1
|
Chen W, Ma H, Li B, Yang F, Xiao Y, Gong Y, Li Z, Li T, Zeng Q, Xu K, Duan Y. Spatiotemporal Regulation of Circular RNA Expression during Liver Development of Chinese Indigenous Ningxiang Pigs. Genes (Basel) 2022; 13:746. [PMID: 35627131 PMCID: PMC9141790 DOI: 10.3390/genes13050746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. METHODS In this study, we systematically analyzed circular RNAs in the liver of Ningxiang pigs, at four time points after birth (30 days, 90 days, 150 days and 210 days). RESULTS A total of 3705 circRNAs were coexpressed in four time periods were found, and KEGG analysis showed that the significantly upregulated pathways were mainly enriched in lipid metabolism and amino acid metabolism, while significantly downregulated pathways were mainly related to signal transduction, such as ECM-receptor interaction, MAPK signaling pathway, etc. Short time-series expression miner (STEM) analysis showed multiple model spectra that were significantly enriched over time in the liver. By constructing a competing endogenous RNA (ceRNA) regulatory network, 9187 pairs of networks related to the change in development time were screened. CONCLUSIONS The expression profiles of circRNAs in Ningxiang pig liver were revealed at different development periods, and it was determined that there is differential coexpression. Through enrichment analysis of these circRNAs, it was revealed that host genes were involved in metabolism-related signaling pathways and fatty acid anabolism. Through STEM analysis, many circRNAs involved in fat metabolism, transport, and deposition pathways were screened, and the first circRNA-miRNA-mRNA regulation network map in Ningxiang pig liver was constructed. The highly expressed circRNAs related to fat deposition were verified and were consistent with RNA-Seq results.
Collapse
Affiliation(s)
- Wenwu Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610000, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Ting Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Kang Xu
- Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang 410600, China; (K.X.); (Y.D.)
| | - Yehui Duan
- Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang 410600, China; (K.X.); (Y.D.)
| |
Collapse
|
2
|
Kułakowska A, Jurkiewicz P, Sýkora J, Benda A, Mely Y, Hof M. Fluorescence Lifetime Tuning—A Novel Approach to Study Flip-Flop Kinetics in Supported Phospholipid Bilayers. J Fluoresc 2009; 20:563-9. [DOI: 10.1007/s10895-009-0581-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
|
3
|
|
4
|
Movileanu L, Popescu D, Victor G, Turcu G. Selective association of phospholipids as a clue for the passive flip-flop diffusion through bilayer lipid membranes. Biosystems 1997; 40:263-75. [PMID: 9116189 DOI: 10.1016/s0303-2647(96)01650-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We showed that the investigation of the selective association of phospholipids might contribute to the insight of the flip-flop diffusion processes. The process of selective association was studied quantitatively by testing the association probabilities for both parallel and anti-parallel orientations of the polar headgroups. The model of double chain binary mixture confirms a high capacity of phospholipids for self-association in parallel configuration of the electric dipole moments whether the cross-sectional area of the polar headgroups are in an usual range of 25-55 A2. It is demonstrated that the aggregation of a class of phospholipids from a binary mixture is strongly dependent on the dipole-dipole interaction between the same phospholipids and is modulated by the magnitude of the electric dipole moment of the other phospholipids from that binary mixture. There are a great number of mechanisms involved in the transbilayer movement of phospholipids. We referred here only to the passive transport of lipids from one monolayer to the other. The flip-flop mechanisms raised in this paper are the breakdown of bilayer due to the increase of the packing density and the inversion of the coupled phospholipids from the opposite monolayers of the same bilayer. Thus, the pair formation promoting a drop in occupied volume decreases the packing pressure in the respective monolayer and consequently triggers a flip-flop into the other direction since the packing pressure in the other monolayer has not dropped. According to the present model for the binary mixtures of double-chain lipids, the rate of the flip-flop diffusion decreased by increasing the number of the methylene groups added to the acyl chain. This dependence may be perturbed whether the phospholipids possesses a very high cross-section area of the polar headgroups (a > 55 A2). We think that the selective association of phospholipids is neither exclusively, nor only involved in promoting the transbilayer diffusion of phospholipids. Most probably, the selective association determines some phospholipid domains that attract certain particular proteins so that it can modulate the protein activity.
Collapse
Affiliation(s)
- L Movileanu
- Biophysical Laboratory, University of Bucharest, Faculty of Biology, Romania
| | | | | | | |
Collapse
|
5
|
Christiansen VJ, Sims PJ, Hamilton KK. Complement C5b-9 increases plasminogen binding and activation on human endothelial cells. Arterioscler Thromb Vasc Biol 1997; 17:164-71. [PMID: 9012652 DOI: 10.1161/01.atv.17.1.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Deposition of the terminal complement proteins (C5b-9) on human endothelial cells can result in cell lysis or nonlytic alterations of cell function including procoagulant responses. Because regulation of fibrinolysis is a central endothelial function and because C9 contains a carboxyl-terminal lysine similar to other proteins that bind and facilitate activation of plasminogen (PG), the effects of complement injury on PG binding and activation on these cells were investigated. Activation of complement through deposition of C5b67 complexes on endothelial cells resulted in a small increase (approximately 20%) in PG binding. Incorporation of C8 into C5b-8 resulted in no further increase in binding; however, specific 125I-PG binding was increased by approximately 100% after C5b-9 deposition. Moreover, PG was found to bind specifically to C7 and C9. The PG bound to endothelial cells after C5b-9 deposition was readily activated by tissue-type plasminogen activator (TPA). In a cell-free system, complement C9 and a synthetic peptide composed of the 20 carboxyl-terminal amino acids of C9 enhanced PG activation by TPA. Removal of the carboxyl-terminal lysine of C9 abolished the enhancement of PG activation without diminishing PG binding. We conclude that membrane C9 may comprise a binding site for PG and serve to enhance activation of this zymogen by TPA. These findings suggest that immune injury to the endothelium may enhance both the fibrin-generating and fibrinolytic capacity of the vessel wall.
Collapse
Affiliation(s)
- V J Christiansen
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA.
| | | | | |
Collapse
|
6
|
Bevers EM, Comfurius P, Zwaal RF. Regulatory mechanisms in maintenance and modulation of transmembrane lipid asymmetry: pathophysiological implications. Lupus 1996; 5:480-7. [PMID: 8902787 DOI: 10.1177/096120339600500531] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The two leaflets of the plasma membrane of eukaryotic cells differ in lipid composition: the outer leaflet comprises mainly neutral choline containing phospholipids, whereas the aminophospholipids reside almost exclusively in the cytoplasmic leaflet. The importance of transmembrane lipid asymmetry may be judged from the fact that the cell invests energy to maintain this situation for which at least two regulatory mechanisms are held responsible. A translocase, selective for aminophospholipids, acts as an ATP-dependent pump for rapid inward movement of phosphatidylserine (PS) and phosphatidylethanolamine; in addition, a non-selective, but also ATP-dependent pump causes outward movement of phospholipids, be it at a much lower rate compared to the inward transport by the aminophospholipid translocase. These two systems, acting in concert, are thought to be the main players in the maintenance of a dynamic equilibrium of the phospholipids over both membrane leaflets. Dissipation of membrane lipid asymmetry can be elicited in different cell types under a variety of conditions; in particular, platelets upon activation rapidly lose their normal plasma membrane lipid distribution, but also in other blood cells, lipid asymmetry can be lost, be it at a much lower rate and extent than in platelets. A putative protein, referred to as "scramblase' has been described, which requires the continuous presence of elevated intracellular Ca(2+)-levels, to allow a rapid, non-selective and bidirectional transbilayer movement of phospholipids. Although scrambling of lipids does not require ATP as such, preliminary studies suggest the possible involvement of one or more phosphorylated proteins. The most prominent consequence of the loss of phospholipid asymmetry is exposure of PS in the outer leaflet of the plasma membrane. Surface-exposed PS serves several important physiological functions: it promotes assembly of enzyme complexes of the coagulation cascade, it forms a signal for cell-cell recognition, which is important for cell scavenging processes. Surface-exposure of PS is an early phenomenon of apoptosis and appears to be involved in efficient removal of these cells. In addition, PS in the outer leaflet of cells is thought to play a role in cell fusion processes. It may be clear from the foregoing, that the amount of PS present at the cell surface needs to be tightly controlled, and that an impairment of this process leads to either excessive- or diminished exposition of PS which may have several pathophysiological consequences.
Collapse
Affiliation(s)
- E M Bevers
- Cardiovascular Research Institute Maastricht, University of Limburg, The Netherlands
| | | | | |
Collapse
|
7
|
Abstract
The membrane attack complex of complement is formed by the molecular fusion of the five terminal complement proteins, C5, C6, C7, C8, and C9. While the assembly process on a target membrane and its modulation by restriction factors present on host cells is now quite well understood the molecular details of the architecture of the complex still need much further clarification. This is especially true for the interaction of the last acting protein C9, which provides the cytotoxic action of the complex, with the precursor C5b-8 complex. Because of this lack of structural details the molecular mechanisms that lead to complement-mediated cell death remain cryptic, however, it is hoped that recent advances in controlling the assembly process and in site-specific modification of the terminal complement proteins by recombinant DNA techniques should change this predicament quickly.
Collapse
Affiliation(s)
- A F Esser
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City 64110
| |
Collapse
|
8
|
Chang C, Zhao J, Wiedmer T, Sims P. Contribution of platelet microparticle formation and granule secretion to the transmembrane migration of phosphatidylserine. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53161-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
9
|
Dahlbäck B, Wiedmer T, Sims PJ. Binding of anticoagulant vitamin K-dependent protein S to platelet-derived microparticles. Biochemistry 1992; 31:12769-77. [PMID: 1463747 DOI: 10.1021/bi00166a009] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vitamin K-dependent protein S is an anticoagulant plasma protein serving as cofactor to activated protein C in degradation of coagulation factors Va and VIIIa on membrane surfaces. In addition, it forms a noncovalent complex with complement regulatory protein C4b-binding protein (C4BP), a reaction which inhibits its anticoagulant function. Both forms of protein S have affinity for negatively charged phospholipids, and the purpose of the present study was to elucidate whether they bind to the surface of activated platelets or to platelet-derived microparticles. Binding of protein S to human platelets stimulated with various agonists was examined with FITC-labeled monoclonal antibodies and fluorescence-gated flow cytometry. Protein S was found to bind to membrane microparticles which formed during platelet activation but not to the remnant activated platelets. Binding to microparticles was saturable and maximum binding was seen at approximately 0.4 microM protein S. It was calcium-dependent and reversed after the addition of EDTA. Inhibition experiments with monoclonal antibodies suggested the gamma-carboxyglutamic acid containing module of protein S to be involved in the binding reaction. An intact thrombin-sensitive region of protein S was not required for binding. The protein S-C4BP complex did not bind to microparticles or activated platelets even though it bound to negatively charged phospholipid vesicles. Intact protein S supported binding of both protein C and activated protein C to microparticles. Protein S-dependent binding of protein C/activated protein C was blocked by those monoclonal antibodies against protein S that inhibited its cofactor function. In conclusion, we have found that free protein S binds to platelet-derived microparticles and stimulates binding of protein C/activated protein C.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- B Dahlbäck
- Department of Clinical Chemistry, University of Lund, Malmö General Hospital, Sweden
| | | | | |
Collapse
|
10
|
Schweinle JE, Nishiyasu M. Sub-minimal inhibitory concentrations of cefmetazole enhance serum bactericidal activity in vitro by amplifying poly-C9 deposition. J Clin Invest 1992; 89:1198-207. [PMID: 1556181 PMCID: PMC442979 DOI: 10.1172/jci115703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Serum-resistant organisms grown in sub-minimal inhibitory concentrations (subMICs) of antibiotics in vitro may be rendered sensitive to complement-mediated, serum bactericidal activity. We measured 125I-C3 and 125I-C9 deposition on genetically serum resistant Salmonella montevideo SH5770 (SH5770) that was rendered serum sensitive by growth in sub-MICs of cefmetazole (CMZ), a parenteral, second generation, cephamycin-group antibiotic. Three times as much C3 and over six times as much C9 bound to SH5770 grown in one-fourth the MIC of CMZ compared to broth-grown bacteria. SDS-PAGE analysis and autoradiography showed that neither the ratio of C3b:iC3b (approximately 1:2.5) nor the nature of the C3-bacterial bond was changed by growing the organisms in CMZ. Large amounts of complement membrane attack complexes containing poly-C9 were seen only on CMZ-grown SH5770 by SDS-PAGE and autoradiography. Poly-C9 was also detected only on CMZ-grown bacteria by indirect immunofluorescence and ELISA using a murine monoclonal antibody directed against a neoantigen of poly-C9. Bacterial hydrophobicity increased after growth in CMZ, and transmission electron micrographs of CMZ-grown SH5770 showed cell wall disruption and blebbing. These results indicate that growth in subMICs of CMZ increases bacterial hydrophobic domains available for interacting with the membrane attack complex, C5b-9, allowing formation and stable insertion of bactericidal complexes containing poly-C9.
Collapse
Affiliation(s)
- J E Schweinle
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510
| | | |
Collapse
|
11
|
Hamilton KK, Sims PJ. The terminal complement proteins C5b-9 augment binding of high density lipoprotein and its apolipoproteins A-I and A-II to human endothelial cells. J Clin Invest 1991; 88:1833-40. [PMID: 1752944 PMCID: PMC295750 DOI: 10.1172/jci115504] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Terminal complement protein complexes C5b-9 have been found in human atherosclerotic lesions. Insertion of C5b-9 in the endothelial cell membrane alters permeability, induces membrane vesiculation, and activates secretion. We hypothesized that complement might also alter interactions of the endothelial surface with lipoproteins, particularly high density lipoprotein (HDL), which is reported to inhibit C5b-9-induced hemolysis. We now demonstrate that exposure to C5b-9 increases (by 2- to 50-fold) specific binding of HDL and its apolipoproteins (apo) A-I and A-II to endothelial cells. Binding to cells exposed to antibody, C5b67, and C5b-8 was virtually unchanged. Enhanced binding was also dependent on the number of C5b-9 complexes deposited on the cells. Other agonists that activate endothelial secretion did not augment binding. Calcium was required for full exposure of new binding sites by C5b-9. The C5b-9-induced increase in binding was independent of the increase observed after cholesterol loading. In addition, apo A-I and A-II appear to compete for the same binding sites on untreated and C5b-9-treated cells. In contrast to the data reported for red cells, we were unable to detect significant inhibition of C5b-9-mediated endothelial membrane permeabilization by HDL (up to 1 mg/ml) or by apo A-I (up to 100 micrograms/ml). These data demonstrate that the C5b-9 proteins enhance endothelial binding of HDL and its apoproteins, suggesting that intravascular complement activation may alter cholesterol homeostasis in the vessel wall.
Collapse
Affiliation(s)
- K K Hamilton
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City 73190
| | | |
Collapse
|
12
|
Abstract
Membranes allow the rapid passage of unchanged lipids. Phospholipids on the other hand diffuse very slowly from one monolayer to another with a half-time of several hours. This slow spontaneous movement in a pure lipid bilayer can be selectively modulated in biological membranes by intrinsic proteins. In microsomes, and probably in bacterial membranes, non-specific phospholipid flippases allow the rapid redistribution of newly synthesized phospholipids. In eukaryotic plasma membranes, aminophospholipid translocase selectively pumps phosphatidylserine (PS) and phosphatidylethanolamine (PE) from the outer to the inner leaflet and establishes a permanent lipid asymmetry. The discovery of an aminophospholipid translocase in chromaffin granules proves that eukaryotic organelles may also contain lipid translocators.
Collapse
Affiliation(s)
- A Zachowski
- Institut de Biologie Physico-Chimique, Paris, France
| | | |
Collapse
|