Specific RNA binding to ordered phospholipid bilayers

The dynamics of the RNA world: insights and challenges

The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture can only emerge if the pieces fit together by either following from one another or coexisting with each other. Here, we review the theory of the origin, maintenance, and enhancement of the RNA world as an evolving population of dynamical systems. The dynamical view of the origin of life allows us to pinpoint the missing and the not fitting pieces: (1) How can the first self-replicating ribozyme emerge in the absence of template-directed information replication? (2) How can nucleotide replicators avoid competitive exclusion despite utilizing the very same resources (nucleobases)? (3) How can the information catastrophe be avoided? (4) How can enough genes integrate into a cohesive system in order to transition to a cellular stage? (5) How can the way information is stored and metabolic complexity coevolve to pave to road leading out of the RNA world to the present protein-DNA world?

Assembly of RNA nanostructures on supported lipid bilayers

The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nano-structures at interfaces is important for many applications. In spite of this, the use of laterally mobile lipid bilayers to control RNA three-dimensional nanostructure formation on surfaces remains largely unexplored. Here, we direct the self-assembly of RNA building blocks into three-dimensional structures of RNA on fluid lipid bilayers composed of cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or mixtures of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and cationic sphingosine. We demonstrate the stepwise supramolecular assembly of discrete building blocks through specific and selective RNA-RNA interactions, based on results from quartz crystal microbalance with dissipation (QCM-D), ellipsometry, fluorescence recovery after photobleaching (FRAP) and total internal reflection fluorescence microscopy (TIRF) experiments. The assembly can be controlled to give a densely packed single layer of RNA polyhedrons at the fluid lipid bilayer surface. We show that assembly of the 3D structure can be modulated by sequence specific interactions, surface charge and changes in the salt composition and concentration. In addition, the tertiary structure of the RNA polyhedron can be controllably switched from an extended structure to one that is dense and compact. The versatile approach to building up three-dimensional structures of RNA does not require modification of the surface or the RNA molecules, and can be used as a bottom-up means of nanofabrication of functionalized bio-mimicking surfaces.

Extracellular microRNAs in Membrane Vesicles and Non-vesicular Carriers

Great excitement has surrounded the finding that small RNAs are stable in various biofluids and carry specific signatures reflecting physiological and pathological states. In this chapter, we briefly describe the impact of this revolutionary discovery and introduce different subclasses of circulating microRNAs based on their mode of transport. Subsequently, we review the current state-of-the art knowledge on microRNA selection for export, secretion and possible uptake mechanisms and their potential function in circulation. Furthermore, we give an overview on the possible use of cell-free microRNAs as biomarkers and as therapeutic targets. Overall, we aim to highlight open questions and address some of the pitfalls of current extracellular RNA research.

Circulating microRNAs in cardiovascular diseases: from biomarkers to therapeutic targets

microRNAs (miRNAs) are a class of conserved, short, non-coding RNAs that have important and potent capacities to regulate gene expression at the posttranscriptional level. In the past several years, the aberrant expressions of miRNAs in the cardiovascular system have been widely reported, and the crucial roles of some special miRNAs in heart development and pathophysiology of various cardiovascular diseases have been gradually recognized. Recently, it was discovered that miRNAs are presented in peripheral circulation abundantly and stably. This has raised the possibility of using circulating miRNAs as biomarkers for diseases. Furthermore, some studies demonstrated that circulating miRNAs may serve as novel extracellular communicators of cell-cell communication. These discoveries not only reveal the functions of circulating miRNAs in cardiovascular system but also inform the development of miRNAs therapeutic strategies. In this review, we discuss the potential roles of circulating miRNAs in a variety of cardiovascular diseases from biomarkers to therapeutic targets to clearly understand the roles of circulating miRNAs in cardiovascular system.

MicroRNA-specific regulatory mechanisms in atherosclerosis

During the past decade, the crucial role of microRNAs (miRs) controlling tissue homeostasis and disease in the cardiovascular system has become widely recognized. By controlling the expression levels of their targets, several miRs have been shown to modulate the function of endothelial cells, vascular smooth muscle cells, and macrophages, thereby regulating the development and progression of atherosclerosis. For instance, miR-155 can exacerbate early stages of atherosclerosis by increasing the inflammatory activation and disturbing efficient lipid handling in macrophages. Conversely, miRs can exert atheroprotective roles, as has been established for the complementary miR-126 strand pair, which forms a dual system sustaining the endothelial proliferative reserve and promoting endothelial regeneration to counteract atherogenic effects of disturbed flow and hyperlipidemia. Under some conditions, miRs are released from cells and are transported by microvesicles, ribonucleoprotein complexes, and lipoproteins, being remarkably stable in circulation. Conferred by such delivery modules, miRs can regulate target mRNAs in recipient cells, representing a new tool for cell-cell communication in the context of atherosclerotic disease. Here, we will discuss novel aspects of miR-mediated regulatory mechanisms, namely the regulation by competing RNA targets, miRNA tandems, or complementary miR strand pairs, as well as their potential diagnostic and therapeutic value in atherosclerosis. This article is part of a Special Issue entitled 'Non-coding RNAs'.

Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription

Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.

The ins and outs of microRNAs as biomarkers in liver disease and transplantation

Ongoing research is being conducted in the field of transplantation to discover novel, noninvasive biomarkers for assessment of graft quality before transplantation and monitoring of graft injury after transplantation. MicroRNAs (miRNAs) are among the most promising in this field. MiRNAs are small noncoding RNAs that function as important regulators of gene expression in response to cellular stress and disease. An advantage that makes miRNAs attractive candidates for biomarker research is their fast release from cells in response to stress and injury, which can occur via different routes. In the context of liver transplantation (LT), noninvasive measurement and stability of extracellular miRNAs in blood, bile, and graft perfusates has been linked to cell-type specific injury and early graft outcome following LT. Furthermore, specific intrahepatic miRNA expression patterns have been associated with graft survival and recurrent disease, like hepatitis C virus-related fibrosis and hepatocellular carcinoma. Therefore, miRNAs with strong predictive value and high sensitivity and specificity might be successfully applied to assess hepatic injury and to diagnose (recurrent) liver disease before, during and after LT. In this review, the current features and future prospects of miRNAs as biomarkers in and out of the liver are discussed.

Analysis of circulating microRNAs that are specifically increased in hyperlipidemic and/or hyperglycemic sera

MicroRNAs (miRNAs) are small non-coding RNA sequences that regulate gene expression post-transcriptionally by translation inhibition or mRNA degradation. The aim of the present study was to analyze serum miRNAs modulated by hyperlipidemia and/or hyperglycemia and to correlate them with biochemical parameters within lipid metabolism. Five selected circulating miRNAs (miR-125a-5p, miR-146a, miR-10a, miR-21 and miR-33a) were individually analyzed by TaqMan miRNA assays along with lipid and inflammation parameters in sera from 20 hyperlipidemic (HL) and/or hyperglycemic (HG) patients, and compared with data from five normolipidemic/normoglycemic subjects. Results showed: (1) the levels of all the analyzed circulating miRNA were increased in HL sera and correlated positively with sera's lipid and inflammatory parameters; (2) circulating miR-125a-5p and miR-146a levels were increased in HG and/or HL sera; (3) all selected miRNAs were detected in α-lipoprotein fraction from sera, and miR-33a was also present in β-lipoprotein fraction; (4) miRNA concentrations were increased in the α-lipoprotein fraction from HL sera. These data show a statistically significant correlation of the analyzed miRNA with increased lipids, specifically with α- and β-lipoproteins, and CRP and IL-1β levels in HL and/or HG sera, suggesting a contribution of these miRNAs to the atherosclerotic process.

Membrane potential-dependent binding of polysialic acid to lipid monolayers and bilayers

Polysialic acids are linear polysaccharides composed of sialic acid monomers. These polyanionic chains are usually membrane-bound, and are expressed on the surfaces of neural, tumor and neuroinvasive bacterial cells. We used toluidine blue spectroscopy, the Langmuir monolayer technique and fluorescence spectroscopy to study the effects of membrane surface potential and transmembrane potential on the binding of polysialic acids to lipid bilayers and monolayers. Polysialic acid free in solution was added to the bathing solution to assess the metachromatic shift in the absorption spectra of toluidine blue, the temperature dependence of the fluorescence anisotropy of DPH in liposomes, the limiting molecular area in lipid monolayers, and the fluorescence spectroscopy of oxonol V in liposomes. Our results show that both a positive surface potential and a positive transmembrane potential inside the vesicles can facilitate the binding of polysialic acid chains to model lipid membranes. These observations suggest that these membrane potentials can also affect the polysialic acid-mediated interaction between cells.

Circulating miRNAs: reflecting or affecting cardiovascular disease?

MicroRNAs are a class of small, noncoding RNAs encoded by the metazoan genome that regulate protein expression. A collection of studies point to vital roles for microRNAs in the onset and development of cardiovascular diseases. So far, microRNAs have been considered as important intracellular mediators in maintaining proper cardiac function and hemostasis, and have been proposed as potential therapeutic targets in cardiovascular disease. The recent discovery that microRNAs circulate in a stable form in many body fluids, including blood, suggests that circulating microRNAs can serve as a new generation of biomarkers for cardiovascular diseases. In this review, we summarize the findings of studies focusing on circulating microRNAs present in human blood cells or plasma/serum, where they potentially could serve as diagnostic or prognostic markers for a variety of cardiovascular pathologies, including acute myocardial infarction, heart failure, coronary artery disease, stroke, diabetes and hypertension. The significance and limitations of microRNAs as the new biomarker generation for cardiovascular disease are also discussed.

Detection of nanosized ordered domains in DOPC/DPPC and DOPC/Ch binary lipid mixture systems of large unilamellar vesicles using a TEMPO quenching method

Nanosized ordered domains formed in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DOPC/DPPC) and DOPC/cholesterol (Ch) liposomes were characterized using a newly developed (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) quenching method. The membrane fluidity of the DOPC/DPPC liposomes, evaluated by the use of 1,6-diphenyl-1,3,5-hexatriene (DPH), increased significantly above their phase-transition temperature. The fluorescence spectra of 6-lauroyl-2-dimethylamino naphthalene (Laurdan) indicated the formation of an immiscible ordered phase in the DOPC/DPPC (50/50) liposomal membrane at 30 °C. The analysis of the membrane polarity indicated that the surface of the liquid-disordered phase was hydrated whereas that of the ordered phase was dehydrated. DOPC/DPPC and DOPC/Ch (70/30) liposomes exhibited heterogeneous membranes, indicating that nanosized ordered domains formed on the surface of the DOPC/DPPC liposomes. The size of these nanosized ordered domains was estimated using the TEMPO quenching method. Because TEMPO can quench DPH distributed in the disordered phases, the remaining fluorescence from DPH is proportional to the size of the ordered domain. The domain sizes calculated for DOPC/DPPC (50/50), DOPC/DPPC (25/75), DOPC/Ch (70/30), and DOPC/DPPC/Ch (40/40/20) were 13.9, 36.2, 13.2, and 35.5 Å, respectively.

Extracellular communication via microRNA: lipid particles have a new message

The complexity of microRNA (miRNA)-mediated pathway control has burgeoned since the discovery that miRNAs are found in the extracellular space and constitute a form of cell-cell communication. miRNAs have been found in plasma, urine, and saliva and have recently been shown to be carried on lipoproteins. This has led to the proposal that circulating miRNAs may be useful biomarkers of various diseases, including cardiovascular disease, diabetes, and other forms of dysregulated metabolism. Although our understanding of the cellular machinery responsible for the secretion of miRNA is incomplete, it has been demonstrated that miRNAs are packaged into exosomes, microvesicles, and apoptotic bodies by a broad range of cell types. Intriguingly, a large portion of extracellular miRNA is found outside of any lipid-containing vesicle, and instead is associated with RNA binding proteins like argonautes 1 and 2, which may aid in their protection from abundant nucleases in the extracellular space. The excitement for miRNAs as biomarkers is mounting as more and more evidence supports that these noncoding RNAs are actively secreted from diseased tissues, possibly before the onset of overt disease. While caution should be taken in these early days, there is little doubt that extracellular miRNAs will hold tremendous potential as both diagnostic and therapeutic agents.

Human tRNA(Sec) associates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers

We have shown previously that simple RNA structures bind pure phospholipid liposomes. However, binding of bona fide cellular RNAs under physiological ionic conditions is shown here for the first time. Human tRNA(Sec) contains a hydrophobic anticodon-loop modification: N⁶-isopentenyladenosine (i⁶A) adjacent to its anticodon. Using a highly specific double-probe hybridization assay, we show mature human tRNA(Sec) specifically retained in HeLa intermediate-density membranes. Further, isolated human tRNA(Sec) rebinds to liposomes from isolated HeLa membrane lipids, to a much greater extent than an unmodified tRNA(Sec) transcript. To better define this affinity, experiments with pure lipids show that liposomes forming rafts or including positively charged sphingosine, or particularly both together, exhibit increased tRNA(Sec) binding. Thus tRNA(Sec) residence on membranes is determined by several factors, such as hydrophobic modification (likely isopentenylation of tRNA(Sec)), lipid structure (particularly lipid rafts), or sphingosine at a physiological concentration in rafted membranes. From prior work, RNA structure and ionic conditions also appear important. tRNA(Sec) dissociation from HeLa liposomes implies a mean membrane residence of 7.6 min at 24°C (t(1/2) = 5.3 min). Clearly RNA with a 5-carbon hydrophobic modification binds HeLa membranes, probably favoring raft domains containing specific lipids, for times sufficient to alter biological fates.

MicroRNAs as biomarkers for myocardial infarction

MicroRNAs (miRs) are short non-coding RNA molecules involved in post-transcriptional gene regulation by binding to the 3' untranslated region of a messenger RNA (mRNA), thereby inhibiting the translation or inducing mRNA destabilization. MiRs are generally considered to act as intracellular mediators essential for normal cardiac function, and their deregulated expression profiles have been associated with cardiovascular diseases. Recent studies have revealed the existence of freely circulating miRs in human peripheral blood, which are present in a stable nature. This has raised the possibility that miRs may be released in the circulation and can serve as novel diagnostic markers for acute or chronic human disorders, including myocardial infarction (MI). This review summarizes the recent findings of miRs that fulfill the criteria of candidate biomarkers for MI.

Circulating MicroRNAs

In the past few years, the crucial role of different micro-RNAs (miRNAs) in the cardiovascular system has been widely recognized. Recently, it was discovered that extracellular miRNAs circulate in the bloodstream and that such circulating miRNAs are remarkably stable. This has raised the possibility that miRNAs may be probed in the circulation and can serve as novel diagnostic markers. Although the precise cellular release mechanisms of miRNAs remain largely unknown, the first studies revealed that these circulating miRNAs may be delivered to recipient cells, where they can regulate translation of target genes. In this review, we will discuss the nature of the stability of miRNAs that circulate in the bloodstream and discuss the available evidence regarding the possible function of these circulating miRNAs in distant cell-to-cell communication. Furthermore, we summarize and discuss the usefulness of circulating miRNAs as biomarkers for a wide range of cardiovascular diseases such as myocardial infarction, heart failure, atherosclerosis, hypertension, and type 2 diabetes mellitus.

C6 pyridinium ceramide influences alternative pre-mRNA splicing by inhibiting protein phosphatase-1

Alternative pre-mRNA processing is a central element of eukaryotic gene regulation. The cell frequently alters the use of alternative exons in response to physiological stimuli. Ceramides are lipid-signaling molecules composed of sphingosine and a fatty acid. Previously, water-insoluble ceramides were shown to change alternative splicing and decrease SR-protein phosphorylation by activating protein phosphatase-1 (PP1). To gain further mechanistical insight into ceramide-mediated alternative splicing, we analyzed the effect of C6 pyridinium ceramide (PyrCer) on alternative splice site selection. PyrCer is a water-soluble ceramide analog that is under investigation as a cancer drug. We found that PyrCer binds to the PP1 catalytic subunit and inhibits the dephosphorylation of several splicing regulatory proteins containing the evolutionarily conserved RVxF PP1-binding motif (including PSF/SFPQ, Tra2-beta1 and SF2/ASF). In contrast to natural ceramides, PyrCer promotes phosphorylation of splicing factors. Exons that are regulated by PyrCer have in common suboptimal splice sites, are unusually short and share two 4-nt motifs, GAAR and CAAG. They are dependent on PSF/SFPQ, whose phosphorylation is regulated by PyrCer. Our results indicate that lipids can influence pre-mRNA processing by regulating the phosphorylation status of specific regulatory factors, which is mediated by protein phosphatase activity.

Conformational change of single-stranded RNAs induced by liposome binding

The interaction between single-stranded RNAs and liposomes was studied using UV, Fourier Transform Infrared spectroscopy (FTIR) and Circular Dichroism spectroscopy (CD). The effect of the surface characteristics of liposomes, which were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and modified with cholesterol (Ch) or 1,2-dioleoyl-3-trimethylammonium propane (DOTAP), on the liposome–RNA interaction was investigated. The fluorescence of 6-(p-toluidino)naphthalene-2-sulfonate (TNS) embedded in the liposome surface (ε = 30–40) was decreased in the presence of tRNA, suggesting that single-stranded tRNA could bind onto the liposome. The dehydration of –PO₂⁻ –, guanine (G) and cytosine (C) of tRNA molecules in the presence of liposomes suggested both an electrostatic interaction (phosphate backbone of tRNA and trimethylammonium group of POPC, DOTAP) and a hydrophobic interaction (guanine or cytosine of tRNA and aliphatic tail of lipid). The tRNA conformation on the liposome was determined by CD spectroscopy. POPC/Ch (70/30) maintained tRNA conformation without any denaturation, while POPC/DOTAP(70/30) drastically denatured it. The mRNA translation was evaluated in an Escherichia coli cell-free translation system. POPC/Ch(70/30) enhanced expression of green fluorescent protein (GFP) (116%) while POPC/DOTAP(70/30) inhibited (37%), suggesting that the conformation of RNAs was closely related to the translation efficiency. Therefore, single-stranded RNAs could bind to liposomal membranes through electrostatic and hydrophobic attraction, after which conformational changes were induced depending on the liposome characteristics.

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment

The ubiquitous SecY/Sec61–complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent solubilized Sec–complexes have been reported. Here, we present a single–particle cryo–electron microscopy structure of the SecYEG complex in a membrane environment at sub–nanometer resolution, bound to a translating ribosome. Using the SecYEG complex reconstituted in a so–called Nanodisc, we could trace the nascent polypeptide chain from the peptidyl transferase center into the membrane. The reconstruction allowed for the identification of ribosome–lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the PCC. Based on our map and molecular dynamics simulations we present a model of a signal anchor–gated PCC in the membrane.

MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins

Circulating microRNAs (miRNA) are relatively stable in plasma and are a new class of disease biomarkers. Here we present evidence that high-density lipoprotein (HDL) transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities. Cellular export of miRNAs to HDL was demonstrated to be regulated by neutral sphingomyelinase. Reconstituted HDL injected into mice retrieved distinct miRNA profiles from normal and atherogenic models. HDL delivery of both exogenous and endogenous miRNAs resulted in the direct targeting of mRNA reporters. Furthermore, HDL-mediated delivery of miRNAs to recipient cells was demonstrated to be scavenger receptor BI-dependent. The human HDL-miRNA profile from normal subjects is significantly different than familial hypercholesterolemia subjects. Notably, HDL-miRNA from atherosclerotic subjects induced differential gene expression, with significant loss of conserved mRNA targets in cultured hepatocytes. Collectively, these observations suggest that HDL participates in a mechanism of intercellular communication involving the transport and delivery of miRNAs.

Liposomes destabilize tRNA during heat stress

Biomembranes play an important role in cellular response to heat stress. In this study, we focus on the interaction between liposomes and tRNA. Upon heat treatment we determined circular dichroism spectra of tRNA in presence of liposomes prepared from POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and cholesterol (Ch). To compare thermal stability, midpoint temperature (T(m)) of tRNA was calculated from normalized theta(208). Addition of POPC/Ch liposomes decreased the T(m) value of tRNA from 48 degrees C to 38 degrees C. We conclude that POPC/Ch liposomes interact with tRNA and destabilize its conformation under heat stress.

The selection of aptamers specific for membrane molecular targets

A growing number of RNA aptamers have been selected experimentally using the SELEX combinatorial approach, and these aptamers have several advantages over monoclonal protein antibodies or peptides with respect to their applications in medicine and nanobiotechnology. Relatively few successful selections have been reported for membrane molecular targets, in contrast to the situation with non-membrane molecular targets. This review compares the procedures and techniques used in selections against membrane proteins and membrane lipids. In the case of membrane proteins, the selections were performed against soluble protein fragments, detergent-membrane protein mixed micelles, whole cells, vesicles derived from cellular membranes, and enveloped viruses. Liposomes were used as an experimental system for the selection of aptamers against membrane lipids. RNA structure-dependent aptamer binding for rafts in lipid vesicles was reported. Based on the selected aptamers against DOPC and the amino acid tryptophan, a specific passive membrane transporter composed of RNA was constructed. The determination of the selectivity of aptamers appears to be a crucial step in a selection, but has rarely been fully investigated. The selections, which use whole cells or vesicles derived from membranes, can yield aptamers not only against proteins but also against membrane lipids.

Membrane transport in primitive cells

Although model protocellular membranes consisting of monoacyl lipids are similar to membranes composed of contemporary diacyl lipids, they differ in at least one important aspect. Model protocellular membranes allow for the passage of polar solutes and thus can potentially support cell-to functions without the aid of transport machinery. The ability to transport polar molecules likely stems from increased lipid dynamics. Selectively permeable vesicle membranes composed of monoacyl lipids allow for many lifelike processes to emerge from a remarkably small set of molecules.

RNA and DNA interactions with zwitterionic and charged lipid membranes - a DSC and QCM-D study

The aim of the present study is to establish under which conditions tRNA associates with phospholipid bilayers, and to explore how this interaction influences the lipid bilayer. For this purpose we have studied the association of tRNA or DNA of different sizes and degrees of base pairing with a set of model membrane systems with varying charge densities, composed of zwitterionic phosphatidylcholines (PC) in mixtures with anionic phosphatidylserine (PS) or cationic dioctadecyl-dimethyl-ammoniumbromide (DODAB), and with fluid or solid acyl-chains (oleoyl, myristoyl and palmitoyl). To prove and quantify the attractive interaction between tRNA and model-lipid membrane we used quartz crystal microbalance with dissipation (QCM-D) monitoring to study the tRNA adsorption to deposit phospholipid bilayers from solutions containing monovalent (Na(+)) or divalent (Ca(2+)) cations. The influence of the adsorbed polynucleic acids on the lipid phase transitions and lipid segregation was studied by means of differential scanning calorimetry (DSC). The basic findings are: i) tRNA adsorbs to zwitterionic liquid-crystalline and gel-phase phospholipid bilayers. The interaction is weak and reversible, and cannot be explained only on the basis of electrostatic attraction. ii) The adsorbed amount of tRNA is higher for liquid-crystalline bilayers compared to gel-phase bilayers, while the presence of divalent cations show no significant effect on the tRNA adsorption. iii) The adsorption of tRNA can lead to segregation in the mixed 1,2-dimyristoyl-sn-glycerol-3-phosphatidylcholine (DMPC)-1,2-dimyristoyl-sn-glycero-3-phosphatidylserine (DMPS) and DMPC-DODAB bilayers, where tRNA is likely excluded from the anionic DMPS-rich domains in the first system, and associated with the cationic DODAB-rich domains in the second system. iv) The addition of shorter polynucleic acids influence the chain melting transition and induce segregation in a mixed DMPC-DMPS system, while larger polynucleic acids do not influence the melting transition in these system. The results in this study on tRNA-phospholipid interactions can have implications for understanding its biological function in, e.g., the cell nuclei, as well as in applications in biotechnology and medicine.

Polysialic acid can mediate membrane interactions by interacting with phospholipids

Polysialic acid (polySia) is expressed on the surface of neural cells, neuroinvasive bacterial cells and several tumor cells. PolySia chains attached to NCAM can influence both trans interactions between membranes of two cells and cis interactions. Here, we report on the involvement of phospholipids in regulation of membrane interactions by polySia. The pH at the surface of liposomes, specific molecular area of phosphatidylcholine molecules, phase transition of DPPC bilayers, cyclic voltammograms of BLMs, and electron micrographs of phosphatidylcholine vesicles were studied after addition of polysialic acid free in solution. The results indicate that polySia chains can associate with phosphatidylcholine bilayers, incorporate into the polar part of a phospholipid monolayer, modulate cis interactions between phosphatidylcholine molecules, and facilitate trans interactions between apposing phospholipid vesicles. These observations imply that polySia attached to NCAM or to lipids can behave similarly.

Structural characterization of cationic lipid-tRNA complexes

Despite considerable interest and investigations on cationic lipid-DNA complexes, reports on lipid-RNA interaction are very limited. In contrast to lipid-DNA complexes where lipid binding induces partial B to A and B to C conformational changes, lipid-tRNA complexation preserves tRNA folded state. This study is the first attempt to investigate the binding of cationic lipid with transfer RNA and the effect of lipid complexation on tRNA aggregation and condensation. We examine the interaction of tRNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant tRNA concentration and various lipid contents. FTIR, UV-visible, CD spectroscopic methods and atomic force microscopy (AFM) were used to analyze lipid binding site, the binding constant and the effects of lipid interaction on tRNA stability, conformation and condensation. Structural analysis showed lipid-tRNA interactions with G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(Chol) = 5.94 (+/- 0.8) x 10(4) M(-1), K(DDAB) = 8.33 (+/- 0.90) x 10(5) M(-1), K(DOTAP) = 1.05 (+/- 0.30) x 10(5) M(-1) and K(DOPE) = 2.75 (+/- 0.50) x 10(4) M(-1). The order of stability of lipid-tRNA complexation is DDAB > DOTAP > Chol > DOPE. Hydrophobic interactions between lipid aliphatic tails and tRNA were observed. RNA remains in A-family structure, while biopolymer aggregation and condensation occurred at high lipid concentrations.

The modern RNP world of eukaryotes

Eukaryote gene expression is mediated by a cascade of RNA functions that regulate, process, store, transport, and translate RNA transcripts. The RNA network that promotes this cascade depends on a large cohort of proteins that partner RNAs; thus, the modern RNA world of eukaryotes is really a ribonucleoprotein (RNP) world. Features of this "RNP infrastructure" can be related to the high cytosolic density of macromolecules and the large size of eukaryote cells. Because of the densely packed cytosol or nucleoplasm (with its severe restriction on diffusion of macromolecules), partitioning of the eukaryote cell into functionally specialized compartments is essential for efficiency. This necessitates the association of RNA and protein into large RNP complexes including ribosomes and spliceosomes. This is well illustrated by the ubiquitous spliceosome for which most components are conserved throughout eukaryotes and which interacts with other RNP-based machineries. The complexes involved in gene processing in modern eukaryotes have broad phylogenetic distributions suggesting that the common ancestor of extant eukaryotes had a fully evolved RNP network. Thus, the eukaryote genome may be uniquely informative about the transition from an earlier RNA genome world to the modern DNA genome world.

Liposome membrane itself can affect gene expression in the Escherichia coli cell-free translation system

A possible role of a model biomembrane, liposome, in gene expression was investigated by using the cell-free translation system. A reporter protein, green fluorescence protein (GFP), was expressed in vitro with and without liposome prepared with 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphatidyl chorine (POPC) and cholesterol (Ch) (5.7 mM lipid concentration). In the presence of POPC/Ch liposome, the fluorescence intensity of produced GFP was found to be 1.67 times higher than that in the control after 18 h of expression. The results of the SDS-PAGE analysis also show the above promotion effect of the liposome on the net expression of the GFP gene (1.58 times more). The amounts of mRNA were found to be promoted to 1.29 times higher than those in the control. The differences among mRNA, net expression of the GFP gene, and GFP fluorescence indicate that the enhanced GFP expression in the presence of POPC/Ch liposome could primarily affect the transcription and translation of the GFP gene among the possible steps of gene expression. The variation of in vitro gene expression with various liposomes also shows that the biomembrane could act as a modulator to split the genotype and phenotype in a biological cell.

Structural co-evolution of viruses and cells in the primordial world

Viruses and cells co-evolve due to the parasitic nature of viruses. Yet there are no models suggesting how the unicellular organisms and their viruses might co-evolve structurally. Here, in this study, we plunge into this unexplored field from a wide perspective and try to describe some of the intriguing ways in which viruses may have shaped the cellular life forms on the ancient Earth. At first we propose a scenario where viruses act as a driving force in the emergence of bacterial cell walls by providing favorable intermediates for the otherwise improbable steps in the cell wall generation. We also discuss the role of viruses in the evolution of cell surface components such as receptors and second membranes. Finally we focus on hypothetical proto-viruses, the selfish abusers of the RNA-world, in explaining some of the very early stages in the origin and evolution of life. Proto-viruses may be responsible for creating the first true cells in order to support their selfish needs. In this model we also suggest a logical pathway to explaining the emergence of modern viruses.