Sugar phosphate activation of the stress sensor eIF2B

The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.

The activity of translation initiation factor eIF2B is known to be modulated through stress-responsive phosphorylation of its substrate eIF2. Here, the authors uncover the regulation of eIF2B by the binding of sugar phosphates, suggesting a link between nutrient status and the rate of protein synthesis.

Quantitative intravital imaging in zebrafish reveals in vivo dynamics of physiological-stress-induced mitophagy

Mitophagy, the selective recycling of mitochondria through autophagy, is a crucial metabolic process induced by cellular stress, and defects are linked to aging, sarcopenia and neurodegenerative diseases. To therapeutically target mitophagy, the fundamental in vivo dynamics and molecular mechanisms must be fully understood. Here, we generated mitophagy biosensor zebrafish lines expressing mitochondrially targeted, pH-sensitive fluorescent probes, mito-Keima and mito-EGFP-mCherry, and used quantitative intravital imaging to illuminate mitophagy during physiological stresses, namely, embryonic development, fasting and hypoxia. In fasted muscle, volumetric mitolysosome size analyses documented organelle stress response dynamics, and time-lapse imaging revealed that mitochondrial filaments undergo piecemeal fragmentation and recycling rather than the wholesale turnover observed in cultured cells. Hypoxia-inducible factor (Hif) pathway activation through physiological hypoxia or chemical or genetic modulation also provoked mitophagy. Intriguingly, mutation of a single mitophagy receptor (bnip3) prevented this effect, whereas disruption of other putative hypoxia-associated mitophagy genes [bnip3la (nix), fundc1, pink1 or prkn (Parkin)] had no effect. This in vivo imaging study establishes fundamental dynamics of fasting-induced mitophagy and identifies bnip3 as the master regulator of Hif-induced mitophagy in vertebrate muscle.

Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy

The PINK1 protein kinase activates the PARK2 ubiquitin ligase to promote mitochondrial ubiquitylation and recruitment of ubiquitin-binding mitophagy receptors typified by OPTN and TAX1BP1. Here, we combine proximity biotinylation of OPTN and TAX1BP1 with CRISPR-Cas9-based screens for mitophagic flux to develop a spatial proteogenetic map of PARK2-dependent mitophagy. Proximity labeling of OPTN allowed visualization of a "mitochondrial-autophagosome synapse" upon mitochondrial depolarization. Proximity proteomics of OPTN and TAX1BP1 revealed numerous proteins at the synapse, including both PARK2 substrates and autophagy components. Parallel mitophagic flux screens identified proteins with roles in autophagy, vesicle formation and fusion, as well as PARK2 targets, many of which were also identified via proximity proteomics. One protein identified in both approaches, HK2, promotes assembly of a high-molecular weight complex of PINK1 and phosphorylation of ubiquitin in response to mitochondrial damage. This work provides a resource for understanding the spatial and molecular landscape of PARK2-dependent mitophagy.

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies

Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.

Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics

Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.

Evaluation of sulphur amino acid requirement of male Korean native ducklings from hatch to 21 day of age

1. A dose-response experiment was conducted with male Korean native ducklings (KND) to evaluate the total sulphur amino acid (TSAA) requirement from hatch to 21 d of age. 2. A completely randomised design with 7 dietary TSAA concentrations (0.62%, 0.65%, 0.68%, 0.71%, 0.74%, 0.77% and 0.80%) were used with 6 replications per treatment. 3. Body weight (BW) and feed intake were measured weekly to calculate average daily gain (ADG), average daily feed intake (ADFI) and feed conversion ratio (FCR). One duckling per pen (n = 6) was killed by cervical dislocation to weigh empty body and drumsticks at the conclusion of experiment. 4. BW was improved significantly with increasing TSAA content, in a non-linear manner. A significant decrease of FCR was shown with increasing TSAA contents. TSAA requirement was determined by taking a mean value after fitting the data to both a linear-plateau and a quadratic-plateau model. Estimated TSAA requirements were 0.70%, 0.70%, 0.66% and 0.70% for the maximum BW, ADG and ADFI and for the minimum FCR, respectively. Increasing TSAA content improved quantity of full body weight (FBW), empty body weight (EBW) and drumstick weight (DSW), but there was no effect on proportion of DSW in relation to EBW and proportion of EBW to FBW. 5. In conclusion, the growth of male KND during 1 to 21 d of age was improved with increasing TSAA content, suggesting optimal TSAA requirements estimated by two analysis models.

True and standardized total tract phosphorus digestibility in canola meals from Brassica napus black and Brassica juncea yellow fed to growing pigs

The aim was to determine the true total tract digestibility (TTTD) and standardized total tract digestibility (STTD) of P in canola meals from Brassica napus black (BNB) and Brassica juncea yellow (BJY) fed to growing pigs. Fifty-four barrows with an initial BW of 19.9 ± 0.22 kg (mean ± SEM) were allocated in 3 consecutive blocks to 1 of 9 dietary treatments in a randomized complete block design to give 6 replicate pigs per diet. Dietary treatments were cornstarch based with increasing concentrations of P, that is, 0.8, 1.6, 2.4, and 3.3 g/kg (as-fed basis) from either BNB or BJY as the sole source of P and a gelatin-based P-free diet. Limestone was added to maintain a Ca:total P ratio of 1.2:1 in all diets. All diets contained titanium dioxide (3 g/kg) as an indigestible marker. Daily feed allowance was calculated to supply 2.6 times the maintenance energy requirement based on the BW at the beginning of each period and offered in 2 equal portions at 0800 and 1600 h as a dry mash. Pigs were individually housed in metabolism crates and fed experimental diets for 16 d, including 9 d for adaptation to feed and 5 d for total but separate collection of feces and urine. The apparent total tract digestibility values of P increased from 19.0 to 30.0% for BNB and from 17.3 to 28.3% for BJY as the dietary P content increased from 0.8 to 3.3 g/kg DM. The TTTD of P was determined using the regression analysis as dietary P content increased from 0.8 to 3.3 g/kg whereas the STTD of P was calculated for the diet with the highest P content (i.e., 3.3 g/kg, as-fed basis) using the P-free diet to estimate endogenous P losses (EPL). The total and basal EPL estimates obtained with regression analysis and the P-free diet were 665 ± 0.03 and 209 ± 96 mg/kg DMI, respectively. The TTTD of P was 33.3 and 32.0% in BNB and BJY, respectively. Respective STTD values were 31.0 and 28.3%. The results indicated that the TTTD and STTD of P were comparable in the 2 canola meals from BNB and BJY canola.

The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy

Damaged mitochondria are detrimental to cellular homeostasis. One mechanism for removal of damaged mitochondria involves the PINK1-PARKIN pathway, which poly-ubiquitylates damaged mitochondria to promote mitophagy. We report that assembly of ubiquitin chains on mitochondria triggers autophagy adaptor recruitment concomitantly with activation of the TBK1 kinase, which physically associates with OPTN, NDP52, and SQSTM1. TBK1 activation in HeLa cells requires OPTN and NDP52 and OPTN ubiquitin chain binding. In addition to the known role of S177 phosphorylation in OPTN on ATG8 recruitment, TBK1-dependent phosphorylation on S473 and S513 promotes ubiquitin chain binding in vitro as well as TBK1 activation, OPTN mitochondrial retention, and efficient mitophagy in vivo. These data reveal a self-reinforcing positive feedback mechanism that coordinates TBK1-dependent autophagy adaptor phosphorylation with the assembly of ubiquitin chains on mitochondria to facilitate efficient mitophagy, and mechanistically links genes mutated in Parkinson's disease and amyotrophic lateral sclerosis in a common selective autophagy pathway.

Net energy content of dry extruded-expelled soybean meal fed with or without enzyme supplementation to growing pigs as determined by indirect calorimetry

Two experiments were conducted to determine the NE content of dry extruded-expelled soybean (DESBM) and the effect of a multienzyme carbohydrase (MC) mixture on the NE content of DESBM and to determine the effect of diet design on NE values in growing pigs using indirect calorimetry (IC). In Exp. 1, 24 barrows (19.6 ± 0.51 kg BW) were allotted in a completely randomized design to 4 dietary treatments: a corn–soybean meal basal diet (Diet A), a diet containing Diet A and DESBM in an 80:20 ratio with a constant CP (Diet B), a diet with an 80:20 ratio of Diet A and DESBM with a constant corn:soybean meal ratio (Diet C), and a diet with simple substitution of Diet A with DESBM in an 80:20 ratio (Diet D). Pigs were fed in metabolism crates for a period of 16 d to determine the DE and ME and thereafter were moved into an indirect calorimeter where O2 consumption and CO2 production were measured to determine heat production and fasting heat production. The NE content of DESBM was calculated (difference method) to be 2,632, 2,548 and 2,540 kcal/kg DM in diets B, C, and D, respectively. Respective values obtained with published prediction equations were 2,624, 2,530 and 2,436 kcal/kg. In Exp. 2, 24 barrows (16.9 ± 0.76 kg BW) were randomly allotted to 1 of 4 treatments. The diets were a corn–soybean meal basal diet and a diet containing the basal diet and DESBM in an 80:20 ratio with a constant corn:soybean meal ratio with or without 2 levels (0.05% and 0.1%) of MC. The experimental procedures were similar to those described in Exp. 1. Enzyme supplementation improved (P < 0.0001) the DE, ME, and NE content of the DESBM. Multienzyme carbohydrase at 0.05% and 0.1% of the diet improved NE values of DESBM by 4.9% and 3.7%, respectively. In conclusion, the NE values of DESBM obtained with the IC method were higher than the values obtained with prediction equations; the disparity was least when diets were formulated with a constant CP level. However, as the difference method was used to determine the NE of ingredient, it is more appropriate to maintain a constant ratio between the ingredients. Also, the NE value of DESBM obtained for diets C and D were not different. Hence, the average NE value of DESBM evaluated was 2,544 kcal/kg DM. Enzyme supplementation improved the NE content of DESBM fed to growing pigs.

Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis

Phosphorylation is often used to promote protein ubiquitylation, yet we rarely understand quantitatively how ligase activation and ubiquitin (UB) chain assembly are integrated with phosphoregulation. Here we employ quantitative proteomics and live-cell imaging to dissect individual steps in the PINK1 kinase-PARKIN UB ligase mitochondrial control pathway disrupted in Parkinson's disease. PINK1 plays a dual role by phosphorylating PARKIN on its UB-like domain and poly-UB chains on mitochondria. PARKIN activation by PINK1 produces canonical and noncanonical UB chains on mitochondria, and PARKIN-dependent chain assembly is required for accumulation of poly-phospho-UB (poly-p-UB) on mitochondria. In vitro, PINK1 directly activates PARKIN's ability to assemble canonical and noncanonical UB chains and promotes association of PARKIN with both p-UB and poly-p-UB. Our data reveal a feedforward mechanism that explains how PINK1 phosphorylation of both PARKIN and poly-UB chains synthesized by PARKIN drives a program of PARKIN recruitment and mitochondrial ubiquitylation in response to mitochondrial damage.

Nutrient digestibility and growth performance of pigs fed diets with different levels of canola meal from Brassica napus black and Brassica juncea yellow

Nutrient digestibility and the effect of high dietary inclusion of canola meals from Brassica napus black (BNB) and Brassica juncea yellow (BJY) on growing and weaned pigs performance were determined. In Exp.1, 6 ileal cannulated barrows (initial BW = 20.7 ± 1.5 kg) were used to determine the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of AA in BNB and BJY. Pigs were allotted to diets containing either BNB or BJY as the sole source of protein in a crossover design to give 6 replicates per diet. The SID of all AA in BNB and BJY were similar. In Exp. 2, 168 weaned pigs (initial BW = 7.61 ± 0.76 kg) were assigned in a randomized complete block design to 7 diets (n = 24) consisting of a wheat-soybean meal-based control diet and 6 diets containing 5, 10 or 15% of canola meal derived from either BNB or BJY to determine the effect of different dietary inclusion on growth performance over a 28-d period postweaning. Diets were formulated to contain similar NE and SID of Lys. There were no differences in growth performance among treatments. In Exp. 3, 162 weaned pigs (initial BW = 7.26 ± 0.70 kg) were used to determine the effect of high BNB and BJY inclusion level without or with multicarbohydrase supplementation on growth performance and apparent total tract digestibility (ATTD) of CP, DM, and GE. A wheat-soybean meal-based control diet and 8 diets containing 20 and 25% of either BNB or BJY without or with added multi-carbohydrase were formulated (n = 18) to contain comparable NE and similar SID of Lys contents. Feeding the diets containing 25% of BNB or BJY supported similar growth performance as those containing 20%. The multi-carbohydrase had no effect on growth performance but improved (P < 0.05) the ATTD of DM, CP, and GE compared with those fed nonsupplemented diets irrespective of canola meal type. Diets containing 25% canola meal had lower (P < 0.05) ATTD of DM, CP, and GE regardless of canola meal type compared with the 20% canola meal diets. There was an interaction (P < 0.05) between canola meal type and inclusion level on ATTD of DM in which ATTD of DM decreased with increasing inclusion of both canola meal types. Results of the current study indicate that both BNB and BJY can be included up to 25% in weaned pig diets without compromising performance as long as the diets are formulated on an NE and SID of Lys basis. Also, enzyme addition improved the ATTD of CP, DM, and GE in weaned pigs in both BNB and BJY diets.

Feeding a diet containing resistant potato starch influences gastrointestinal tract traits and growth performance of weaned pigs

The aim was to evaluate the effects of feeding resistant potato starch (RPS) as a natural source of resistant starch to weaned pigs for 28 d immediately after weaning. Sixty piglets (Yorkshire-Landrace × Duroc) weaned at 21 ± 2 d (1:1 male:female) with an initial BW of 7.2 ± 0.78 kg were assigned in a completely randomized design to 1 of 5 dietary treatments to give 6 observations per treatment and 2 pigs per pen. Dietary treatments consisted of a negative control corn-soybean meal-wheat-wheat middlings-based diet (NC; no antimicrobial agents added) or the NC supplemented with RPS either as powder or in capsules and each included at 0.5 or 1.0% as a top-dressing on each day. Diets were formulated to meet 1998 NRC specifications. Pigs were offered the experimental diets on an ad libitum basis for 28 d and water was available at all times. The ADG, ADFI, and G:F were determined weekly. Fecal score was determined daily for 14 d after weaning. At the conclusion of study, 1 pig from each pen was randomly selected and euthanized (n = 6 per treatment) to determine visceral organ weight, digesta pH, VFA, and ammonia N (NH3-N) concentrations. Resistant potato starch supplementation improved (P < 0.001) fecal score, and pigs offered 1.0% RPS had more solid feces (P < 0.05) than those offered 0.5% RPS during the first 14 d after weaning, independent of the form of RPS. Resistant potato starch supplementation decreased (P < 0.05) ileal and cecal digesta pH regardless of the levels of RPS or mode of delivery. The total VFA concentrations in cecal digesta were greater (P < 0.05) but the molar proportion of branched-chain fatty acids were lower (P < 0.05) for pigs fed the RPS-containing diets compared with those fed the NC, irrespective of the RPS levels or the form of RPS. However, there were no differences (P > 0.10) in visceral organ weights, growth performance, and digestibilities of DM, CP, Ca, and P among treatments. The results of this experiment indicate that supplementing a weaner pig diet with at least 0.5% RPS independent of mode of delivery has the potential to enhance outcomes characteristic of a functional gut in weaned pigs without adverse effects on growth.

Standardized ileal amino acid digestibility in egg from hyperimmunized hens fed to weaned pigs

The study was conducted to determine the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of AA in egg from hens hyperimmunized with Escherichia coli K88 antigens (EGG) fed to weaned pigs. Spray dried porcine plasma (SDPP) was included for comparison. Eight barrows (Yorkshire-Landrace × Duroc; initial BW of 17 ± 1 kg) were fitted with a T-cannula at the distal ileum and fed 2 diets in a completely randomized design to give 4 replicates per diet. The diets were corn (Zea mays) starch based with either EGG or SDPP as the sole source of protein and were formulated to contain 130 g/kg CP. At the end of the study, a 50 g/kg casein diet was fed to all pigs (n = 8) to quantify endogenous N and AA losses to determine SID. Titanium dioxide (3 g/kg) was included in the diets as an indigestible maker. Each period lasted for 7 d. Pigs were adapted to their respective diets for 5 d followed by 12 h of continuous ileal digesta collection on days 6 and 7. Daily feed allowance was set at 4% BW at the beginning of each period and offered in 2 equal portions at 0800 and 1600 h as a dry mash. Pigs had unlimited access to water via low pressure nipple drinkers. The AID (%) of CP and indispensable AA were lower (P < 0.05) in EGG compared with SDPP. The SID (%) of CP (82 vs. 96) and indispensable AA were lower (P < 0.05) in pigs fed EGG compared with SDPP. In conclusion, the average AID and SID of N and indispensable AA in EGG are lower than in SDPP when fed at high levels.

Intramolecular interactions control Vms1 translocation to damaged mitochondria

Mitochondrial dysfunction is associated with the development of many age-related human diseases. Therefore recognizing and correcting the early signs of malfunctioning mitochondria is of critical importance for cellular welfare and survival. We previously demonstrated that VCP/Cdc48-associated mitochondrial stress responsive 1 (Vms1) is a component of a mitochondrial surveillance system that mediates the stress-responsive degradation of mitochondrial proteins by the proteasome. Here we propose novel mechanisms through which Vms1 monitors the status of mitochondria and is recruited to damaged or stressed mitochondria. We find that Vms1 contains a highly conserved region that is necessary and sufficient for mitochondrial targeting (the mitochondrial targeting domain [MTD]). Of interest, MTD-mediated mitochondrial targeting of Vms1 is negatively regulated by a direct interaction with the Vms1 N-terminus. Using laser-induced generation of mitochondrial reactive oxygen species, we also show that Vms1 is preferentially recruited to mitochondria subjected to oxidative stress. These studies define cellular and biochemical mechanisms by which Vms1 locali-zation to mitochondria is controlled to enable an efficient protein quality control system.

Gastrointestinal health and function in weaned pigs: a review of feeding strategies to control post-weaning diarrhoea without using in-feed antimicrobial compounds

For the last several decades, antimicrobial compounds have been used to promote piglet growth at weaning through the prevention of subclinical and clinical disease. There are, however, increasing concerns in relation to the development of antibiotic-resistant bacterial strains and the potential of these and associated resistance genes to impact on human health. As a consequence, European Union (EU) banned the use of antibiotics as growth promoters in swine and livestock production on 1 January 2006. Furthermore, minerals such as zinc (Zn) and copper (Cu) are not feasible alternatives/replacements to antibiotics because their excretion is a possible threat to the environment. Consequently, there is a need to develop feeding programs to serve as a means for controlling problems associated with the weaning transition without using antimicrobial compounds. This review, therefore, is focused on some of nutritional strategies that are known to improve structure and function of gastrointestinal tract and (or) promote post-weaning growth with special emphasis on probiotics, prebiotics, organic acids, trace minerals and dietary protein source and level.

Identification of a protein mediating respiratory supercomplex stability

The complexes of the electron transport chain associate into large macromolecular assemblies, which are believed to facilitate efficient electron flow. We have identified a conserved mitochondrial protein, named respiratory supercomplex factor 1 (Rcf1-Yml030w), that is required for the normal assembly of respiratory supercomplexes. We demonstrate that Rcf1 stably and independently associates with both Complex III and Complex IV of the electron transport chain. Deletion of the RCF1 gene caused impaired respiration, probably as a result of destabilization of respiratory supercomplexes. Consistent with the hypothetical function of these respiratory assemblies, loss of RCF1 caused elevated mitochondrial oxidative stress and damage. Finally, we show that knockdown of HIG2A, a mammalian homolog of RCF1, causes impaired supercomplex formation. We suggest that Rcf1 is a member of an evolutionarily conserved protein family that acts to promote respiratory supercomplex assembly and activity.

Ubiquitin-dependent mitochondrial protein degradation

Progressive mitochondrial failure is tightly associated with the onset of many age-related human pathologies. This tight connection results from the double-edged sword of mitochondrial respiration, which is responsible for generating both ATP and ROS, as well as from risks that are inherent to mitochondrial biogenesis. To prevent and treat these diseases, a precise understanding of the mechanisms that maintain functional mitochondria is necessary. Mitochondrial protein quality control is one of the mechanisms that protect mitochondrial integrity, and increasing evidence implicates the cytosolic ubiquitin/proteasome system (UPS) as part of this surveillance network. In this review, we will discuss our current understanding of UPS-dependent mitochondrial protein degradation, its roles in diseases progression, and insights into future studies.

Infestation status of head louse and treatment with lindane shampoo in children of primary school and kindergarten in Chinju-shi, Kyongsangnam-do, Korea

The infestation status of head louse among children attending primary schools and kindergartens in Chinju-shi, Kyongsangnam-do, Korea, was investigated between June and July 1999. Out of 2,288 children examined, 3.9% of boys (48/1,242) and 23.5% of girls (246/1,046) were infested with nits or adult/nymphs of lice. The effectiveness of lindane shampoo (1% gamma benzene hexachloride solution) was evaluated after one or two time applications to all the children infested. The negative conversion rate of pediculosis was 93.5%. Effective control measures are needed to control and prevent such ectoparasite infestation amongst children.