Control Of Pathways Research Articles

Phosphate Limitation Enhances Heterologous Enzyme Production in Bacillus subtilis: Mechanistic Insights and Universal Applicability.

Bacillus subtilis is one of the commonly used hosts for heterologous enzyme expression, depending on media rich in carbon, nitrogen, and phosphate sources for optimal growth and enzyme production. Interestingly, our investigation of maltotetraose-forming amylase, a key enzyme for efficient maltotetraose synthesis, revealed that phosphate limitation significantly enhances the growth rate and production of heterologous enzymes in recombinant B. subtilis. Under phosphate-limited conditions in a 15 L fermenter, the enzyme activity reached 679.15 U/mL, an improvement of 101% over the initial levels and a 12 h reduction in fermentation time. Transcriptomic analysis indicated that phosphate limitation promotes sustained enzyme production by upregulating protein synthesis and quality control pathways while optimizing energy utilization. This strategy was validated across various enzyme systems, highlighting its general applicability for enhancing heterologous protein expressions. These findings provide valuable insights for the industrial production of maltotetraose-forming amylase and other high-value enzymes, supporting the advancement of microbial fermentation technology.

Stalled disomes marked by Hel2-dependent ubiquitin chains undergo Ubp2/Ubp3-mediated deubiquitination upon translational run-off

Stalled ribosomes cause collisions, impair protein synthesis, and generate potentially harmful truncated polypeptides. Eukaryotic cells utilize the ribosome-associated quality control (RQC) and no-go mRNA decay (NGD) pathways to resolve these problems. In yeast, the E3 ubiquitin ligase Hel2 recognizes and polyubiquitinates disomes and trisomes at the 40S ribosomal protein Rps20/uS10, thereby priming ribosomes for further steps in the RQC/NGD pathways. Recent studies have revealed high concentrations of disomes and trisomes in unstressed cells, raising the question of whether and how Hel2 selects long-term stalled disomes and trisomes. This study presents quantitative analysis of in vivo-formed Hel2•ribosome complexes and the dynamics of Hel2-dependent Rps20 ubiquitination and Ubp2/Ubp3-dependent deubiquitination. Our findings show that Hel2 occupancy progressively increases from translating monosomes to disomes and trisomes. We demonstrate that disomes and trisomes with mono- or di-ubiquitinated Rps20 resolve independently of the RQC component Slh1, while those with tri- and tetra-ubiquitinated Rps20 do not. Based on the results, we propose a model in which Hel2 translates the duration of ribosome stalling into polyubiquitin chain length. This mechanism allows for the distinction between transient and long-term stalling, providing the RQC machinery with a means to select fatally stalled ribosomes over transiently stalled ones.

Cytoplasmic mRNA decay and quality control machineries in eukaryotes.

mRNA degradation pathways have key regulatory roles in gene expression. The intrinsic stability of mRNAs in the cytoplasm of eukaryotic cells varies widely in a gene- and isoform-dependent manner and can be regulated by cellular cues, such as kinase signalling, to control mRNA levels and spatiotemporal dynamics of gene expression. Moreover, specialized quality control pathways exist to rid cells of non-functional mRNAs produced by errors in mRNA processing or mRNA damage that negatively impact translation. Recent advances in structural, single-molecule and genome-wide methods have provided new insights into the central machineries that carry out mRNA turnover, the mechanisms by which mRNAs are targeted for degradation and the general principles that govern mRNA stability at a global level. This improved understanding of mRNA degradation in the cytoplasm of eukaryotic cells is finding practical applications in the design of therapeutic mRNAs.

Autophagy in Plant Health and Disease.

Autophagy has emerged as an essential quality control pathway in plants that selectively and rapidly removes damaged or unwanted cellular components to maintain cellular homeostasis. It can recycle a broad range of cargoes, including entire organelles, protein aggregates, and even invading microbes. It involves the de novo biogenesis of a new cellular compartment, making it intimately linked to endomembrane trafficking pathways. Autophagy is induced by a wide range of biotic and abiotic stress factors, and autophagy mutant plants are highly sensitive to stress, making it an attractive target for improving plant stress resilience. Here, we critically discuss recent discoveries related to plant autophagy and highlight open questions and future research areas.

Polyglycidamides: from Backbone-Promoted Amidation to Degradable Polyether with Wide-Range LCST.

Amide groups occur extensively in natural and synthetic polymers cultivating their vital roles in biological and industrial worlds. We report here an efficient and controlled pathway to amide-functionalized polyethers through ring-opening polymerization (ROP) of commercially available ethyl glycidate followed by amidation of the pendant ester groups. Transesterification is inhibited during the ROP by use of a two-component organocatalyst. Surprisingly, amidation can be completed even at 0 °C uncatalyzed, which is attributed to the electron-withdrawing effect of the oxygenated backbone as well as the inter-/intra-chain hydrogen bonding. Also interestingly, ethylene glycol and water are found to further accelerate the amidation while suppressing backbone degradation. The obtained polyglycidamides (PGAms) exhibit aqueous thermoresponsive properties, similar to their carbon-chain counterparts (polyacrylamides). Cloud point can be linearly modulated by co-amidation using two amines of varied ratios. Unlike polyacrylamides and regular polyethers, PGAm is degradable through retro-oxa-Michael addition under basic conditions.

FUT10 and FUT11 are protein O-fucosyltransferases that modify protein EMI domains.

O-Fucosylation plays crucial roles in various essential biological events. Alongside the well-established O-fucosylation of epidermal growth factor-like repeats by protein O-fucosyltransferase 1 (POFUT1) and thrombospondin type 1 repeats by POFUT2, we recently identified a type of O-fucosylation on the elastin microfibril interface (EMI) domain of Multimerin-1 (MMRN1). Here, using AlphaFold2 screens, co-immunoprecipitation, enzymatic assays combined with mass spectrometric analysis and CRISPR-Cas9 knockouts, we demonstrate that FUT10 and FUT11, originally annotated in UniProt as α1,3-fucosyltransferases, are actually POFUTs responsible for modifying EMI domains; thus, we renamed them as POFUT3 and POFUT4, respectively. Like POFUT1/2, POFUT3/4 function in the endoplasmic reticulum, require folded domain structures for modification and participate in a non-canonical endoplasmic reticulum quality control pathway for EMI domain-containing protein secretion. This finding expands the O-fucosylation repertoire and provides an entry point for further exploration in this emerging field of O-fucosylation.

Role and modulation of various spinal pathways for human upper limb control in different gravity conditions.

Humans can perform movements in various physical environments and positions (corresponding to different experienced gravity), requiring the interaction of the musculoskeletal system, the neural system and the external environment. The neural system is itself comprised of several interactive components, from the brain mainly conducting motor planning, to the spinal cord (SC) implementing its own motor control centres through sensory reflexes. Nevertheless, it remains unclear whether similar movements in various environmental dynamics necessitate adapting modulation at the brain level, correcting modulation at the spinal level, or both. Here, we addressed this question by focusing on upper limb motor control in various gravity conditions (magnitudes and directions) and using neuromusculoskeletal simulation tools. We integrated supraspinal sinusoidal commands with a modular SC model controlling a musculoskeletal model to reproduce various recorded arm trajectories (kinematics and EMGs) in different contexts. We first studied the role of various spinal pathways (such as stretch reflexes) in movement smoothness and robustness against perturbation. Then, we optimised the supraspinal sinusoidal commands without and with a fixed SC model including stretch reflexes to reproduce a target trajectory in various gravity conditions. Inversely, we fixed the supraspinal commands and optimised the spinal synaptic strengths in the different environments. In the first optimisation context, the presence of SC resulted in easier optimisation of the supraspinal commands (faster convergence, better performance). The main supraspinal commands modulation was found in the flexor sinusoid's amplitude, resp. frequency, to adapt to different gravity magnitudes, resp. directions. In the second optimisation context, the modulation of the spinal synaptic strengths also remarkably reproduced the target trajectory for the mild gravity changes. We highlighted that both strategies of modulation of the supraspinal commands or spinal stretch pathways can be used to control movements in different gravity environments. Our results thus support that the SC can assist gravity compensation.

FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis.

Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.

The contributions of language and inhibitory control to false belief reasoning over time.

The role of language in false belief reasoning has been much debated for twenty-five years or more, especially the relative contributions of general language development, complement syntax, vocabulary, and executive function. However, the empirical studies so far have fallen short, in that they generally have too few participants for adequate statistical modeling; they do not include control variables; or they are cross-sectional rather than longitudinal, making inferences about causal direction much more tenuous. The present study considers the role of these different variables in the development of false belief reasoning over several months of testing, with 258 children aged three to five years. The children are also from under-resourced communities, broadening the populations that generally contribute such data. A cross-sectional and a longitudinal regression analysis reveals the contribution of each variable to the children's success on the false belief measures. Finally, a structural equation model tests the relative contribution of the different potential factors over time, how they interact, and change. The model is an excellent fit to the data. Inhibitory control, complement comprehension and vocabulary all have effects on false belief reasoning at the first time point (T1). However, at T3, the major proximal contribution is the child's comprehension of complements, though the longitudinal pathways of vocabulary and inhibitory control also pave the way. Our data confirm the specific contribution of complement syntax but also makes clear, as do training studies, that a certain amount of preparedness in vocabulary and in executive function skills is also necessary.

Proteomic changes upon treatment with semaglutide in individuals with obesity

Obesity and type 2 diabetes are prevalent chronic diseases effectively managed by semaglutide. Here we studied the effects of semaglutide on the circulating proteome using baseline and end-of-treatment serum samples from two phase 3 trials in participants with overweight or obesity, with or without diabetes: STEP 1 (n = 1,311) and STEP 2 (n = 645). We identified evidence supporting broad effects of semaglutide, implicating processes related to body weight regulation, glycemic control, lipid metabolism and inflammatory pathways. Several proteins were regulated with semaglutide, after accounting for changes in body weight and HbA1c at end of trial, suggesting effects of semaglutide on the proteome beyond weight loss and glucose lowering. A comparison of semaglutide with real-world proteomic profiles revealed potential benefits on disease-specific proteomic signatures including the downregulation of specific proteins associated with cardiovascular disease risk, supporting its reported effects of lowering cardiovascular disease risk and potential drug repurposing opportunities. This study showcases the potential of proteomics data gathered from randomized trials for providing insights into disease mechanisms and drug repurposing opportunities. These data also highlight the unmet need for, and importance of, examining proteomic changes in response to weight loss pharmacotherapy in future trials.

Convergence of orphan quality control pathways at a ubiquitin chain-elongating ligase

Convergence of orphan quality control pathways at a ubiquitin chain-elongating ligase

Alpha-Synuclein Effects on Mitochondrial Quality Control in Parkinson's Disease.

The maintenance of healthy mitochondria is essential for neuronal survival and relies upon mitochondrial quality control pathways involved in mitochondrial biogenesis, mitochondrial dynamics, and mitochondrial autophagy (mitophagy). Mitochondrial dysfunction is critically implicated in Parkinson's disease (PD), a brain disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra. Consequently, impaired mitochondrial quality control may play a key role in PD pathology. This is affirmed by work indicating that genes such as PRKN and PINK1, which participate in multiple mitochondrial processes, harbor PD-associated mutations. Furthermore, mitochondrial complex-I-inhibiting toxins like MPTP and rotenone are known to cause Parkinson-like symptoms. At the heart of PD is alpha-synuclein (αS), a small synaptic protein that misfolds and aggregates to form the disease's hallmark Lewy bodies. The specific mechanisms through which aggregated αS exerts its neurotoxicity are still unknown; however, given the vital role of both αS and mitochondria to PD, an understanding of how αS influences mitochondrial maintenance may be essential to elucidating PD pathogenesis and discovering future therapeutic targets. Here, the current knowledge of the relationship between αS and mitochondrial quality control pathways in PD is reviewed, highlighting recent findings regarding αS effects on mitochondrial biogenesis, dynamics, and autophagy.

Formyl-methionine-mediated eukaryotic ribosome quality control pathway for cold adaptation.

Protein synthesis in the eukaryotic cytosol can start using both conventional methionine and formyl-methionine (fMet). However, a mechanism, if such exists, for detecting and regulating the incorporation of fMet (instead of Met) during translation, thereby preventing cellular toxicity of nascent fMet-bearing (fMet-) polypeptides, remains unknown. Here, we describe the fMet-mediated ribosome quality control (fMet-RQC) pathway in Saccharomyces cerevisiae. A eukaryotic translation initiation factor 3 subunit c, Nip1, specifically recognizes N-terminal fMet in nascent polypeptides, recruiting a small GTPase, Arf1, to induce ribosome stalling, largely with 41-residue fMet-peptidyl tRNAs. This leads to ribosome dissociation and subsequent stress granule formation. Loss of the fMet-RQC pathway causes the continued synthesis of fMet polypeptides, which inhibits essential N-terminal Met modifications and promotes their coaggregation with ribosomes. This fMet-RQC pathway is important for the adaptation of yeast cells to cold stress by promoting stress granule formation and preventing a buildup of toxic fMet polypeptides.

Restoration of lysosomal function attenuates autophagic flux impairment in nucleus pulposus cells and protects against mechanical overloading-induced intervertebral disc degeneration

ABSTRACT Intervertebral disc degeneration (IVDD) is a leading cause of low back pain that incurs large socioeconomic burdens. Growing evidence reveals that macroautophagy/autophagy dysregulation contributes to IVDD, but the exact role of autophagy and its regulatory mechanisms remain largely unknown. Here, we found that mechanical overloading impaired the autophagic flux of nucleus pulposus (NP) cells in vivo and in vitro. Mechanistically, the impairment of autophagic flux was attributed to lysosomal dysfunction induced by overloading. Overloading could also lead to lysosomal membrane permeabilization and consequent lysosome-dependent cell death. As critical effectors of lysosomal quality control pathways, CHMP4B (charged multivesicular body protein 4B) and TFEB (transcription factor EB) were downregulated in overloading-treated NP cells and degenerative discs. Restoring lysosomal function by CHMP4B or TFEB overexpression attenuated autophagic flux impairment of NP cells and protected against overloading-induced IVDD. Additionally, human IVDD was associated with impaired autophagy, and defective lysosomal quality control was also linked to human IVDD. Collectively, these findings highlighted that lysosomal defects were crucial for mechanical overloading-induced autophagic flux impairment and death of NP cells, suggesting the potential therapeutic relevance of restoring lysosomal function for IVDD.

Challenges and coping strategies of cancer screening research and practice in China: Taking esophageal cancer as an example

For most cancers, clear intervention targets for primary prevention are lacking, due to unidentified high-risk causal factors. Consequently, the focus of cancer prevention and control in China has shifted towards early screening and treatment within the general population. This review outlines the significant challenges in research and practice of cancer prevention and control in China, including: ①inadequate understanding of the natural history of cancer; ② limited high-level evidence supporting cancer screening effectiveness and value; ③compromised efficiency and accuracy in current screening modality; and ④ insufficient universality and sustainability of the current screening practices, taking esophageal cancer as an example. To address these challenges, we propose potential coping strategies: ① establishing tailored technologies and pathways for cancer prevention and control based on population-based and clinical epidemiological studies using high-quality designs; ②breaking conventional constraints to establish a novel, efficient, and precision cancer screening strategy and modality that aligned with the frontline needs of cancer prevention and control; and ③establishing enhanced communication platforms among government policymaking departments, scientific research teams, and industrial institutions to foster collaboration and translation in the field of cancer prevention and control. Ultimately, through the collaboration of multiple disciplines and departments, we will jointly achieve the long-term goal of cancer prevention and treatment.

Insights into Dentatorubral-Pallidoluysian Atrophy from a new Drosophila model of disease.

Dentatorubral-pallidoluysian atrophy (DRPLA) is a neurodegenerative disorder that presents with ataxia, dementia and epilepsy. As a member of the polyglutamine family of diseases, DRPLA is caused by abnormal CAG triplet expansion beyond 48 repeats in the protein-coding region of ATROPHIN 1 (ATN1), a transcriptional co-repressor. To better understand DRPLA, we generated new Drosophila lines that express full-length, human ATN1 with a normal (Q7) or pathogenic (Q88) repeat. Expression of ATN1 is toxic, with the polyglutamine-expanded version being consistently more problematic than wild-type ATN1. Fly motility, longevity and internal structures are negatively impacted by pathogenic ATN1. RNA-seq identified altered protein quality control and immune pathways in the presence of pathogenic ATN1. Based on these data, we conducted genetic experiments that confirmed the role of protein quality control components that ameliorate or exacerbate ATN1 toxicity. Hsc70-3, a chaperone, arose as a likely suppressor of toxicity. VCP (a proteasome-related AAA ATPase), Rpn11 (a proteasome-related deubiquitinase) and select DnaJ proteins (co-chaperones) were inconsistently protective, depending on the tissues where they were expressed. Lastly, informed by RNA-seq data that exercise-related genes may also be involved in this model of DRPLA, we conducted short-term exercise, which improved overall fly motility. This new model of DRPLA will prove important to understanding this understudied disease and will help to identify therapeutic targets for it.

Exploring the Link between Premature Ovarian Insufficiency, Insomnia and Circadian Pathways.

To establish an interaction network for genes related to premature ovarian insufficiency (POI) and insomnia, and to identify biological processes that connect POI to the physiological clock. Previously reported lists of genes associated to POI and insomnia were contrasted and their intersection was used as input on protein-protein interaction analyses. POI-associated genes were contrasted with gene expression markers for neural circadian control and enriched pathways among their shared content were dissected. The functional network generated from the intersection between POI and insomnia gene lists pointed to the central nervous system as the most relevant cellular context for this connection. After identifying POI-associated genes that play a role in neural circadian patterns, we observed the disruption of pathways related to the hypothalamic-pituitary-gonadal axis as the major genetic link between ovarian function and circadian neural circuits. These findings highlight neurological mechanisms that support the POI-insomnia interplay.

Interferon gamma-mediated prevention of tumor progression in a mouse model of multiple myeloma.

Malignant plasma cells in multiple myeloma patients reside in the bone marrow and continuously interact with local immune cells. Progression and therapy response are influenced by this immune environment, highlighting the need for a detailed understanding of endogenous immune responses to malignant plasma cells. Here we used the 5TGM1 murine transfer model of multiple myeloma to dissect early immune responses to myeloma cells. We modeled stable and progressive disease by transferring 5TGM1 murine myeloma cells into C57Bl/6 mice and KaLwRij mice, respectively. We used flow cytometry and single-cell and bulk transcriptomic analyses to characterize differential immune responses in stable and progressive disease. Transfer of 5TGM1 cells in C57Bl/6 mice led to stable disease with low tumor burden in a subset of animals. Stable disease was associated with sustained activation and expansion of NK cells, ILC1, and CD8+ T cells, a response that was lost upon disease progression. Single-cell RNA-sequencing of immune cells and bulk RNA sequencing of immune and mesenchymal stromal cells implicated the activation of interferon responses as a central immune pathway during stable disease. Experimentally, neutralization of IFNγ significantly increased myeloma development and progression in C57Bl/6 mice, testifying to the importance of this pathway in early disease control. In conclusion, we provide a framework for studying immune responses to multiple myeloma progression in immunocompetent and genetically modifiable mice and highlight the importance of bone marrow immunity in tumor control.

Are the knowledge, tools and resources to control foot and mouth disease available?

Foot and mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed animals. Together with other diseases highlighted in this special edition of the Scientific and Technical Review, the circulation of FMD virus in different parts of the world has shaped the work of the World Organisation for Animal Health (WOAH) over the past hundred years. In 2012, the Global Framework for the Progressive Control of Transboundary Animal Diseases, led by WOAH and the Food and Agriculture Organization of the United Nations, established a joint FMD working group and a strategy for the control of FMD. Control of FMD requires political commitment to deliver the sustained investment and deploy the resources required to break the cycle of infection. This article highlights recent improvements in diagnostic and genomic tools, as well as new vaccine platform technologies that, if strategically deployed, have the potential to improve the control of this disease. The article also reflects on global and regional initiatives using the Progressive Control Pathway for FMD, which remains relevant and has wider positive benefits for the control of other transboundary animal diseases.

Cellular Regulation and Oncogenesis of Primary Tumors in the Central Nervous System

AbstractThe World Health Organization's system for classifying and grading primary tumors of the Central Nervous System conjectures the clinical-biological course of the oncogenic process based on morphological, genetic, histological, and immunohistochemical parameters. These principles are fundamental for a progression in the classification of these tumors, to guarantee the promotion of a more precise diagnosis. In this sense, it is important to understand the process of oncotic cell formation, which is the result of mutations in intra and extracellular control pathways. In this way, genes that act to induce the cell cycle, under normal conditions, when mutated, can result in a dysregulation of the progress of the cycle, causing alterations in the control factors and, consequently, phenotypic transformations in the cell. Thus, to understand the role of genes in modulating primary tumors in the Central Nervous System, mutations in the genes most prevalently related to Gliomas, Meningiomas, and Medulloblastomas were addressed highlighting their influences on the development of these tumors.