Activation loop phosphorylation regulates B‐Raf in vivo and transformation by B‐Raf mutants

Despite being mutated in cancer and RASopathies, the role of the activation segment (AS) has not been addressed for B‐Raf signaling in vivo. Here, we generated a conditional knock‐in mouse allowing the expression of the B‐Raf^AVKA mutant in which the AS phosphoacceptor sites T599 and S602 are replaced by alanine residues. Surprisingly, despite producing a kinase‐impaired protein, the Braf^AVKA allele does not phenocopy the lethality of Braf‐knockout or paradoxically acting knock‐in alleles. However, Braf^AVKA mice display abnormalities in the hematopoietic system, a distinct facial morphology, reduced ERK pathway activity in the brain, and an abnormal gait. This phenotype suggests that maximum B‐Raf activity is required for the proper development, function, and maintenance of certain cell populations. By establishing conditional murine embryonic fibroblast cultures, we further show that MEK/ERK phosphorylation and the immediate early gene response toward growth factors are impaired in the presence of B‐Raf^AVKA. Importantly, alanine substitution of T599/S602 impairs the transformation potential of oncogenic non‐V600E B‐Raf mutants and a fusion protein, suggesting that blocking their phosphorylation could represent an alternative strategy to ATP‐competitive inhibitors.     

Stimulation of autophagy suppresses the intracellular survival of Burkholderia pseudomallei in mammalian cell lines

Burkholderia pseudomallei is the causative agent of melioidosis, a tropical infection of humans and other animals. The bacterium is an intracellular pathogen that can escape from endosomes into the host cytoplasm, where it replicates and infects adjacent cells. We investigated the role played by autophagy in the intracellular survival of B. pseudomallei in phagocytic and non-phagocytic cell lines. Autophagy was induced in response to B. pseudomallei invasion of murine macrophage (RAW 264.7) cells and a proportion of the bacteria co-localized with the autophagy effector protein LC3, a marker for autophagosome formation. Pharmacological stimulation of autophagy in RAW 264.7 and murine embryonic fibroblast (MEF) cell lines resulted in increased co-localization of B. pseudomallei with LC3 while basal levels of co-localization could be abrogated using inhibitors of the autophagic pathway. Furthermore, induction of autophagy decreased the intracellular survival of B. pseudomallei in these cell lines, but bacterial survival was not affected in MEF cell lines deficient in autophagy. Treatment of infected macrophages with chloramphenicol increased the proportion of bacteria within autophagosomes indicating that autophagic evasion is an active process relying on bacterial protein synthesis. Consistent with this hypothesis, we identified a B. pseudomallei type III secreted protein, BopA, which plays a role in mediating bacterial evasion of autophagy. We conclude that the autophagic pathway is a component of the innate defense system against invading B. pseudomallei, but which the bacteria can actively evade. However, when autophagy is pharmacologically induced using rapamycin, bacteria are actively sequestered in autophagosomes, ultimately decreasing their survival.     

ER-localized phosphatidylethanolamine synthase plays a conserved role in lipid droplet formation

The asymmetric distribution of phospholipids in membranes is a fundamental principle of cellular compartmentalization and organization. Phosphatidylethanolamine (PE), a nonbilayer phospholipid that contributes to organelle shape and function, is synthesized at several subcellular localizations via semiredundant pathways. Previously, we demonstrated in budding yeast that the PE synthase Psd1, which primarily operates on the mitochondrial inner membrane, is additionally targeted to the ER. While ER-localized Psd1 is required to support cellular growth in the absence of redundant pathways, its physiological function is unclear. We now demonstrate that ER-localized Psd1 sublocalizes on the ER to lipid droplet (LD) attachment sites and show it is specifically required for normal LD formation. We also find that the role of phosphatidylserine decarboxylase (PSD) enzymes in LD formation is conserved in other organisms. Thus we have identified PSD enzymes as novel regulators of LDs and demonstrate that both mitochondria and LDs in yeast are organized and shaped by the spatial positioning of a single PE synthesis enzyme.     

Malnutrition is Common and Increases the Risk of Adverse Medical Events in Older Adults With Femoral Fragility Fractures

BackgroundFemoral fragility fractures are one of the most common injuries managed by orthopedic surgeons. Malnutrition influences the poor outcomes observed in this population. Our purpose was to assess the annual trends of malnutrition diagnosis and determine risk factors for malnutrition and complications in patients 65 years and older presenting with femoral fragility fractures. We hypothesized that malnutrition would increase the risk of postoperative wound infection, wound dehiscence, non-union, and mortality.MethodsThe PearlDiver database was reviewed from 2010 to 2020. Patients ≥ 65-years-old with femur fractures treated with operative fixation were identified by CPT code. A preoperative diagnosis of malnourished state was defined by ICD-9 and ICD-10 codes and patients were divided into malnourished and non-malnourished cohorts. Patients were tracked for one year following operative fixation of a femoral fragility fracture for the occurrence of infection, wound dehiscence, nonunion and mortality. The rates of these complications were compared between malnourished and nonmalnourished cohorts.ResultsThere were 178,283 total femoral fragility fractures identified in patients aged 65-years or older. The overall prevalence of malnutrition diagnosis in this geriatric population was 12.8%. Documented malnutrition in femoral fragility fractures increased from 1.6% to 32.9% from 2010-2020 (P<0.0001). Compared to patients without malnutrition, patients with malnutrition are at increased risk of mortality (OR 1.31, 95% CI 1.2558 – 1.3752, p < 0.0001), are more likely to develop a wound infection (OR 1.49; 95% CI 1.252 – 1.7626; p < 0.0001), more likely to have a wound dehiscence (OR 1.55; 95% CI 1.3416 – 1.7949; p < 0.0001), and more likely to develop non-union (1.89; 95% CI 1.6946 – 2.1095; p < 0.0001). Multiple demographic variables were associated with malnutrition diagnosis including higher age, higher Charlson Comorbidity Index, female sex, dementia, and institutionalization. Parkinson’s disease, feeding difficulty and institutionalization demographic variables had the highest risk of malnutrition.ConclusionThe current study found that malnutrition diagnosis significantly increases the risk of adverse medical events in elderly adults with femoral fragility fractures. The rates of malnutrition increased steadily from 2010-2020. This trend is likely a result of increased awareness and testing for malnutrition, not reflecting an actual increased prevalence of malnutrition. Multiple expected demographic variables are associated with diagnosis of malnutrition. Level of Evidence: III     

Metagenomics versus total RNA sequencing: most accurate data-processing tools,microbial identification accuracy and perspectives for ecological assessments

Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.     

Activation of a PGC-1-related Coactivator (PRC)-dependent Inflammatory Stress Program Linked to Apoptosis and Premature Senescence

PGC-1-related coactivator (PRC), a growth-regulated member of the PGC-1 coactivator family, contributes to the expression of the mitochondrial respiratory apparatus. PRC also orchestrates a robust response to metabolic stress by promoting the expression of multiple genes specifying inflammation, proliferation, and metabolic reprogramming. Here, we demonstrate that this PRC-dependent stress program is activated during apoptosis and senescence, two major protective mechanisms against cellular dysfunction. Both PRC and its targets (IL1α, SPRR2D, and SPRR2F) were rapidly induced by menadione, an agent that promotes apoptosis through the generation of intracellular oxidants. Menadione-induced apoptosis and the PRC stress program were blocked by the antioxidant N-acetylcysteine. The PRC stress response was also activated by the topoisomerase I inhibitor 7-ethyl-10-hydroxycamptothecin (SN-38), an inducer of premature senescence in tumor cells. Cells treated with SN-38 displayed morphological characteristics of senescence and express senescence-associated β-galactosidase activity. In contrast to menadione, the SN-38 induction of the PRC program occurred over an extended time course and was antioxidant-insensitive. The potential adaptive function of the PRC stress response was investigated by treating cells with meclizine, a drug that promotes glycolytic energy metabolism and has been linked to cardio- and neuroprotection against ischemia-reperfusion injury. Meclizine increased lactate production and was a potent inducer of the PRC stress program, suggesting that PRC may contribute to the protective effects of meclizine. Finally, c-MYC and PRC were coordinately induced under all conditions tested, implicating c-MYC in the biological response to metabolic stress. The results suggest a general role for PRC in the adaptive response to cellular dysfunction.     

Effects of corticosterone and amyloid-beta on proteins essential for synaptic function: Implications for depression and Alzheimer's disease

The relationship between Alzheimer's disease (AD) and depression has been well established in terms of epidemiological and clinical observations. Depression has been considered to be both a symptom and risk factor of AD. Several genetic and neurobiological mechanisms have been described to underlie these two disorders. Despite the accumulating knowledge on this topic, the precise neuropathological mechanisms remain to be elucidated. In this study, we propose that synaptic degeneration plays an important role in the disease progression of depression and AD. Using primary culture of hippocampal neurons treated with oligomeric Aβ and corticosterone as model agents for AD and depression, respectively, we found significant changes in the pre-synaptic vesicle proteins synaptophysin and synaptotagmin. We further investigated whether the observed protein changes affected synaptic functions. By using FM^®4-64 fluorescent probe, we showed that synaptic functions were compromised in treated neurons. Our findings led us to investigate the involvement of protein degradation mechanisms in mediating the observed synaptic protein abnormalities, namely, the ubiquitin–proteasome system and autophagy. We found up-regulation of ubiquitin-mediated protein degradation, and the preferential signaling for the autophagic–lysosomal degradation pathway. Lastly, we investigated the neuroprotective role of different classes of antidepressants. Our findings demonstrated that the antidepressants Imipramine and Escitalopram were able to rescue the observed synaptic protein damage. In conclusion, our study shows that synaptic degeneration is an important common denominator underlying depression and AD, and alleviation of this pathology by antidepressants may be therapeutically beneficial.     

Regulation of ripening and opportunities for control in tomato and other fruits

Fruits are an important part of a healthy diet. They provide essential vitamins and minerals, and their consumption is associated with a reduced risk of heart disease and certain cancers. These important plant products can, however, be expensive to purchase, may be of disappointing quality and often have a short shelf life. A major challenge for crop improvement in fleshy fruit species is the enhancement of their health‐promoting attributes while improving quality and reducing postharvest waste. To achieve these aims, a sound mechanistic understanding of the processes involved in fruit development and ripening is needed. In recent years, substantial insights have been made into the mechanistic basis of ethylene biosynthesis, perception and signalling and the identity of master regulators of ripening that operate upstream of, or in concert with a regulatory pathway mediated by this plant hormone. The role of other plant hormones in the ripening process has, however, remained elusive, and the links between regulators and downstream processes are still poorly understood. In this review, we focus on tomato as a model for fleshy fruit and provide an overview of the molecular circuits known to be involved in ripening, especially those controlling pigment accumulation and texture changes. We then discuss how this information can be used to understand ripening in other fleshy fruit‐bearing species. Recent developments in comparative genomics and systems biology approaches are discussed. The potential role of epigenetic changes in generating useful variation is highlighted along with opportunities for enhancing the level of metabolites that have a beneficial effect on human health.