Evaluating the roles of energetic functional constraints on teleost mitochondrial-encoded protein evolution

Mitochondria are the power plant of cells, which play critical roles not only in energy metabolism but also in thermoregulation. These two roles have been individually suggested to influence mitochondrial DNA (mtDNA) evolution, however their relative importance is still rarely considered. Here, we conduct a comparative genomic analysis of 401 teleost complete mitochondrial genomes and test the roles of these dual functional constraints on mitochondria to provide a more complete view of mtDNA evolution. We found that mitochondrial protein-coding genes of migratory fishes have significantly smaller Ka/Ks than nonmigratory fishes. The same data set showed that the genes of fishes living in cold climates have significantly smaller Ka/Ks than tropical fishes. In contrast, these trends were not observed for two nuclear genes that are not involved in energy metabolism. The differences in selection patterns observed between mitochondrial and nuclear genes suggest that the functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mitochondrial-encoded proteins in teleosts.     

Peripheral effects of FAAH deficiency on fuel and energy homeostasis: role of dysregulated lysine acetylation

Background

FAAH (fatty acid amide hydrolase), primarily expressed in the liver, hydrolyzes the endocannabinoids fatty acid ethanolamides (FAA). Human FAAH gene mutations are associated with increased body weight and obesity. In our present study, using targeted metabolite and lipid profiling, and new global acetylome profiling methodologies, we examined the role of the liver on fuel and energy homeostasis in whole body FAAH^−/− mice.

Methodology/Principal Findings

FAAH^−/− mice exhibit altered energy homeostasis demonstrated by decreased oxygen consumption (Indirect calorimetry). FAAH^−/− mice are hyperinsulinemic and have adipose, skeletal and hepatic insulin resistance as indicated by stable isotope phenotyping (SIPHEN). Fed state skeletal muscle and liver triglyceride levels was increased 2–3 fold, while glycogen was decreased 42% and 57% respectively. Hepatic cholesterol synthesis was decreased 22% in FAAH^−/− mice. Dysregulated hepatic FAAH^−/− lysine acetylation was consistent with their metabolite profiling. Fasted to fed increases in hepatic FAAH^−/− acetyl-CoA (85%, p<0.01) corresponded to similar increases in citrate levels (45%). Altered FAAH^−/− mitochondrial malate dehydrogenase (MDH2) acetylation, which can affect the malate aspartate shuttle, was consistent with our observation of a 25% decrease in fed malate and aspartate levels. Decreased fasted but not fed dihydroxyacetone-P and glycerol-3-P levels in FAAH^−/− mice was consistent with a compensating contribution from decreased acetylation of fed FAAH^−/− aldolase B. Fed FAAH^−/− alcohol dehydrogenase (ADH) acetylation was also decreased.

Conclusions/Significance

Whole body FAAH deletion contributes to a pre-diabetic phenotype by mechanisms resulting in impairment of hepatic glucose and lipid metabolism. FAAH^−/− mice had altered hepatic lysine acetylation, the pattern sharing similarities with acetylation changes reported with chronic alcohol treatment. Dysregulated hepatic lysine acetylation seen with impaired FAA hydrolysis could support the liver''s role in fostering the pre-diabetic state, and may reflect part of the mechanism underlying the hepatic effects of endocannabinoids in alcoholic liver disease mouse models.     

Myosin II regulatory light chain is required for trafficking of bile salt export protein to the apical membrane in Madin-Darby canine kidney cells

BSEP, MDR1, and MDR2 ATP binding cassette transporters are targeted to the apical (canalicular) membrane of hepatocytes, where they mediate ATP-dependent secretion of bile acids, drugs, and phospholipids, respectively. Sorting to the apical membrane is essential for transporter function; however, little is known regarding cellular proteins that bind ATP binding cassette proteins and regulate their trafficking. A yeast two-hybrid screen of a rat liver cDNA library identified the myosin II regulatory light chain, MLC2, as a binding partner for BSEP, MDR1, and MDR2. The interactions were confirmed by glutathione S-transferase pulldown and co-immunoprecipitation assays. BSEP and MLC2 were overrepresented in a rat liver subcellular fraction enriched in canalicular membrane vesicles, and MLC2 colocalized with BSEP in the apical domain of hepatocytes and polarized WifB, HepG2, and Madin-Darby canine kidney cells. Expression of a dominant negative, non-phosphorylatable MLC2 mutant reduced steady state BSEP levels in the apical domain of polarized Madin-Darby canine kidney cells. Pulse-chase studies revealed that Blebbistatin, a specific myosin II inhibitor, severely impaired delivery of newly synthesized BSEP to the apical surface. These findings indicate that myosin II is required for BSEP trafficking to the apical membrane.     

Synthesis of α- and β-glycosides containing spin labels,as probes for studies of carbohydrate-protein interaction

Nitroxide spin-labeled α-d-glycopyranosides were synthesized in good yield and in a highly stereoselective manner by reaction of per-O-benzyl-α-d-glycopyranosyl bromides with 2,2,6,6-tetramethyl-4-piperidinol under the bromide ion-catalyzed conditions devised by Lemieux etal. After hydrogenolysis, the deblocked intermidiates were oxidized to give the desired, spin-labeled α-d-glycopyranosides. Nitroxide spin-labeled α-d-glycopyranosides, as well as a β-maltoside, were synthesized by standard methods. The synthesis is also described of 2-amino-2-deoxy-d-glucose and -d-galactose derivatives having a spin label at C-2, and of the spin-labeled compound 1-[4-(β-d-galactopyranosyloxy)phenyl]-3-(2,2,6,6-tetramethylpiperidin-1-oxyl-4-yl)-2-thiourea.     

Changes in intranuclear chromatin architecture induce bipolar nuclear localization of histone variant H1T2 in male haploid spermatids

Spermiogenesis entails a major biochemical and morphological restructuring of the germ cell packing the DNA into the condensed spermatid nucleus. H1T2 is a histone H1 variant selectively and transiently expressed in male haploid germ cells during spermiogenesis that specifically localizes to a chromatin domain at the apical pole under the acrosome. We explored the mechanisms determining polar localization of H1T2 in spermatids. In acrosome-deficient round spermatids of hrb -/- and gopc -/- mice, H1T2 localization is not altered, indicating that proper acrosome development is not required for specifying nuclear polarity. In contrast, in late round spermatids from trf2 -/- or hmgb2 -/- mice, a bipolar H1T2 localization was observed revealing that polarity is modified by loss of proteins specifying chromatin architecture. Our results show that intranuclear chromatin organization is critical for correct polar localization of H1T2 and that H1T2 can be a useful molecular marker revealing chromatin disorganization in spermatids.     

Bone inflammation and altered gene expression with type I diabetes early onset

Type I diabetes is associated with bone loss and marrow adiposity. To identify early events involved in the etiology of diabetic bone loss, diabetes was induced in mice by multiple low dose streptozotocin injections. Serum markers of bone metabolism and inflammation as well as tibial gene expression were examined between 1 and 17 days post‐injection (dpi). At 3 dpi, when blood glucose levels were significantly elevated, body, fat pad and muscle mass were decreased. Serum markers of bone resorption and formation significantly decreased at 5 dpi in diabetic mice and remained suppressed throughout the time course. An osteoclast gene, TRAP5 mRNA, was suppressed at early and late time points. Suppression of osteogenic genes (runx2 and osteocalcin) and induction of adipogenic genes (PPARγ2 and aP2) were evident as early as 5 dpi. These changes were associated with an elevation of serum cytokines, but more importantly we observed an increase in the expression of cytokines in bone, supporting the idea that bone, itself, exhibits an inflammatory response during diabetes induction. This inflammation could in turn contribute to diabetic bone pathology. IFN‐γ (one of the key cytokines elevated in bone and known to be involved in bone regulation) deficiency did not prevent diabetic bone pathology. Taken together, our findings indicate that bone becomes inflamed with the onset of T1‐diabetes and during this time bone phenotype markers become altered. However, inhibition of one cytokine, IFN‐γ was not sufficient to prevent the rapid bone phenotype changes. J. Cell. Physiol. 218: 575–583, 2009. © 2008 Wiley‐Liss, Inc.     

Are bird density,species richness and community structure similar between native woodlands and non-native plantations in an area with a generalist bird fauna?

This study compared the bird assemblages of native semi-natural woodlands and non-native Sitka spruce (Picea sitchensis) plantations in Ireland to identify what vegetation variables most influenced birds and to identify management targets in plantations to maximise future bird conservation. Point counts were conducted in 10 Oak (Quercus spp.) and 10 Ash (Fraxinus excelsior) native woodlands and in five Mid-rotation (20–30 years old) and five Mature (30–50 years old) Sitka spruce plantations. Ordination was used to characterise woodland types according to their constituent bird species. Total bird density (calculated using Distance software) and species richness were assessed for the different woodland types. Oak and Ash woodland bird assemblages were separated from Mid-rotation and Mature plantations by the ordination. There was no difference in total bird density between any of the woodland types. Oak woodlands had significantly higher species richness than either Mid-rotation or Mature Sitka spruce plantations. Ash had higher species richness than Mature Sitka spruce plantations. Understorey vegetation was negatively associated with total bird density, which also varied with survey year. Understorey vegetation was positively associated with species richness. Reasons for the relationships between vegetation and bird assemblages are discussed. Management should seek to increase shrub and understorey vegetation in the Mid-rotation phase to improve the contribution of plantations to bird conservation.     

Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions

By generating classes of random structures for trypsin inhibitor and carp myogen, each consistent with a given set of experimental or theoretical information, we have assessed the relative utility of various experiments and theories in deducing the conformation of macromolecules. We compare the calculated structures with known x-ray coordinates and compute for each class an average error. Small errors mean that the experimental or theoretical constraints limit the structures to the vicinity of the crystal structure, whereas large errors show that the constraints permit a wide variety of tertiary conformations. We find the following points to hold true: (1) Qualitative information on all the distances, as might be obtained from the correct prediction of interresidue contacts, effectively determines the structure (error approximately 1 Å). (2) Quantitative information on a limited number of distances, as might be obtained from nmr or crosslinking experiments, significantly restricts the range of possible structures only when the number of distances given is comparable to the number of residues (error approximately 3 Å). (3) Quantitative information on the distances of each residue to the center of mass of the molecule, as might in part be obtained from solvent accessibility and solution x-ray studies, is not particularly restrictive by itself (error approximately 5 Å). (4) Complete qualitative local distance information, as might be obtained from secondary prediction and CD/ORD studies, is clearly consistent with a wide variety of tertiary structures (error approximately 7 Å).     

Hemoglobin-water interactions in normal and sickle erythrocytes by proton magnetic resonance T1ϱ measurements

The dependence of the water proton magnetic resonance spin-lattice relaxation rate (T_1?^?1) in the rotating frame on the strength of the spin-locking (H₁) field has been investigated for packed oxy and deoxy normal and sickle erythrocytes at temperatures from 9 to 40 °C. The T_1?^?1 of oxy or deoxy normal erythrocytes shows no dependence on H₁ up to ~7 G at any temperature studied. On the other hand, T_1?^?1 decreases from about 40 s^?1 to 15 s^?1 (H₁ from 0 to ~7 G) for deoxygenated packed sickle cells at 40 °C. The magnitude of this variation of T_1?^?1 with H₁ decreases with decreasing temperature. Oxy packed sickle cells also show a dependence of T_1?^?1 on H₁ but the magnitude is <10% of that of the deoxygenated samples. These results suggest that water proton T_1?^?1 measurements are a sensitive probe of hemoglobin S polymerization and provide a novel technique for the study of slow water motions in these systems. The T_1?^?1 results are compared with low frequency T₁^?1 results of other investigators on hemoglobin S solutions. Analysis of the data suggests that water proton motions with correlation times of the order of 10^?5 s are present in the deoxygenated sickle cell samples at temperatures above 10 °C.     

ON THE ACCUMULATION OF DYE IN NITELLA

Living cells of Nitella were placed in different concentrations of brilliant cresyl blue solutions at pH 6.9. It was found that the greater the concentration of the external dye solution, the greater was the speed of accumulation of the dye in the cell sap and higher was the concentration of dye found in the sap at equilibrium. Analysis of the time curves showed that the process may be regarded as a reversible pseudounimolecular reaction. When the concentration in the sap is plotted as ordinates and the concentration in the outside solution as abscissae the curve is convex toward the abscissae. There is reason to believe that secondary changes involving injury take place as the dye accumulates and that if these changes did not occur the curve would be concave toward the abscissae. The process may be explained as a chemical combination of the dye with a constituent of the cell. This harmonizes with the fact that the temperature coefficient is high (about 4.9). Various other possible explanations are discussed.