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Chen DX, Chu WY, Liu XL, Nong XX, Li YL, Du SJ, Zhang JS. Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. ACTA ACUST UNITED AC 2012; 23:70-6. [PMID: 22409749 DOI: 10.3109/19401736.2011.653799] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.
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Affiliation(s)
- Dun-Xue Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, People's Republic of China
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2
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Abstract
Apocytochrome c has a potent ability to insert spontaneously into membrane. To identify which sequences were critical for this insertion activity, a series of peptides N19, C8, C15 and C21, corresponding to sequences 1-19, 81-88, 74-88 and 68-88 of apocytochrome c, respectively, were synthesized and purified. Insertion ability into phospholipid monolayer, intrinsic fluorescence emission spectra, and the accessibility of peptide C21 to fluorescence quenchers: KI, acrylamide and HB showed that only segment 68-88 could insert into membrane, while other segments did not. CD spectra demonstrated that its interaction with liposomes containing negatively charged phospholipid could induce a partial alpha-helical conformation in peptide C21. It is interesting to note that a cooperation exists between segment 68-88 and 1-19 in the insertion of apocytochrome c and consequently translocation across membrane.
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Affiliation(s)
- Xiaoping Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, The Chinese Academy of Sciences, Beijing, China
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3
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Wang X, Han X, Jia S, Yang F. Change of apocytochrome c translocation across membrane in consequence of hydrophobic segment deletion. Mol Cell Biochem 2002; 233:39-47. [PMID: 12083378 DOI: 10.1023/a:1015502800914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Wild-type apocytochrome c and its hydrophobic segment deleted mutants, named delta28-39, delta72-86 and delta28-29/72-86 were constructed, expressed and highly purified respectively. Insertion ability into phospholipid monolayer, inducing leakage of entrapped fluorescent dye fluorescein sulfonate (FS) from liposomes, and translocation across model membrane system showed that the wild-type apoprotein and delta28-39 almost exhibited the same characteristics, while mutants with segment 72-86 deletion did not. Furthermore, CD spectra, intrinsic fluorescence emission spectra, and the accessibility of the protein to the fluorescence quenchers: KI, acrylamide and HB demonstrated that the segment 72-86 deletion has a significant effect on the conformational changes of apocytochrome c following its interaction with phospholipid. On the basis of these results it is postulated that the C-terminal hydrophobic segment 72-86 plays an important role in the translocation of apocytochrome c across membrane.
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Affiliation(s)
- Xiaoping Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, The Chinese Academy of Sciences, Beijing
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4
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Bryson EA, Rankin SE, Goormaghtigh E, Ruysschaert JM, Watts A, Pinheiro TJ. Structure and dynamics of lipid-associated states of apocytochrome c. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:1390-6. [PMID: 10691976 DOI: 10.1046/j.1432-1327.2000.01138.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Apocytochrome c (apocyt c), which in aqueous solution is largely unstructured, acquires an alpha-helical conformation upon association with lipid membranes. The extent of alpha-helix induced in apocyt c is lipid-dependent and this folding process is driven by both electrostatic and hydrophobic lipid-protein interactions. The structural and dynamic properties of apocyt c in lipid membranes were investigated by attenuated total reflection Fourier transform infrared spectroscopy combined with amide H-D exchange kinetics. Apocyt c acquires a higher content of alpha-helical structure with negatively charged membranes than with zwitterionic ones. For all membranes studied here, the helices of these partially folded states of apocyt c have a preferential orientation perpendicular to the plane of the lipid membrane. The H-D exchange revealed that a small fraction of amide protons of apocyt c, possibly associated with a stable folded domain protected by the lipid, remained protected from exchange over 20 min. However, a large fraction of amide protons exchanged in less than 20 min, indicating that the helical states of apocyt c in lipid membranes are very dynamic.
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Affiliation(s)
- E A Bryson
- Department of Biological Sciences, University of Warwick, Coventry, UK
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5
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Wang X, Dumont ME, Sherman F. Sequence Requirements for Mitochondrial Import of Yeast Cytochrome c. J Biol Chem 1996. [DOI: 10.1074/jbc.271.12.6594] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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6
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de Jongh HH, Brasseur R, Killian JA. Orientation of the alpha-helices of apocytochrome c and derived fragments at membrane interfaces, as studied by circular dichroism. Biochemistry 1994; 33:14529-35. [PMID: 7981214 DOI: 10.1021/bi00252a020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The orientation of the different helical regions of the mitochondrial precursor protein apocytochrome c has been studied using circular dichroism on isolated fragments of this protein associated with oriented films composed of various phospholipids [de Jongh, H. H. J., Goormaghtigh, E., & Killian, J. A. (1994) Biochemistry (preceding article in this issue)]. Both the N and C terminus adopt helical structures in a membrane environment. The middle region can also be helical, but only in the presence of the N-terminal domain of the protein. In the presence of the unsaturated lipids dioleoylphosphatidylcholine and dioleoylphosphatidylglycerol, all three helices are found to have a preferred orientation perpendicular to the membrane normal, whereas in the presence of the saturated lipids dimyristoylphosphatidylcholine and dimyristoylphosphatidylglycerol, the terminal helices are preferentially oriented parallel to the membrane normal. In films composed of dioleoylphosphatidylserine, it is found that the N-terminal helix is oriented preferentially perpendicular, whereas the C-terminal helix is aligned more parallel to the membrane normal. The differences in preferred orientation between the terminal helices are demonstrated by molecular modeling of the helices at a water-lipid interface. The results are discussed in light of the translocation of apocytochrome c over the outer mitochondrial membrane, an important step in the import process of this protein in mitochondria.
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Affiliation(s)
- H H de Jongh
- Department of Biochemistry of Membranes, University of Utrecht, The Netherlands
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7
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Zhang F, Rowe ES. Calorimetric studies of the interactions of cytochrome c with dioleoylphosphatidylglycerol extruded vesicles: ionic strength effects. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1193:219-25. [PMID: 8054342 DOI: 10.1016/0005-2736(94)90156-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cytochrome c has been studied as an example of a peripheral membrane protein which interacts with the lipids as well as the proteins of the inner mitochondrial membrane. In order to elucidate the thermodynamic properties of these interactions, isothermal titration calorimetry and differential scanning calorimetry (DSC) were used to study the binding of cytochrome c to negatively charged dioleoylphosphatidylglycerol (DOPG) extruded vesicles as a function of ionic strength. The binding constant and enthalpy of association decrease with increasing ionic strength, with no binding detected above 0.5 M NaCl. The enthalpy of the binding of cytochrome c to DOPG-extruded vesicles was 15 kcal/mol, and the binding constant was 6 x 10(6) M-1 at the lowest ionic strengths. The minimum size of the lipid cluster to which the protein bound was found to be approx. 9 lipid molecules in the titration calorimetry measurements and as low as 5 lipid molecules in the DSC measurements. The stability of the bound cytochrome c was found to be reduced; the thermal denaturation temperature was lowered from 83 to 50 degrees when bound to DOPG. The results of this study support previous suggestions that cytochrome c may undergo a conformational change when it binds to charged lipids such as DOPG. The results also support the suggestion that the protein penetrates partially into the lipid bilayer.
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Affiliation(s)
- F Zhang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City 66103
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8
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de Jongh HH, Killian JA, de Kruijff B. A water-lipid interface induces a highly dynamic folded state in apocytochrome c and cytochrome c, which may represent a common folding intermediate. Biochemistry 1992; 31:1636-43. [PMID: 1310614 DOI: 10.1021/bi00121a008] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, we have used CD and NMR techniques to investigate the secondary structure of (apo-) cytochrome c both in solution and when associated with micelles. In aqueous solution, the holoprotein cytochrome c is tightly folded at secondary and tertiary levels and differs strongly from its random-coiled precursor. However, in the presence of 12-PN/12-Pglycol (9:1) micelles, we observed a remarkable resemblance between the CD spectra of these partially helical proteins. The water-lipid interface induces a secondary folding of apocytochrome c, whereas cytochrome c is suggested to partially lose its tertiary structure. The exchange of all amide protons and, using deuterium-labeled proteins, of all amide deuterons with the solvent was monitored by NMR. A rapid exchange rate was observed, indicating that these folding states are highly dynamic. Saturation-transfer NMR of micelle-associated apocytochrome c showed that the exchange takes place at the (sub-) second time scale. The holoprotein in the presence of micelles was found to have two distinct exchange rates: (1) a fast rate, comparable to that found for the micelle-associated precursor and 4.5 times slower than that of the random-coiled apocytochrome c, and (2) a slow rate which is 75 times slower than the precursor in solution. Urea denaturation studies showed the micelle-bound proteins to have a low helix stability, which explains the inability of the lipid-induced secondary structure to prevent its labile protons from rapid exchange. The uniqueness of this lipid-induced highly dynamic folding state of (apo-) cytochrome c is demonstrated by comparison with amphiphilic polypeptides like melittin, and its implications for membrane translocation and functioning are discussed.
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Affiliation(s)
- H H de Jongh
- Centre for Biomembranes and Lipid Enzymology, University of Utrecht, The Netherlands
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9
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Hakvoort TB, Sprinkle JR, Margoliash E. Reversible import of apocytochrome c into mitochondria. Proc Natl Acad Sci U S A 1990; 87:4996-5000. [PMID: 2164215 PMCID: PMC54248 DOI: 10.1073/pnas.87.13.4996] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
35S-labeled Drosophila melanogaster apocytochrome c was made by in vitro transcription/translation of the gene and purified to the monomeric, fully reduced form. It was found that in the presence of a wheat germ extract factor there was a high-affinity phase of the uptake into mouse liver mitochondria at 10-300 pM apocytochrome c, and a lower-affinity phase through 4000 pM. Without the factor, the high-affinity phase was absent. The stimulatory effect of the factor could not be elicited with various reductants, such as NADH, FMN, and ferrous protoheme IX. Conversely, when mitochondria loaded with apocytochrome c were resuspended in fresh medium, the protein readily reequilibrated. Successive washings depleted greater than 95% of the associated apoprotein but removed no holoprotein. Proteases (proteinase K or trypsin) added to a suspension of mitochondria loaded with apoprotein digested an amount of apoprotein similar to that which would have been dissociated during the same time, as measured by successive washings in the absence of protease. Mitochondria loaded with apoprotein and similarly treated with protease continued exporting the apoprotein, even after the protease was inhibited and removed, suggesting that most of the apoprotein associated with the organelle was in a protease-resistant compartment. Apocytochrome c mutants in which serines or alanines replaced cysteines 14 and 17, which bind the prosthetic group, behaved like the cysteine-containing protein, indicating that the covalent attachment of the heme is unrelated to the translocation of the apoprotein.
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Affiliation(s)
- T B Hakvoort
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208
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Jordi W, de Kroon AI, Killian JA, de Kruijff B. The mitochondrial precursor protein apocytochrome c strongly influences the order of the headgroup and acyl chains of phosphatidylserine dispersions. A 2H and 31P NMR study. Biochemistry 1990; 29:2312-21. [PMID: 2159798 DOI: 10.1021/bi00461a015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Deuterium and phosphorus nuclear magnetic resonance techniques were used to study the interaction of the mitochondrial precursor protein apocytochrome c with headgroup-deuterated (dioleoylphosphatidyl-L-[2-2H1]serine) and acyl chain deuterated (1,2-[11,11-2H2]dioleoylphosphatidylserine) dispersions. Binding of the protein to dioleoylphosphatidylserine liposomes results in phosphorus nuclear magnetic resonance spectra typical of phospholipids undergoing fast axial rotation in extended liquid-crystalline bilayers with a reduced residual chemical shift anisotropy and an increased line width. 2H NMR spectra on headgroup-deuterated dioleoylphosphatidylserine dispersions showed a decrease in quadrupolar splitting and a broadening of the signal on interaction with apocytochrome c. Addition of increasing amounts of apocytochrome c to the acyl chain deuterated dioleoylphosphatidylserine dispersions results in the gradual appearance of a second component in the spectra with a 44% reduced quadrupolar splitting. Such large reduction of the quadrupolar splitting has never been observed for any protein studied yet. The lipid structures corresponding to these two components could be separated by sucrose gradient centrifugation, demonstrating the existence of two macroscopic phases. In mixtures of phosphatidylserine and phosphatidylcholine similar effects are observed. The induction of a new spectral component with a well-defined reduced quadrupolar splitting seems to be confined to the N-terminus since addition of a small hydrophilic amino-terminal peptide (residues 1-38) also induces a second component with a strongly reduced quadrupolar splitting. A chemically synthesized peptide corresponding to amino acid residues 2-17 of the presequence of the mitochondrial protein cytochrome oxidase subunit IV also has a large perturbing effect on the order of the acyl chains, indicating that the observed effects may be a property shared by many mitochondrial precursor proteins. In contrast, binding of the mature protein, cytochrome c, to acyl chain deuterated phosphatidylserine dispersions has no effect on the deuterium and phosphorus nuclear magnetic resonance spectra, thereby demonstrating precursor-specific perturbation of the phospholipid order. The inability of holocytochrome c to perturb the phospholipid order is due to folding of this protein, since unfolding of cytochrome c by heat or urea treatment results in similar effects on dioleoylphosphatidylserine bilayers, as observed for the unfolded precursor. Implications of these data for the import of apocytochrome c into mitochondria will be discussed.
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Affiliation(s)
- W Jordi
- Centre for Biomembranes and Lipid Enzymology, State University of Utrecht, The Netherlands
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11
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Abstract
Intracellular phosphorylation is an important step in active uptake and utilization of carbohydrates. For example glucose and glycerol enter the liver cell along the extra intracellular gradient by facilitated diffusion through specific carriers and are concentrated inside the cell by phosphorylation via hexokinase or glycerol kinase. Depending on the function of the respective tissue the uptake of carbohydrates serves different metabolic purposes. In brain and kidney medulla cells which depend on carbohydrates, glucose and glycerol are taken up according to the energy demand. However, in tissues such as muscle which synthesize glycogen or like liver which additionally produce fat from glucose, the uptake of carbohydrates has to be regulated according to the availability of glucose and glycerol. How the reversible coupling of the kinases to the outer membrane pore and the mitochondrial ATP serves to fulfil these specific requirements will be explained as well as how this regulates the carbohydrate uptake in brain according to the activity of the oxidative phosphorylation and how this allows glucose uptake in liver and muscle to persist in the presence of high glucose 6-phosphate without activating the rate of glycolysis.
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Affiliation(s)
- D Brdiczka
- Fakultät für Biologie, Universität Konstanz, Federal Republic of Germany
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12
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Jordi W, Nibbeling R, de Kruijff B. Phenethyl alcohol disorders phospholipid acyl chains and promotes translocation of the mitochondrial precursor protein apocytochrome c across a lipid bilayer. FEBS Lett 1990; 261:55-8. [PMID: 1689674 DOI: 10.1016/0014-5793(90)80635-v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction of phenethyl alcohol with model membranes and its effect on translocation of the chemically prepared mitochondrial precursor protein apocytochrome c across a lipid bilayer was studied. Phenethyl alcohol efficiently penetrates into monolayers and causes acyl chain disordering judged from deuterium nuclear magnetic resonance measurements with specific acyl chain-deuterated phospholipids. Translocation of apocytochrome c across a phospholipid bilayer was stimulated on addition of phenethyl alcohol indicating that the efficiency of translocation of this precursor protein is enhanced due to a disorder of the acyl chain region of the bilayer.
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Affiliation(s)
- W Jordi
- Centre for Biomembranes and Lipid Enzymology, State University of Utrecht, The Netherlands
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13
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Yan SC, Grinnell BW, Wold F. Post-translational modifications of proteins: some problems left to solve. Trends Biochem Sci 1989; 14:264-8. [PMID: 2672445 DOI: 10.1016/0968-0004(89)90060-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Three major questions regarding the post-translational modification of amino acid side chains in proteins are briefly considered: (1) What are the biological functions of the reactions, (2) what is the specificity of the processing reactions in selecting only a few or sometimes even only one residue for modification, and (3) how do we solve the uniqueness of the processing steps in the production of recombinant proteins? The answers to these questions are not obvious at this time.
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14
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De Vrije T, Batenburg AM, Jordi W, De Kruijff B. Inhibition of PhoE translocation across Escherichia coli inner-membrane vesicles by synthetic signal peptides suggests an important role of acidic phospholipids in protein translocation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 180:385-92. [PMID: 2466667 DOI: 10.1111/j.1432-1033.1989.tb14660.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To obtain insight into the mechanism of precursor protein translocation across membranes, the effect of synthetic signal peptides and other relevant (poly)peptides on in vitro PhoE translocation was studied. The PhoE signal peptide, associated with inner membrane vesicles, caused a concentration-dependent inhibition of PhoE translocation, as a result of a specific interaction with the membrane. Using a PhoE signal peptide analog and PhoE signal peptide fragments, it was demonstrated that the hydrophobic part of the peptide caused the inhibitory effect, while the basic amino terminus is most likely important for an optimal interaction with the membrane. A quantitative analysis of our data and the known preferential interaction of synthetic signal peptides with acidic phospholipids in model membranes strongly suggest the involvement of negatively charged phospholipids in the inhibitory interaction of the synthetic PhoE signal peptide with the inner membrane. The important role of acidic phospholipids in protein translocation was further confirmed by the observation that other (poly)peptides, known to have both a high affinity for acidic lipids and hydrophobic interactions with model membranes, also caused strong inhibition of PhoE translocation. The implication of these results with respect to the role of signal peptides in protein translocation is indicated.
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Affiliation(s)
- T De Vrije
- Centre for Biomembranes and Lipid Enzymology, University of Utrecht, The Netherlands
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15
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Differential interactions of apo- and holocytochrome c with acidic membrane lipids in model systems and the implications for their import into mitochondria. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84950-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Jordi W, Zhou LX, Pilon M, Demel RA, de Kruijff B. The importance of the amino terminus of the mitochondrial precursor protein apocytochrome c for translocation across model membranes. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94175-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Nicholson DW, Hergersberg C, Neupert W. Role of cytochrome c heme lyase in the import of cytochrome c into mitochondria. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37385-x] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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