Study of polytopic membrane protein topological organization as a function of membrane lipid composition.

A protocol is described using lipid mutants and thiol-specific chemical reagents to study lipid-dependent and host-specific membrane protein topogenesis by the substituted-cysteine accessibility method as applied to transmembrane domains (SCAM). SCAM is adapted to follow changes in membrane protein topology as a function of changes in membrane lipid composition. The strategy described can be adapted to any membrane system.

THE EFFECTS OF STREPTOZOTOCIN DIABETES AND DIETARY IRON INTAKE ON CATALASE, GLUTATHIONE PEROXIDASE, SUPEROXIDE DISMUTASE AND LIPID PEROXIDATION IN CARDIAC AND SKELETAL MUSCLES OF RATS

Catalase, glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) prevent oxygen free radical mediated tissue damage. Diabetes increases and a low dietary intake of iron decreases catalase activity in muscle. Therefore, the combined effects of diabetes and iron deficiency on the free radical scavenging enzyme system and lipid peroxidation were studied. Male, weanling rats were injected with streptozotocin (65 mg/kg, IV) and fed diets containing either 35 ppm iron (Db + Fe) or 8 ppm iron (Db $-$ Fe). Sham injected animals served as iron adequate (C + Fe) or iron deficient (C $-$ Fe) controls. Heart, gastrocnemius (GT), soleus and tibialis anterior (TA) muscles were dissected, weighted and analyzed for catalase, GSH-Px and SOD activities after 3, 6 or 9 weeks on the respective diets. The TBA assay was used to assess lipid peroxidation in the GT muscle. Diabetes elevated catalase activity in all muscles while it had a slight lowering effect on SOD and GSH-Px activities in the GT and TA muscles. In the C $-$ Fe rats, catalase activity declined and remained depressed in all muscles except the heart. There was an elevation in GSH-Px and SOD in the GT muscles of these animals after 6 weeks but not after 9 weeks of consuming the low iron diet. The Db $-$ Fe animals were unable to respond to the diabetic state with catalase activity as high as observed in the Db + Fe rats. Treatment with insulin or iron returned catalase to control levels. The C $-$ Fe animals had significantly lower levels of lipid peroxidation than the other groups at 6 and 9 weeks. Refeeding an iron adequate diet resulted in an increase in lipid peroxidation levels. These studies indicate that skeletal muscle free radical scavenging enzymes are sensitive to metabolic states and that dietary iron influences lipid peroxidation in this tissue. ^

Lipid-protein interactions drive membrane protein topogenesis in accordance with the positive inside rule.

Transmembrane domain orientation within some membrane proteins is dependent on membrane lipid composition. Initial orientation occurs within the translocon, but final orientation is determined after membrane insertion by interactions within the protein and between lipid headgroups and protein extramembrane domains. Positively and negatively charged amino acids in extramembrane domains represent cytoplasmic retention and membrane translocation forces, respectively, which are determinants of protein orientation. Lipids with no net charge dampen the translocation potential of negative residues working in opposition to cytoplasmic retention of positive residues, thus allowing the functional presence of negative residues in cytoplasmic domains without affecting protein topology.

Molecular genetic approaches to defining lipid function.

Lipids fulfill multiple and diverse functions in cells. Establishing the molecular basis for these functions has been challenging due to the lack of catalytic activity of lipids and the pleiotropic effects of mutations that affect lipid composition. By combining molecular genetic manipulation of membrane lipid composition with biochemical characterization of the resulting phenotypes, the molecular details of novel lipid functions have been established. This review summarizes the results of such a combined approach to defining lipid function in bacteria.

Redistribution of plasma membrane phosphatidylserine during erythroid development

Phosphatidylserine (PS) is not only one of the structural components of the plasma membrane, it also plays an important role in blood coagulation, and cell-cell interactions during aging and apoptosis.^ Here we studied some alterations that occur in membrane phosphatidylserine asymmetry during erythroid differentiation-associated apoptosis and erythrocyte aging and characterized some aspects in the regulation of PS asymmetry.^ Erythroleukemia cells, frequently used to study erythroid development, undergo apoptosis when induced to differentiate along the erythroid lineage. In the case of K562 cells induced to differentiate with hemin, this event is characterized by DNA fragmentation that correlates with downregulation of the survival protein BCL-xL and ultimately the result is cell death. We showed here that reorientation of PS from the inner-to-outer plasma membrane leaflet and inhibition of the aminophospholipid translocase are also events observed upon hemin treatment. We observed that constitutive expression of BCL-2 did not inhibit the alterations caused by hemin in membrane lipid asymmetry and only slightly prevented hemin-induced DNA fragmentation. On the other hand, BCL-2 effectively inhibited actinomycin D and staurosporine-induced DNA fragmentation and the appearance of PS at the outer leaflet of these cells. z.VAD.fmk, a widely used caspases inhibitor, blocked DNA fragmentation induced by both hemin and actinomycin D but only inhibited PS externalization in cells treated with actinomycin D.^ These results showed that PS externalization occurs during differentiation-related apoptosis. Unlike the pharmacologically-induced event, however, hemin-induced PS redistribution seems to be regulated by a mechanism independent of BCL-2 and caspases.^ Membrane PS is externalized not only during apoptosis but also during red blood cell senescence. To study this event, we artificially induced cellular aging by in vitro storage or vesiculation in the presence of the amphipathic lipid dilauroylphosphatidylcholine. These cells were monitored for age-dependent changes in cell density by Percoll gradient centrifugation and assessed for alterations in membrane lipid asymmetry and their ability to be cleared in vivo. These experiments demonstrated a progressive increase in red cell density upon vesiculation and in vitro aging. The clearance rate of cells obtained after vesiculation, was biphasic in nature, showing a very rapid component together with a second component consistent with the clearance rates of control populations. Quantitation of PS in the outer leaflet of red cells revealed that membrane redistribution of PS occurred upon in vitro storage and vesiculation. Inhibition of the aminophospholipid translocase with the sulfhydryl-oxidant reagent pyridyldithioethylamine resulted in higher PS externalization and enhanced clearance of vesiculated RBC.^ These observations not only suggest that vesiculation may be the mechanism responsible for some of the characteristic changes in cell density and PS asymmetry that occur upon cell aging, but also confirm the role of PS in the recognition and clearance of senescent cells. ^

Membrane trafficking from lysosomes to the plasma membrane regulates phosphatidylserine externalization during apoptosis

Programmed cell death is characterized by tightly controlled temporal and spatial intracellular Ca2+ responses that regulate the release of key proapoptotic proteins from mitochondria to the cytosol. Since apoptotic cells retain their ability to exclude membrane impermeable dyes, it is possible that the cells evoke repair mechanisms that, similar to those in normal cells, patch any damaged areas of the plasma membrane that preclude dye permeation. One critical distinction between plasma membrane repair in normal and apoptotic cells is the preservation of membrane lipid asymmetry. In normal cells, phosphatidylserine (PS) retains its normal asymmetric distribution in the inner membrane leaflet. In apoptotic cells, PS redistributes to the outer membrane leaflet by a Ca2+ dependent mechanism where it serves as a recognition ligand for phagocytes(1). In this study Ca 2+-specific fluorescent probes were employed to investigate the source of Ca2+ required for PS externalization. Experiments employing Rhod2-AM, calcium green 1, fura2-AM and the aqueous space marker FITC-dextran, demonstrated that exogenous Ca2+ imported with endocytotic vesicles into the cell was released into the cytosol in an apoptosis dependent manner. Labeling of the luminal side of the endocytotic vesicles with FITC-annexin 5, revealed that membrane lipid asymmetry was disrupted upon endosome formation. Specific labeling of the lysosomal luminal surface with the non-exchangeable membrane lipid probe, N-rhodamine-labeled-phosphatidylethanolamine (N-Rho-PE) and the lysosomal specific probe, lysotracker green, facilitated real-time monitoring of plasma membrane-to-endosome-to-lysosome transitions. Enforced elevation of cytosolic [Ca2+] with ionophore resulted in the redistribution of N-Rho-PE and PS from the inner membrane leaflet to the PM outer membrane leaflet. Identical results were obtained during apoptosis, however, the redistribution of both N-RhoPE and PS was dependent on the release of intra-lysosomal Ca2+ to the cytosol. Additional experiments suggested that lipid redistribution was dependent on the activity of lysosomal phospholipase A2 activity since lipid trafficking was abolished in the presence of chloroquine and lipase inhibitors. These data indicate that endosomal/lysosomal Ca2+ and the fusion of hybrid organelles to the plasma membrane regulates the externalization of PS during apoptosis. ^

THE HISTONE DEACETYLASE INHIBITOR, MS-275, SENSITIZES METASTATIC OSTEOSARCOMA TO FASL-INDUCED CELL DEATH: A ROLE FOR C-FLIP

The purpose of this study was to determine the effects of the histone deacetylase inhibitor, MS-275, on the Fas signaling pathway and susceptibility of osteosarcoma (OS) to Fas ligand (FasL)-induced cell death. OS metastasizes almost exclusively to the lungs. We have shown that Fas expression in OS cells is inversely correlated with their metastatic potential. Fas+ cells are rapidly eliminated when they enter the lungs via interaction with FasL, which is constitutively expressed in the lungs. Fas- OS cells escape this FasL-induced apoptosis and survive in the lung microenvironment. Moreover, upregulation of Fas in established OS lung metastases results in tumor regression. Therefore, agents that upregulate Fas expression or activate the Fas signaling pathway may have therapeutic potential. Treatment of Fas- metastatic OS cell lines with 2 μM MS-275 sensitized cells to FasL-induced cell death in vitro. We found that MS-275 did not alter the expression of Fas on the cell surface; rather it resulted in increased levels of Fas within the membrane lipid rafts, as demonstrated by an increase in Fas expression in detergent insoluble lipid raft fractions. We further demonstrated that following MS-275 treatment, Fas colocalized with GM1+ lipid rafts and that there was a decrease in c-FLIP (cellular FLICE-inhibitory protein) mRNA and protein. Downregulation of c-FLIP correlated with caspase activation and apoptosis induction. Transfection of cells with shRNA to c-FLIP also resulted in the localization of Fas to lipid rafts. These studies indicate that MS-275 sensitizes OS cells to FasL by upregulating the expression of Fas in membrane lipid rafts, which correlated with the downregulation of c-FLIP. Treatment of nu/nu-mice with established OS lung metastases with oral MS-275 resulted in increased apoptosis, a significant inhibition of c-FLIP expression in tumors and tumor regression. Histopathological examination of mice showed no significant organ toxicity. Overall, these results suggest that the mechanism by which MS-275 sensitizes OS cells and lung metastases to FasL-induced cell death may be by a reduction in the expression of c-FLIP.

Functional analysis of anionic phospholipids in cell metabolism in {\it Escherichia coli\/}

The major goal of this work was to understand the function of anionic phospholipid in E. coli cell metabolism. One important finding from this work is the requirement of anionic phospholipid for the DnaA protein-dependent initiation of DNA replication. An rnhA mutation, which bypasses the need for the DnaA protein through induction of constitutive stable DNA replication, suppressed the growth arrest phenotype of a $pgsA$ mutant in which the synthesis of anionic phospholipid was blocked. The maintenance of plasmids dependent on an $oriC$ site for replication, and therefore DnaA protein, was also compromised under conditions of limiting anionic phospholipid synthesis. These results provide support for the involvement of anionic phospholipids in normal initiation of DNA replication at oriC in vivo by the DnaA protein. In addition, structural and functional requirements of two major anionic phospholipids, phosphatidylglycerol and cardiolipin, were examined. Introduction into cells of the ability to make phosphatidylinositol did not suppress the need for the naturally occurring phosphatidylglycerol. The requirement for phosphatidylglycerol was concluded to be more than maintenance of the proper membrane surface charge. Examination of the role of cardiolipin revealed its ability to replace the zwitterionic phospholipid, phosphatidylethanolamine, in maintaining an optimal membrane lipid organization. This work also reported the DNA sequence of the cls gene, which encodes the CL synthase responsible for the synthesis of cardiolipin. ^

The role of BCL-2 in regulation of apoptosis susceptibility by modulation of glutathione

The role of oxidative stress and apoptosis has recently been recognized as an important determinant in the development of a variety of diseases known to man. The oncogene BCL-2 is known to regulate sensitivity to induction of apoptosis and appears to function in an antioxidant pathway by regulating glutathione. We have investigated various steps in the oxidative stress cascade to determine possible sites of action for BCL-2. The fluorescent probes H2DCFDA, dihydroethidium and cis-parinaric acid were used to quantitate generation of peroxides, superoxide and lipid peroxidation, respectively. While each of these agents was able to detect substantial increases in oxidative stress following exposure of cells to ionizing radiation, there was no significant difference between cells expressing high or low levels of BCL-2. Investigation of mitochondrial dysfunction during apoptosis revealed a possible site of bcl-2 intervention, but, analysis of kinetic events occurring during apoptosis suggested that the observed effect is not in the direct apoptotic effector pathway. When glutathione was studied, localization to the nucleus was observed in cells overexpressing BCL-2 that did not occur in cells lacking BCL-2. Additionally, nuclear accumulation of glutathione was sufficient to block granzyme b-mediated nuclear DNA fragmentation, poly (ADP-ribose) polymerase cleavage and caspase activity suggesting that nuclear accumulation of glutathione via a bcl-2 dependent process is functionally relevant to suppression of apoptosis. Thus, a model system emerges where BCL-2 is able to regulate a cell's ability to prevent apoptosis by modifying the cell's antioxidant systems at the organelle level to compensate for oxidative stresses placed upon it. ^

ROLE OF GLUTATHIONE IN FORMALDEHYDE METABOLISM AND TOXICITY

Glutathione (GSH) is involved in the detoxication of numerous chemicals exogenously exposed or endogenously generated. Exposure to these agents cause depletion of cellular GSH rendering these cells more susceptible to the toxic action of these same agents. Formaldehyde (CH(,2)O) was found to deplete cellular GSH, presumably by the formation of the GSH-CH(,2)O complex, S-hydroxymethylglutathione, and its rapid extrusion into the extracellular medium.^ The metabolism and toxicity of CH(,2)O were determined to be dependent upon cellular GSH in vitro and in vivo. The rate of CH(,2)O oxidation decreased and the extent of toxicity increased when isolated rat hepatocytes or strain A/J mice were pretreated with the GSH-depleting agent, diethyl maleate (DEM). Additional experiments were designed to further study the role GSH plays in detoxication using isolated rat hepatocytes.^ L-Methionine protected against the extent of lipid peroxidation and leakage of the cytosolic enzyme, lactate dehydrogenase (LDH), caused by CH(,2)O in DEM-pretreated hepatocytes, further supporting the protective role of GSH against cellular toxicity. The antioxidants, ascorbate, butylated hydroxytoluene, and (alpha)-tocopherol, were all protective against the extent of lipid peroxidation and leakage of LDH in isolated rat hepatocytes. Whereas L-methionine may be protective by increasing the cellular concentration of GSH which is used to detoxify free radicals or by facilitating the rate of CH(,2)O oxidation, the antioxidant, ascorbate, was protective without altering the rate of CH(,2)O oxidation or increasing cellular GSH levels. These results suggest that the free radical-mediated toxicity caused by CH(,2)O in DEM-pretreated hepatocytes is due to the further depletion of GSH by CH(,2)O and not to increased CH(,2)O persistence. How this further depletion in GSH by CH(,2)O in DEM-pretreated hepatocytes results in lipid peroxidation and cell death was further investigated.^ The further decrease in GSH caused by CH(,2)O in DEM-pretreated hepatocytes, suspected of stimulating lipid peroxidation and cell death, was found not to be due to depletion of mitochondrial GSH but to depletion of protein sulfhydryl groups. In addition, cellular toxicity appears more closely correlated with depletion of protein sulfhydryl groups than with an increase in cytosolic free Ca('2+). The combination of CH(,2)O and DEM may be a useful tool in identifying these critical sulfhydryl-protein(s) and to further understand the role GSH plays in detoxication. ^

INVESTIGATIONS ON THE INTRACELLULAR LOCALIZATION OF PHOSPHATIDYLSERINE SYNTHASE FROM ESCHERICHIA COLI

Phosphatidylserine synthase catalyzes the committed step in the synthesis of the major lipid of Escherichia coli, phosphatidylethanolamine, and may be involved in regulating the balance of the zwitterionic and anionic phospholipids in the membrane. Unlike the other enzymes involved in the biosynthesis of phospholipids in E. coli, phosphatidylserine synthase is not membrane associated but seems to have a high affinity for the ribosomal fraction of cells broken by various methods. Investigations on the enzyme in cell free extracts using glycerol gradient centrifugation revealed that the binding of the synthase to ribosomes may be prevented by the presence of highly basic compounds such as spermidine and by the presence of detergent-lipid substrate micelles under assay conditions. Thus phosphatidylserine synthase may not be ribosome associated under physiological conditions but associated with its membrane bound substrate (Louie and Dowhan (1980) J. Biol. Chem. 255, 1124).^ In addition homogeneous enzyme shows many of the properties of a membrane associated protein. It binds nonionic detergent such as Triton X-100, which is also required during purification of the enzyme. Optimal catalytic activity is also dependent on micelle or surface bound substrate. Phosphatidylserine synthase has been synthesized in vitro using a coupled transcription-translation system dependent on the presence of the cloned structural gene. The translation product was found to preferentially associate with the ribosomal fraction even in the presence of added E. coli membranes. Preferential membrane binding could be induced if the membranes were supplemented with the lipid substrate CDP-diacylglycerol. Similar effects were obtained with the acidic lipids phosphatidylglycerol and cardiolipin. On the other hand the zwitterionic lipid phosphatidylethanolamine and the lipid product phosphatidylserine did not cause any detectable membrane association. These results are consistent with the enzyme recognizing membrane bound substrate (Carman and Dowhan (1979) J. Biol. Chem. 254, 8391) and with the lipid charge influencing membrane interaction.^ Phosphatidylserine synthase is at a branch point in lipid metabolism, which may determine the distribution of the zwitterionic and anionic phospholipids in the membrane. The results obtained here indicate phosphatidylserine synthase may play a significant role in membrane lipid biosynthesis by maintaining charge balance of the E. coli membrane. In determining the localization of phosphatidylserine synthase in vitro one may have a better understanding of its function and control in vivo and may also have a better understanding of its role in membrane assembly.^

Role of phosphatidylethanolamine in the function and assembly of phenylalanine-specific permease of Escherichia coli

Transmembrane segments of polytopic membrane proteins once inserted are generally considered stably oriented due to the large free energy barrier for topological reorientation of adjacent extra-membrane domains. However, proper topology and function of the polytopic membrane protein lactose permease (LacY) of Escherichia coli is dependent on the membrane phospholipid composition revealing topological dynamics of transmembrane domains (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107–2116). The high affinity phenylalanine permease PheP shares many topological similarities with LacY. In this study, mutant E. coli cells lacking phosphatidylethanolamine (PE) as a membrane component were used to evaluate the role of PE in the function and assembly of PheP. Active transport of phenylalanine by cells lacking PE was severely inhibited (both Vmax and Km were altered), whereas the PheP protein level in membranes was unaffected. Cysteine residues were introduced into predicted periplasmic or cytoplasmic segments of cysteine-less PheP, and the topology of the protein was explored using a membrane-impermeable thiol-specific biotinylated probe. Based on the biotinylation patterns of PheP in whole cells, the N-terminus and adjoining transmembrane hairpin of PheP adopted an inverted topological orientation in PE-lacking cells. Introduction of PE following the assembly of PheP triggered a reorientation of the N-terminus and adjacent hairpin to their native orientation associated with regain of wild type transport function. These results coupled with the results for LacY support a specific role for membrane lipid composition in determining topological organization and function of membrane proteins. Several other secondary symporters are compromised for activity in PE-lacking cells suggesting that lipid-assisted topogenesis is a general property of such transporters. The reversible orientation of these secondary transport proteins in response to a change of phospholipid composition might be a result of inherent conformational flexibility necessary for transport function or during protein assembly. ^

Dysregulated CD40-NF-kappaB signaling in the pathophysiology of aggressive non -Hodgkin's lymphoma B cells

Non-Hodgkin's Lymphomas (NHL) are a group (>30) of important human lymphoid cancers that unlike other tumors today, are showing a marked increase in incidence. The lack of insight to the pathogenesis of B-cell NHL poses a significant problem in the early detection and effective treatment of these malignancies. This study shows that large B-cell lymphoma (LBCL) cells, the most common type of B-cell NHL (account for more than 30% of cases), have developed a novel mechanism for autonomous neoplastic B cell growth. We have identified that the key transcription factor NF-κB, is constitutively activated in LBCL cell lines and primary biopsy-derived LBCL cells, suggesting that they are autonomously activated, and do not require accessory T-cell signaling for cell growth and survival. Further studies have indicated that LBCL cells ectopically express an important T-cell associated co-mitogenic factor, CD154 (CD40 ligand), that is able to internally activate the CD401NF-κB pathway, through constitutive binding to its cognate receptor, CD40, on the lymphoma cell surface. CD40 activation triggers the formation of a “Signalosome” comprising virtually the entire canonical CD40/NF-κB signaling pathway that is anchored by CD40 in plasma membrane lipid rafts. The CD40 Signalosome is vulnerable to interdiction by antibody against CD40 that disrupts the Signalosome and induces cell death in the malignant cells. In addition to constitutive NF-κB activation, we have found that the nuclear factor of activated T cells (NFAT) transcription factor is also constitutively activated in LBCL cells. We have demonstrated that the constitutively active NFATc1 and c-rel members of the NFAT and NF-κB families of transcription factors, respectively, interact with each other, bind to the CD154 promoter, and synergistically activate CD154 gene transcription. Down-regulation of NFATc1 and c-rel with small interfering RNA inhibits CD154 gene transcription and lymphoma cell growth. Our findings suggest that continuous CD40 activation not only provides dysregulated proliferative stimuli for lymphoma cell growth and extended tumor cell survival, but also allows continuous regeneration of the CD40 ligand in the lymphoma cell and thereby recharges the system through a positive feedback mechanism. Targeting the CD40/NF-κB signaling pathway could provide potential therapeutic modalities for LBCL cells in the future. ^

Plasticity of lipid-protein interactions in the function and topogenesis of the membrane protein lactose permease from Escherichia coli.

Phosphatidylcholine (PC) has been widely used in place of naturally occurring phosphatidylethanolamine (PE) in reconstitution of bacterial membrane proteins. However, PC does not support native structure or function for several reconstituted transport proteins. Lactose permease (LacY) of Escherichia coli, when reconstituted in E. coli phospholipids, exhibits energy-dependent uphill and energy-independent downhill transport function and proper conformation of periplasmic domain P7, which is tightly linked to uphill transport function. LacY expressed in cells lacking PE and containing only anionic phospholipids exhibits only downhill transport and lacks native P7 conformation. Reconstitution of LacY in the presence of E. coli-derived PE, but not dioleoyl-PC, results in uphill transport. We now show that LacY exhibits uphill transport and native conformation of P7 when expressed in a mutant of E. coli in which PC completely replaces PE even though the structure is not completely native. E. coli-derived PC and synthetic PC species containing at least one saturated fatty acid also support the native conformation of P7 dependent on the presence of anionic phospholipids. Our results demonstrate that the different effects of PE and PC species on LacY structure and function cannot be explained by differences in the direct interaction of the lipid head groups with specific amino acid residues alone but are due to more complex effects of the physical and chemical properties of the lipid environment on protein structure. This conclusion is supported by the effect of different lipids on the proper folding of domain P7, which indirectly influences uphill transport function.

Lipid-dependent topogenesis and function of membrane proteins

Membranes are essential for the integrity and function of the cell. The collective property of the lipid bilayer is critical in providing an optimal functioning environment for membrane proteins. The simple yet well-characterized bacterium Escherichia coli serves an ideal model system to study the function of specific lipids since its lipid content can be easily manipulated. The most abundant lipid in E. coli membrane is phosphatidylethanolamine (PE, 70-80%). A PE-lacking E. coli mutant displays a complex mixture of deficient phenotypes, suggesting a profound role for PE in different aspects of cell function. A novel role of PE as a topological and functional determinant for membrane proteins has been established using lactose permease (LacY) as a model protein. PE is found to be required for energy-dependent uphill transport process of LacY. In PE-lacking membranes, LacY undergoes a dramatic conformational change, and the first half of the protein adopts an inverted topology with respect to the bilayer plane. ^ The work reported here was initiated to understand the molecular properties of lipids that enable their function as topological and functional determinants for membrane proteins. A glycolipid, monoglucosyldiacylglycerol (MGlcDAG) which shares physicochemical similarities with PE, was introduced to PE-lacking E. coli membranes. The introduction of MGlcDAG suppresses many of the PE-deficient phenotypes, and in particular supports the function and native topology of LacY. ^ The lipid-sensitive topogenic signals encoded in the amino acid sequence of LacY were also identified. Native LacY adopts an inverted topology when synthesized without PE, but mutation of specific acidic residues in the cytoplasmic extra-membrane domains can prevent this inversion and supports a native topological organization of LacY in PE-lacking membranes. These results suggest that it is the interplay between the collective charge properties of the lipid bilayer and extra-membrane loops of protein that determines the final orientation of transmembrane domains. By comparing the similarities as well as differences between these two lipids, we established how specific physical and chemical properties of lipids influence various cell functions and elucidated the molecular basis for the novel role of lipids in determining membrane protein topology. ^