Inactivation of ntcA gene revealed differential proteome expression and induction of some hypothetical proteins in the cyanobacterium Anabaena sp. PCC 7120 and its derivative ntcA mutant under different levels of calcium

Abstract

Calcium is an important macronutrient for both prokaryotes and eukaryotes. It acts as an important second messenger mediating rapid response to environmental conditions. The present investigation deals with proteome profiling of Anabaena 7120 and its derivative ntcA mutant in response to varied calcium doses (0, 1 and 10?mM CaCl₂). Concentration of 1?mM CaCl₂ salt was the optimum concentration whereas 10?mM CaCl₂ was the inhibitory concentration for both the wild type and mutant strains. The results showed highly significant alteration in terms of protein abundance and differential response related to key processes of photosynthesis, energy and metabolism, nitrogen metabolism, oxidative and antioxidative defence, transport and signalling and fatty acid metabolism. In the wild type proteins related to photosynthesis and nitrogen metabolism showed upregulation at 1?mM CaCl₂ concentration while antioxidative defence related proteins were down-regulated. In the mutant however, proteins related to photosynthesis and nitrogen metabolism exhibited severe down-regulation. Some hypothetical proteins were also realized during proteome analysis. Overall, our results suggested that NtcA have a potential role in regulation of calcium ion dependent key processes underlying in various metabolic activities of the cyanobacterium Anabaena 7120.     

Down‐regulation of Pyruvate Dehydrogenase Phosphatase in Obese Subjects is a Defect that Signals Insulin Resistance

Objective: The objective of this study was to determine whether down‐regulation of pyruvate dehydrogenase phosphatase (PDP) is responsible for poorly active pyruvate dehydrogenase (PDH) in circulating lymphocytes (CLs) of obese subjects (ObS), and if so, whether it improves when their plasma insulin rises. Research Methods and Procedures: PDH activity was compared in lysed CLs of 10 euglycemic ObS and 10 sex‐ and age‐matched controls before and during plasma insulin enhancement in an oral glucose tolerance test. It was evaluated without (PDHa) or with Mg/Ca or Mg at various concentrations to assess PDP1 or PDP2 activities or with Mg/Ca and exogenous PDP to determine total PDH activity (PDHt), which is an indirect measure of the amount of PDH. The insulin sensitivity index was calculated, and PDP1 and PDP2 mRNA was sought in the CLs. Results: At T₀ in ObS, PDHt was normal, whereas PDHa and PDP1 activity was below normal at all Mg/Ca concentrations. PDP2 activity was undetectable in both groups. PDP1 and PDP2 mRNA was identified, and insulin sensitivity index and PDHa were directly correlated. During the oral glucose tolerance test, plasma insulin rose considerably more in ObS than in controls; PDHa and PDP1 activity also increased but remained significantly below normal, and PDHt was unvaried in both groups. Discussion: PDP1 is down‐regulated in CLs of ObS because it is poorly sensitive to Mg/Ca; this defect is attenuated when plasma insulin is greatly enhanced.     

The role of ethanol oxidation during carboxydotrophic growth of Clostridium autoethanogenum

The Wood–Ljungdahl pathway is an ancient metabolic route used by acetogenic carboxydotrophs to convert CO into acetate, and some cases ethanol. When produced, ethanol is generally seen as an end product of acetogenic metabolism, but here we show that it acts as an important intermediate and co-substrate during carboxydotrophic growth of Clostridium autoethanogenum. Depending on CO availability, C. autoethanogenum is able to rapidly switch between ethanol production and utilization, hereby optimizing its carboxydotrophic growth. The importance of the aldehyde ferredoxin:oxidoreductase (AOR) route for ethanol production in carboxydotrophic acetogens is known; however, the role of the bifunctional alcohol dehydrogenase AdhE (Ald–Adh) route in ethanol metabolism remains largely unclear. We show that the mutant strain C. autoethanogenum ∆adhE1a, lacking the Ald subunit of the main bifunctional aldehyde/alcohol dehydrogenase (AdhE, CAETHG_3747), has poor ethanol oxidation capabilities, with a negative impact on biomass yield. This indicates that the Adh–Ald route plays a major role in ethanol oxidation during carboxydotrophic growth, enabling subsequent energy conservation via substrate-level phosphorylation using acetate kinase. Subsequent chemostat experiments with C. autoethanogenum show that the wild type, in contrast to ∆adhE1a, is more resilient to sudden changes in CO supply and utilizes ethanol as a temporary storage for reduction equivalents and energy during CO-abundant conditions, reserving these ‘stored assets’ for more CO-limited conditions. This shows that the direction of the ethanol metabolism is very dynamic during carboxydotrophic acetogenesis and opens new insights in the central metabolism of C. autoethanogenum and similar acetogens.     

Energy consumption by embryos of a viviparous lizard, Eulamprus tympanum, during development

Energy consumption during development has been measured in many oviparous lizards, but not in viviparous lizards in utero. It has always been assumed that energy consumption by embryos of viviparous lizards during development is similar to that of oviparous species. Estimation of energy consumption of viviparous lizards in vivo are confounded by the possible influence of pregnancy on maternal metabolism. Here we separated maternal and embryonic metabolism in measurements of pregnant Eulamprus tympanum throughout pregnancy. Our data support the hypothesis that the energetic cost of development in viviparous lizards (19.8 kJ g⁻¹) is similar to that in oviparous lizards (mean 16.2 kJ g⁻¹), at least for a species with a simple placenta. An increase in maternal metabolism of 29% above that for non-pregnant E. tympanum goes to maintain pregnancy, and represents an important component of the reproductive effort in E. tympanum.     

PINK1 autophosphorylation is required for ubiquitin recognition

Mutations in PINK1 cause autosomal recessive Parkinson's disease (PD), a neurodegenerative movement disorder. PINK1 is a kinase that acts as a sensor of mitochondrial damage and initiates Parkin‐mediated clearance of the damaged organelle. PINK1 phosphorylates Ser65 in both ubiquitin and the ubiquitin‐like (Ubl) domain of Parkin, which stimulates its E3 ligase activity. Autophosphorylation of PINK1 is required for Parkin activation, but how this modulates the ubiquitin kinase activity is unclear. Here, we show that autophosphorylation of Tribolium castaneum PINK1 is required for substrate recognition. Using enzyme kinetics and NMR spectroscopy, we reveal that PINK1 binds the Parkin Ubl with a 10‐fold higher affinity than ubiquitin via a conserved interface that is also implicated in RING1 and SH3 binding. The interaction requires phosphorylation at Ser205, an invariant PINK1 residue (Ser228 in human). Using mass spectrometry, we demonstrate that PINK1 rapidly autophosphorylates in trans at Ser205. Small‐angle X‐ray scattering and hydrogen–deuterium exchange experiments provide insights into the structure of the PINK1 catalytic domain. Our findings suggest that multiple PINK1 molecules autophosphorylate first prior to binding and phosphorylating ubiquitin and Parkin.     

Quantitative proteomic analysis of hepatic tissue in allotetraploid hybridized from red crucian carp and common carp identified crucial proteins and pathways associated with metabolism and growth rate

Allotetraploid is a new species produced by distant hybridization between red crucian carp (Carassius auratus red var., abbreviated as RCC) and common carp (Cyprinus carpio L., abbreviated as CC). There is a significant difference in growth rate between allotetraploid and its parents. However, the underlying molecular mechanism is largely unknown. In this study, to find direct evidence associated with metabolism and growth rate in protein level, we performed quantitative proteomics analysis on liver tissues between allotetraploid and its parents. A total of 2502 unique proteins were identified and quantified by SWATH-MS in our proteomics profiling. Subsequently, comprehensive bioinformatics analyses including gene ontology enrichment analysis, pathway and network analysis, and protein–protein interaction analysis (PPI) were conducted based on differentially expressed proteins (DEPs) between allotetraploid and its parents. The results revealed several significant DEPs involved in metabolism pathways in liver. More specifically, the integrative analysis highlighted that the DEPs ACSBG1, OAT, and LDHBA play vital roles in metabolism pathways including “pentose phosphate pathway,” “TCA cycle,” and “glycolysis and gluconeogenesis.” These could directly affect the growth rate in fresh water fishes by regulating the metabolism, utilization, and exchange of substance and energy. Since the liver is the central place for metabolism activity in animals, we firstly established the comprehensive and quantitative proteomics knowledge base for liver tissue from freshwater fishes, our study may serve as an irreplaceable reference for further studies regarding fishes’ culture and growth.     

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint‐based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time‐dependent changes, albeit using a static model. By performing an in silico knock‐out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.     

Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer's disease

Deficient energy metabolism and network hyperactivity are the early symptoms of Alzheimer's disease (AD). In this study, we show that administration of exogenous oxidative energy substrates (OES) corrects neuronal energy supply deficiency that reduces the amyloid‐beta‐induced abnormal neuronal activity in vitro and the epileptic phenotype in AD model in vivo. In vitro, acute application of protofibrillar amyloid‐β_1–42 (Aβ_1–42) induced aberrant network activity in wild‐type hippocampal slices that was underlain by depolarization of both the neuronal resting membrane potential and GABA‐mediated current reversal potential. Aβ_1–42 also impaired synaptic function and long‐term potentiation. These changes were paralleled by clear indications of impaired energy metabolism, as indicated by abnormal NAD(P)H signaling induced by network activity. However, when glucose was supplemented with OES pyruvate and 3‐beta‐hydroxybutyrate, Aβ_1–42 failed to induce detrimental changes in any of the above parameters. We administered the same OES as chronic supplementation to a standard diet to APPswe/PS1dE9 transgenic mice displaying AD‐related epilepsy phenotype. In the ex‐vivo slices, we found neuronal subpopulations with significantly depolarized resting and GABA‐mediated current reversal potentials, mirroring abnormalities we observed under acute Aβ_1‐42 application. Ex‐vivo cortex of transgenic mice fed with standard diet displayed signs of impaired energy metabolism, such as abnormal NAD(P)H signaling and strongly reduced tolerance to hypoglycemia. Transgenic mice also possessed brain glycogen levels twofold lower than those of wild‐type mice. However, none of the above neuronal and metabolic dysfunctions were observed in transgenic mice fed with the OES‐enriched diet. In vivo, dietary OES supplementation abated neuronal hyperexcitability, as the frequency of both epileptiform discharges and spikes was strongly decreased in the APPswe/PS1dE9 mice placed on the diet. Altogether, our results suggest that early AD‐related neuronal malfunctions underlying hyperexcitability and energy metabolism deficiency can be prevented by dietary supplementation with native energy substrates.     

Variation between field and laboratory populations of Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae)

Rates of development and pupal weights were compared between seven field populations and two laboratory strains of Tribolium castaneum. Rates of development did not differ significantly between field populations, but pupal weights did vary. Laboratory strains were both slower to develop and heavier than the field populations. The data support the hypothesis that field populations undergo selection for fast development in transient habitats. The findings are discussed in the context of r and K selection in field populations and laboratory cultures.     

Phenols from Potentilla anserina L. Improve Insulin Sensitivity and Inhibit Differentiation in 3T3-L1 Adipocytes in Vitro

Potentilla anserina L., a well-known perennial herb, is widely used in traditional Tibetan medicine and used as a delicious food in humans. The present investigation reports on the activity of P. anserina phenols (PAP) in regulating glycolipid metabolism in 3T3-L1 adipocytes. Insulin sensitivity tests showed that PAP improved insulin-stimulated glucose uptake by promoting the phosphorylation of serine/threonine kinase Akt. Moreover, an assay involving the differentiation of 3T3-L1 preadipocytes demonstrated that PAP also decreased the accumulation of lipid droplets by suppressing the expression of adipokines during the differentiation process. In addition, the underlying mechanism from the aspects of energy metabolism and oxidative stress is also discussed. The improvement in energy metabolism was supported by an increase in mitochondrial membrane potential (MMP) and intracellular ATP. Amelioration of oxidative stress was supported by decreased levels of intracellular reactive oxygen species (ROS). In summary, our findings suggest that PAP can ameliorate the disorder of glycolipid metabolism in insulin resistant 3T3-L1 adipocytes by improving energy metabolism and oxidative stress and might be an attractive candidate for the treatment of diabetes.     

Pyruvate dehydrogenase phosphatase 1 (<Emphasis Type="Italic">PDP1</Emphasis>) null mutation produces a lethal infantile phenotype

Pyruvate dehydrogenase phosphatase deficiency has previously only been confirmed at the molecular level in two brothers and two breeds of dog with exercise intolerance. A female patient, who died at 6 months, presented with lactic acidemia in the neonatal period with serum lactate levels ranging from 2.5 to 17 mM. Failure of dichloroacetate to activate the PDH complex in skin fibroblasts was evident, but not in early passages. A homozygous c.277G > T (p.E93X) nonsense mutation in the PDP1 gene was identified in genomic DNA and immunoblotting showed a complete absence of PDP1 protein in mitochondria. Native PDHC activity could be restored by the addition of either recombinant PDP1 or PDP2. This highlights the role of PDP2, the second phosphatase isoform, in PDP1-deficient patients for the first time. We conclude that the severity of the clinical course associated with PDP1 deficiency can be quite variable depending on the exact nature of the molecular defect.     

Genetic and biochemical basis for alternative routes of tocotrienol biosynthesis for enhanced vitamin E antioxidant production

Vitamin E tocotrienol synthesis in monocots requires homogentisate geranylgeranyl transferase (HGGT), which catalyzes the condensation of homogentisate and the unsaturated C20 isoprenoid geranylgeranyl diphosphate (GGDP). By contrast, vitamin E tocopherol synthesis is mediated by homogentisate phytyltransferase (HPT), which condenses homogentisate and the saturated C20 isoprenoid phytyl diphosphate (PDP). An HGGT‐independent pathway for tocotrienol synthesis has also been shown to occur by de‐regulation of homogentisate synthesis. In this paper, the basis for this pathway and its impact on vitamin E production when combined with HGGT are explored. An Arabidopsis line was initially developed that accumulates tocotrienols and homogentisate by co‐expression of Arabidopsis hydroxyphenylpyruvate dioxygenase (HPPD) and Escherichia coli bi‐functional chorismate mutase/prephenate dehydrogenase (TyrA). When crossed into the vte2–1 HPT null mutant, tocotrienol production was lost, indicating that HPT catalyzes tocotrienol synthesis in HPPD/TyrA‐expressing plants by atypical use of GGDP as a substrate. Consistent with this, recombinant Arabidopsis HPT preferentially catalyzed in vitro production of the tocotrienol precursor geranylgeranyl benzoquinol only when presented with high molar ratios of GGDP:PDP. In addition, tocotrienol levels were highest in early growth stages in HPPD/TyrA lines, but decreased strongly relative to tocopherols during later growth stages when PDP is known to accumulate. Collectively, these results indicate that HPPD/TyrA‐induced tocotrienol production requires HPT and occurs upon enrichment of GGDP relative to PDP in prenyl diphosphate pools. Finally, combined expression of HPPD/TyrA and HGGT in Arabidopsis leaves and seeds resulted in large additive increases in vitamin E production, indicating that homogentisate concentrations limit HGGT‐catalyzed tocotrienol synthesis.     

Silencing pyruvate kinase (NlPYK) leads to reduced fecundity in brown planthoppers,Nilaparvata lugens (Stål) (Hemiptera: Delphacidae)

Pyruvate kinase (PYK) operates in the glycolytic pathway, responsible for regulating the balance between glycolysis and gluconeogenesis. The previous work indicates PYK acts in development of Drosophila embryos and in embryonic muscle growth, from which it may be inferred that PYK acts in insect fecundity. More to the point, as a central enzyme in the glycolytic pathway, PYK acts in many energy‐spending functions in most organisms. On the background findings that triazophos (TZP) stimulates fecundity via increase activities of several genes in brown planthoppers, Nilaparvata lugens, we investigated the combined influence of TZP and silencing a N. lugens PYK (NlPYK) on reproduction‐linked biological performance parameters. Here, we report that TZP+dsNlPYK treatments led to reduced (by 26%) ovarian, but not fat body, protein content relative to controls. Ovarian (35%) and fat body (54%) soluble sugar contents were reduced. TZP+dsNlPYK treatments also led to reduced (by about 24%) fecundity, expressed as numbers of eggs laid. These data show directly that NlPYK acts in insect fecundity, probably via increases in glucose metabolism.     

动植物中COP1泛素连接酶介导的信号转导与蛋白质稳态调控

COP1 E3泛素连接酶最初是在植物中作为光形态建成的关键抑制因子被发现和广泛研究的，是植物生长发育和环境适应过程中的核心“开关”。光受体接收外界环境信号后传递给COP1,COP1再靶向调控下游核心转录因子，从而完成光形态建成等生命过程。在哺乳动物中，尽管大部分光受体都消失，但COP1仍在代谢调控和肿瘤发生过程中靶向重要的转录因子。通过比较动植物中COP1调控过程的异同发现，哺乳动物中COP1所感知的上游信号几乎是未知的，其中COP1结合CRL4形成的复合体E3泛素连接酶的组装机制调控仍不清楚。植物中光是其主要能量来源和COP1的主要上游信号，而作为动物的主要能量来源，葡萄糖和相关激素很可能也是动物COP1的上游信号。同时，通过总结医学研究中针对蛋白质泛素化相关过程的丰富靶点和相关药物，可以为植物COP1等E3泛素连接酶的研究提供有效工具。COP1在细胞生命过程调控中至关重要，其功能和作用机制随着进化而产生多样性，尚有待继续深入探究。     

ON THE MECHANISM OF THE INHIBITION OF GROWTH BY XYLULOSE IN CHLOROCOCCUM ECHINOZYGOTUM1,2

We previously established that xylulose inhibits the growth of the green alga Chlorococcum echinozygotum. Utilizing experiments involving exposure of the alga to NaHC¹⁴O₃, it was possible to show by counting the C¹⁴ activity of methanolic extracts of the algal cells that xylulose inhibited CO₂ uptake. Subsequently it was shown that xylulose does not inhibit or otherwise influence the Hill reaction in this alga. Several enzymes related to xylulose metabolism were investigated. It was found that xylulokinase was active in C. echinozygotum while phosphoketolase activity was absent. Transketolase was present but its activity was not notably affected by xylulose. Crude carboxydismutase preparations were found to be inhibited by xylulose and xylulose 5-phosphate. However, as carboxydismutase was purified further, this inhibition was relatively less. When xylulose 1,5-diphosphate was prepared synthetically, this compound was found to be the most effective inhibitor of purified algal carboxydismutase. We conclude that d -xylulose enters the cells of C. echinozygotum where it is converted to d -xylulose 1,5-diphosphate which acts as a competitive inhibitor of carboxydismutase.     

GROWTH RATES OF BIRDS IN THE HUMID NEW WORLD TROPICS

The growth curves of 40 species of lowland neotropical birds were fitted by logistic equation. The birds were mostly from Panama, Trinidad and Surinam. The growth constants of the fitted equations (asymptote A and growth rate K) were compared within and among species, and with previously published data on temperate species. Growth parameters of tropical passerines are about as variable within species as they are within temperate species. In both cases, variation in A and K between broods is greater than it is within broods. Panamanian birds breed during the dry-wet transition and conditions for growth apparently improve as rainfall increases. Asymptotes of growth curves are higher, and mortality within broods lower, as the breeding season progresses. Asynchronous hatching and the reduction of brood-size by selective starvation of young is a prominent phenomenon during the early part of the breeding season. Several instances are reported, however, of young persisting in nests with inadequate feeding and greatly subnormal weights. Slowed development under conditions of poor nutrition may be adaptive in the tropics if periods of low food availability are short and allow the possibility of recovery from undernourishment. As a group, neotropical lowland passerines (30 species) grow 23% more slowly than a sample of 51 temperate passerines. Variation of growth rates among these tropical species is similar to variation among temperate species, and it is related to adult body-size the length of the nestling period. Young of tropical and temperate species attain similar asymptotes, relative to adult body-weight, by the end of the nestling period. Hypotheses are advanced which might explain the slower growth rate of tropical species, and tested to the extent available data permits. (1) Because brood-size can be changed only by adding or removing whole young, changes in growth rate could provide finer adjustment of the energy requirements of the young to the feeding capacity of the parents. This model predicts different means and variances for growth rate within groups of species with different clutch-sizes, predictions not supported by available data. (2) Growth rate is shown to increase the maximum energy requirement of a nestling only if K exceeds some value determined by the energy requirement of the young, growth rate should vary in proportion to the level of basal maintenance metabolism. In a small sample of tropical species, rates of basal metabolism were 25% lower than in a comparable sample of temperate species. These data therefore support the hypothesis, although the cause of the lower metabolic rate of the tropical nestlings is not known. (3) Daily periods of hypothermia could reduce the energy requirement of the young and at the same time reduce their growth rate; but observations of body temperatures of tropical nestlings are contrary to this hypothesis. (4) The short day-length of tropical climates reduces the time during which young can assimilate energy relative to their energy expenditures. This model predicts that tropical nestlings would have less productive energy available, (consistent with their reduced growth rates), but it also predicts that arctic birds should grow faster than temperate species, which is not confirmed by available data. (5) The low nitrogen content of fruits may cause the slow growth of a few strictly frugivorous species (Oilbird and Bearded Bellbird), but among other tropical species growth rate is not correlated with the estimated proportion of fruit in the diet.     

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Highly conserved among eukaryotic cells, the AMP‐activated kinase (AMPK) is a central regulator of carbon metabolism. To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite levels in wild type, Δsnf1, Δsnf4, and Δsnf1Δsnf4 knockout strains. Using four newly developed computational tools, including novel DOGMA sub‐network analysis, we showed the benefits of three‐level ome‐data integration to uncover the global Snf1 kinase role in yeast. We for the first time identified Snf1's global regulation on gene and protein expression levels, and showed that yeast Snf1 has a far more extensive function in controlling energy metabolism than reported earlier. Additionally, we identified complementary roles of Snf1 and Snf4. Similar to the function of AMPK in humans, our findings showed that Snf1 is a low‐energy checkpoint and that yeast can be used more extensively as a model system for studying the molecular mechanisms underlying the global regulation of AMPK in mammals, failure of which leads to metabolic diseases.