulate sodium channel gating. Additional 'non-canonical' functions of FHFs in excitable and non-excitable cells, including cancer cells, have been reported over the past dozen years. This review summarizes and evaluates reported canonical and non-canonical FHF functions.