Functional similarities of human and chicken apolipoprotein A-I: dependence on secondary and tertiary rather than primary structure

ApoPred: Identification of Apolipoproteins and Their Subfamilies With Multifarious Features

Apolipoprotein is a group of plasma proteins that are associated with a variety of diseases, such as hyperlipidemia, atherosclerosis, Alzheimer's disease, and diabetes. In order to investigate the function of apolipoproteins and to develop effective targets for related diseases, it is necessary to accurately identify and classify apolipoproteins. Although it is possible to identify apolipoproteins accurately through biochemical experiments, they are expensive and time-consuming. This work aims to establish a high-efficiency and high-accuracy prediction model for recognition of apolipoproteins and their subfamilies. We firstly constructed a high-quality benchmark dataset including 270 apolipoproteins and 535 non-apolipoproteins. Based on the dataset, pseudo-amino acid composition (PseAAC) and composition of k-spaced amino acid pairs (CKSAAP) were used as input vectors. To improve the prediction accuracy and eliminate redundant information, analysis of variance (ANOVA) was used to rank the features. And the incremental feature selection was utilized to obtain the best feature subset. Support vector machine (SVM) was proposed to construct the classification model, which could produce the accuracy of 97.27%, sensitivity of 96.30%, and specificity of 97.76% for discriminating apolipoprotein from non-apolipoprotein in 10-fold cross-validation. In addition, the same process was repeated to generate a new model for predicting apolipoprotein subfamilies. The new model could achieve an overall accuracy of 95.93% in 10-fold cross-validation. According to our proposed model, a convenient webserver called ApoPred was established, which can be freely accessed at http://tang-biolab.com/server/ApoPred/service.html. We expect that this work will contribute to apolipoprotein function research and drug development in relevant diseases.

Affinity binding of chicken apolipoprotein A1 to a novel flax orbitide (linusorb)

Bioactive orbitides (linusorbs, LOs) from flaxseed (Linum usitatissimum L.) were ligated through methionine with resin to form an affinity column. The affinity resin was characterized using elemental analysis and the resin bound 70% of its weight in LOs. Chicken serum was passed over the column and washed to remove non-binding materials. The column was eluted with unbound orbitide to competitively release bound protein. A single 28 kDa protein was found in the affinity binding pool. The protein MW and sequence were identical to apolipoprotein A1 (Apo A1), a major serum protein. Its role includes reverse cholesterol transport and cholesterol efflux. The affinity technique allowed convenient and rapid isolation of Apo A1 with a recyclable affinity column. LO binding to a cholesterol carrier molecule might also help us to understand the mechanism of action of LOs in health and the biological activity of flaxseed products.

Bioactive orbitides (linusorbs) from flaxseed (Linum usitatissimum L.) were ligated through methionine with resin to form an affinity column that selectively binds chicken apolipoprotein A1 from chicken serum.

Comparative proteome analysis of abdominal adipose tissues between fat and lean broilers

Background

The molecular mechanism underlying broiler fat deposition is still poorly understood.

Method

Currently, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in abdominal adipose tissues of birds at 4 week of age derived from Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF).

Results

Thirteen differentially expressed protein spots were screened out and identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The protein spots were matched to thirteen proteins by searching against the NCBInr database. These identified proteins were apolipoprotein A-I (Apo A-I), cytokeratin otokeratin, ATP synthase subunit alpha, peptidyl-prolyl cis-trans isomerase FKBP4 (PPIase FKBP4), aspartate aminotransferase, carbonic anhydrase II (CA-II), prostaglandin-H2 D-isomerase precursor, fibrinogen alpha chain, lamin-A (LMNA), superoxide dismutase [Mn] (MnSOD), heat shock protein beta-1 (HSPβ1) and two predicted proteins. These differentially expressed proteins are involved mainly in lipid metabolism, amino acid metabolism, signal transduction, energy conversion, antioxidant, and cytoskeleton. Differential expression of Apo A-I, PPIase FKBP4, and cytokeratin otokeratin proteins were further confirmed by Western blot analysis. Quantitative real-time RT-PCR analyses showed that, of these 13 differentially expressed proteins, only PPIase FKBP4 and cytokeratin otokeratin were differentially expressed at mRNA level between the two lines.

Conclusions

Our results have provided further information for understanding the basic genetics control of growth and development of broiler adipose tissue.

Structure of the Dispase Autolysis-inducing Protein from Streptomyces mobaraensis and Glutamine Cross-linking Sites for Transglutaminase

Transglutaminase from Streptomyces mobaraensis (MTG) is an important enzyme for cross-linking and modifying proteins. An intrinsic substrate of MTG is the dispase autolysis-inducing protein (DAIP). The amino acid sequence of DAIP contains 5 potential glutamines and 10 lysines for MTG-mediated cross-linking. The aim of the study was to determine the structure and glutamine cross-linking sites of the first physiological MTG substrate. A production procedure was established in Escherichia coli BL21 (DE3) to obtain high yields of recombinant DAIP. DAIP variants were prepared by replacing four of five glutamines for asparagines in various combinations via site-directed mutagenesis. Incorporation of biotin cadaverine revealed a preference of MTG for the DAIP glutamines in the order of Gln-39 ≫ Gln-298 > Gln-345 ∼ Gln-65 ≫ Gln-144. In the structure of DAIP the preferred glutamines do cluster at the top of the seven-bladed β-propeller. This suggests a targeted cross-linking of DAIP by MTG that may occur after self-assembly in the bacterial cell wall. Based on our biochemical and structural data of the first physiological MTG substrate, we further provide novel insight into determinants of MTG-mediated modification, specificity, and efficiency.

Effects of chicory inulin on serum metabolites of uric acid, lipids, glucose, and abdominal fat deposition in quails induced by purine-rich diets

Inulin, a group of dietary fibers, is reported to improve the metabolic disorders. In the present study, we investigated the effects of chicory inulin on serum metabolites of uric acid (UA), lipids, glucose, and abdominal fat deposition in quail model induced by a purine-rich diet. In this study, 60 male French quails were randomly allocated to five groups: CON (control group), MOD (model group), BEN (benzbromarone-treated group), CHI-H (high-dosage chicory inulin-treated group), and CHI-L (low-dosage chicory inulin-treated group). The serum UA level was significantly increased in the model group from days 7 to 28, as well as triglyceride (TG) and free fatty acid (FFA) increased later in the experimental period. The abdominal fat ratio was increased on day 28. Benzbromarone can decrease UA levels on days 14 and 28. The high and low dosage of chicory inulin also decreased serum UA levels on days 7, 14, and 28. The abdominal fat ratio, activity, and protein of acetyl-CoA carboxylase (ACC) were decreased in chicory inulin-treated groups. The activities of xanthine oxidase (XOD) and fatty acid synthase (FAS) were increased in the model group and decreased in the benzbromarone and chicory inulin groups. This study evaluated a quail model of induced hyperuricemia with other metabolic disorders caused by a high-purine diet. The results indicated that a purine-rich diet might contribute to the development of hyperuricemia, hypertriglyceridemia, and abdominal obesity. Chicory inulin decreased serum UA, TG, and abdominal fat deposition in a quail model of hyperuricemia by altering the ACC protein expression and FAS and XOD activities.

Novel N-terminal mutation of human apolipoprotein A-I reduces self-association and impairs LCAT activation

We have identified a novel mutation in apoA-I (serine 36 to alanine; S36A) in a human subject with severe hypoalphalipoproteinemia. The mutation is located in the N-terminal region of the protein, which has been implicated in several functions, including lipid binding and lecithin:cholesterol acyltransferase (LCAT) activity. In the present study, the S36A protein was produced recombinantly and characterized both structurally and functionally. While the helical content of the mutant protein was lower compared with wild-type (WT) apoA-I, it retained its helical character. The protein stability, measured as the resistance to guanidine-induced denaturation, decreased significantly. Interestingly, native gel electrophoresis, cross-linking, and sedimentation equilibrium analysis showed that the S36A mutant was primarily present as a monomer, notably different from the WT protein, which showed considerable oligomeric forms. Although the ability of S36A apoA-I to solubilize phosphatidylcholine vesicles and bind to lipoprotein surfaces was not altered, a significantly impaired LCAT activation compared with the WT protein was observed. These results implicate a region around S36 in apoA-I self-association, independent of the intact C terminus. Furthermore, the region around S36 in the N-terminus of human apoA-I is necessary for LCAT activation.

The helix bundle: a reversible lipid binding motif

Apolipoproteins are the protein components of lipoproteins that have the innate ability to inter convert between a lipid-free and a lipid-bound form in a facile manner, a remarkable property conferred by the helix bundle motif. Composed of a series of four or five amphipathic alpha-helices that fold to form a helix bundle, this motif allows the en face orientation of the hydrophobic faces of the alpha-helices in the protein interior in the lipid-free state. A conformational switch then permits helix-helix interactions to be substituted by helix-lipid interactions upon lipid binding interaction. This review compares the apolipoprotein high-resolution structures and the factors that trigger this switch in insect apolipophorin III and the mammalian apolipoproteins, apolipoprotein E and apolipoprotein A-I, pointing out the commonalities and key differences in the mode of lipid interaction. Further insights into the lipid-bound conformation of apolipoproteins are required to fully understand their functional role under physiological conditions.

Microarray analysis of adipose tissue gene expression profiles between two chicken breeds

The chicken is an important model organism that bridges the evolutionary gap between mammals and other vertebrates and provides a major protein source from meat and eggs throughout the world. Excessive accumulation of lipids in the adipose tissue is one of the main problems faced by the broiler industry nowadays. In order to visualize the mechanisms involved in the gene expression and regulation of lipid metabolism in adipose tissue, cDNA microarray containing 9024 cDNA was used to construct gene expression profile and screen differentially expressed genes in adipose tissue between broilers and layers of 10 wk of age. Sixty-seven differentially expressed sequences were screened out, and 42 genes were found when blasted with the GenBank database. These genes are mainly related to lipid metabolism, energy metabolism, transcription and splicing factor, protein synthesis and degradation. The remained 25 sequences had no annotation available in the GenBank database. Furthermore, Northern blot and semi-quantitative RT-PCR were developed to confirm 4 differentially expressed genes screened by cDNA microarray, and it showed great consistency between the microarray data and Northern blot results or semi-quantitative RT-PCR results. The present study will be helpful for clarifying the molecular mechanism of obesity in chickens.