From self-assembly of life to present-day bacteria: a possible role for nanocells

A proposed sequence of major events for the self-assembly of life on Earth is examined. This sequence starts with a construction kit of elements and simple compounds from which a primitive membrane and then a nanocell with a minimal genome is self-assembled. The genome and cell increase in size and complexity and become capable of cell division, similar to present-day bacteria. Another factor to understanding this self-assembly of life is identifying the energy source(s) the first self-assembling nanocells were capable of using. This will also be examined from an evolutionary perspective with hydrogen as the postulated universal energy source [Morita, R. (2000) Microb. Ecol. 38, 307-320].     

Molecular evolution: first enzymes, gases as substrates and genetic templates.

A fundamental problem in biology is the self-assembly of the first cells capable of growth and division under anoxic conditions on the Earth. Evolution proceeded by self-assembling and self-replicating cells that reproduced their own genetic information and also changed their genetic code over time. Was it also possible that some of the first proteins were catalytic and used gases as substrates and also acted as genetic templates? This paper explores the possibility that primitive protein enzymes used gases as their substrates, and reverse translation may have been a feature in the self-assembly of the first cell(s).     

Live-Cell Imaging in Caenorhabditis elegans Reveals the Distinct Roles of Dynamin Self-Assembly and Guanosine Triphosphate Hydrolysis in the Removal of Apoptotic Cells

Dynamins are large GTPases that oligomerize along membranes. Dynamin''s membrane fission activity is believed to underlie many of its physiological functions in membrane trafficking. Previously, we reported that DYN-1 (Caenorhabditis elegans dynamin) drove the engulfment and degradation of apoptotic cells through promoting the recruitment and fusion of intracellular vesicles to phagocytic cups and phagosomes, an activity distinct from dynamin''s well-known membrane fission activity. Here, we have detected the oligomerization of DYN-1 in living C. elegans embryos and identified DYN-1 mutations that abolish DYN-1''s oligomerization or GTPase activities. Specifically, abolishing self-assembly destroys DYN-1''s association with the surfaces of extending pseudopods and maturing phagosomes, whereas inactivating guanosine triphosphate (GTP) binding blocks the dissociation of DYN-1 from these membranes. Abolishing the self-assembly or GTPase activities of DYN-1 leads to common as well as differential phagosomal maturation defects. Whereas both types of mutations cause delays in the transient enrichment of the RAB-5 GTPase to phagosomal surfaces, only the self-assembly mutation but not GTP binding mutation causes failure in recruiting the RAB-7 GTPase to phagosomal surfaces. We propose that during cell corpse removal, dynamin''s self-assembly and GTP hydrolysis activities establish a precise dynamic control of DYN-1''s transient association to its target membranes and that this control mechanism underlies the dynamic recruitment of downstream effectors to target membranes.     

A single amino acid in VP2 is critical for the attachment of infectious bursal disease subviral particles to immobilized metal ions and DF-1 cells

VP2 protein is the primary host-protective immunogen of infectious bursal disease virus (IBDV). His249 and His253 are two surface histidine residues in IBDV subviral particles (SVP), which is formed by twenty VP2 trimers when the VP2 protein of a local isolate is expressed. Here, a systemic study was performed to investigate His249 or/and His253 on self-assembly, cell attachment and immunogenicity of SVP. Point-mutagenesis of either or both histidine residues to alanine did not affect self-assembly of the SVP, but the SVP lost its Ni-NTA binding affinity when the His253 was mutated. Indirect immunofluorescence assays and inhibitory experiments also showed that His253 is essential for SVP to attach onto the DF-1 cells and to inhibit IBDV infection of DF-1 cells. Finally, enzyme-linked immunosorbent assays and chicken protection assays demonstrated that SVP with a mutation of His253 to alanine induced comparable neutralizing antibody titers in chickens as the wild-type SVP did. It was concluded that VP2's His253, a site not significant for the overall immunogenicity induced by SVP, is crucial for the binding affinity of SVP to Ni-NTA and the attachment of an IBDV host cell line. This is the first paper to decipher the role of His253 played in receptor interaction and immunogenicity.     

Golgi apparatus activity and membrane flow during scale biogenesis in the green flagellateScherffelia dubia (Prasinophyceae). II: Cell wall secretion and assembly

Summary Secretion of the cell wall (theca) in the scaly green flagellateScherffelia dubia (Prasinophyceae) has been examined by electron microscopy during cytokinesis. The bi-laminate wall forms by the extracellular amalgamation of two layers of scales produced in the Golgi apparatus (GA). Each mature GA cisterna contains ca. 12,000 scales of two distinct varieties arranged in two layers on the cisternal membrane. GA cisternae undergo turnover and one scale containing cisterna matures from thetransface of each dictyosome every 3–4 minutes. Cisternae then fuse with the plasma membrane at the anterior end of the cell releasing the scales onto the cell surface. The two layers of wall scales integrate on the cell surface in a time-dependent self-assembly process. The first scales deposited commence assembly at the cell posterior and the wall develops anteriorly by edge growth. The daughter cell wall is composed of ca. 1.2 million scales deposited in about 3 hours. Calculations of net membrane flow strongly indicate extensive endocytosis during wall deposition.     

HPRT and the Lesch—Nyhan syndrome

The view is presented that extracellular architecture in plant cell walls results from an interplay between molecular self-assembly and mechanical reorientation due to growth forces. A key initial self-assembly step may involve hemicelluloses. It is suggested that hemicelluloses may self-assemble into a helicoid via a cholesteric liquid crystalline phase; the detailed molecular structure of hemicelluloses (stiff backbone, bulky side chains, and the presence of asymmetric carbon atoms) is shown to be consistent with cholesteric requirements for such self-assembly. Since hemicelluloses are hydrogen-bonded to the periphery of cellulose microfibrils, the cellulose could then itself become helicoidally arranged. Such ‘universal plywood’ structure is found in the walls of a wide variety of plants, and in several types of cell (including wood). The permanent effects of growth stresses on patterns seen in sections of helicoids are displayed by computer graphics plots, and the expected changes in stiffness are calculated.     

Self-assembly of plant cell walls

The object of this paper is to define criteria for distinguishing between self-assembly and template-based assembly in plant cell walls. The example of cellulose shows that cell wall polymers biosynthesized at a membrane may retain parallel chain packing arrangements that are thermodynamically unstable and cannot be reproduced in vitro, making the experimental testing of the self-assembly hypothesis difficult. Also, natural cellulose is ordered on a number of scales of pattern, each of which may be constructed by either self- or template-based assembly independently of the rest. These conceptual problems apply equally to the self-assembly of complete cell walls and other cell wall polymers. It is suggested that the self-assembly concept should be applied only to one stage or level in the synthesis of a cell wall, and that an additional concept of parallel assembly may be useful for understanding the synthesis of some polysaccharides.     

Histone Deacetylase 2 (HDAC2) Protein-dependent Deacetylation of Mortality Factor 4-like 1 (MORF4L1) Protein Enhances Its Homodimerization

Histone acetyltransferase mortality factor 4-like 1 (MORF4L1) is a relatively new histone acetyltransferase component that exists as a homodimer to exert its epigenetic function. The mechanism of MORF4L1 self-assembly is unknown. Here we report that Lys-148 deacetylation is indispensable for facilitating MORF4L1 self-assembly into a homodimeric unit. Among a stretch of ∼10 amino acids in the NH₂ terminus between the chromodomain and MORF4-related gene (MRG) domain within MORF4L1, Lys-148 is normally acetylated. Substitution of Lys-148 with arginine augments MORF4L1 self-assembly. However, acetylation mimics of MORF4L1, including K148L and K148Q, abolished its self-assembly of the histone acetyltransferase component. HDAC2, a deacetylase, interacts with and keeps MORF4L1 in a deacetylation status at Lys¹⁴⁸ that triggers MORF4L1 self-assembly. Knockdown of HDAC2 reduces MORF4L1 self-assembly. HDAC2-dependent deacetylation of MORF4L1 enhances MORF4L1 homodimerization, thus facilitating the functionality of complex formation to repress cell proliferation.     

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry

The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.     

Self-assembled polyhydroxy fatty acids vesicles: a mechanism for plant cutin synthesis

Despite its biological importance, the mechanism of formation of cutin, the polymeric matrix of plant cuticles, has not yet been fully clarified. Here, for the first time, we show the participation in the process of lipid vesicles formed by the self-assembly of endogenous polyhydroxy fatty acids. The accumulation and fusion of these vesicles (cutinsomes) at the outer part of epidermal cell wall is proposed as the mechanism for early cuticle formation.     

Pollen wall development in flowering plants

The outer pollen wall, or exine, is more structurally complex than any other plant cell wall, comprising several distinct layers, each with its own organizational pattern. Since elucidation of the basic events of pollen wall ontogeny using electron microscopy in the 1970s, knowledge of their developmental genetics has increased enormously. However, self-assembly processes that are not under direct genetic control also play an important role in pollen wall patterning. This review integrates ultrastructural and developmental findings with recent models for self-assembly in an attempt to understand the origins of the morphological complexity and diversity that underpin the science of palynology.     

Asymmetry as the Key to Clathrin Cage Assembly

The self-assembly of clathrin proteins into polyhedral cages is simulated for the first time (to our knowledge) by introducing a coarse-grain triskelion particle modeled after clathrin's characteristic shape. The simulations indicate that neither this shape, nor the antiparallel binding of four legs along the lattice edges, is sufficient to induce cage formation from a random solution. Asymmetric intersegmental interactions, which probably result from a patchy distribution of interactions along the legs' surfaces, prove to be crucial for the efficient self-assembly of cages.     

Self-assembly product formation of the Bacillus stearothermophilus PV72/p6 S-layer protein SbsA in the course of autolysis of Bacillus subtilis

In order to achieve high level expression and to study the release of a protein capable of self-assembly, the gene encoding the crystalline cell surface (S-layer) protein SbsA of Bacillus stearothermophilus PV72/p6, including its signal sequence, was cloned and expressed in Bacillus subtilis. To obtain high level expression, a tightly regulated, xylose-inducible, stably replicating multicopy-plasmid vector was constructed. After induction of expression, the S-layer protein made up about 15% of the total cellular protein content, which was comparable to the SbsA content of B. stearothermophilus PV72/p6 cells. During all growth stages, SbsA was poorly secreted to the ambient cellular environment by B. subtilis. Extraction of whole cells with guanidine hydrochloride showed that in late stationary growth phase cells 65% of the synthesised SbsA was retained in the peptidoglycan-containing layer, indicating that the rigid cell wall layer was a barrier for efficient SbsA secretion. Electron microscopic investigation revealed that SbsA release from the peptidoglycan-containing layer started in the late stationary growth phase at distinct sites at the cell surface leading to the formation of extracellular self-assembly products which did not adhere to the cell wall surface. In addition, intracellular sheet-like SbsA self-assembly products which followed the curvature of the cell became visible in partly lysed cells. Intracellularly formed self-assembly products remained intact even after complete lysis of the rigid cell envelope layer.     

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

A requirement for concentrated and chemically homogeneous pools of molecular building blocks would severely restrict plausible scenarios for the origin of life. In the case of membrane self-assembly, models of prebiotic lipid synthesis yield primarily short, single-chain amphiphiles that can form bilayer vesicles only at very high concentrations. These high critical aggregation concentrations (cacs) pose significant obstacles for the self-assembly of single-chain lipid membranes. Here, we examine membrane self-assembly in mixtures of fatty acids with varying chain lengths, an expected feature of any abiotic lipid synthesis. We derive theoretical predictions for the cac of mixtures by adapting thermodynamic models developed for the analogous phenomenon of mixed micelle self-assembly. We then use several complementary methods to characterize aggregation experimentally, and find cac values in close agreement with our theoretical predictions. These measurements establish that the cac of fatty acid mixtures is dramatically lowered by minor fractions of long-chain species, thereby providing a plausible route for protocell membrane assembly. Using an NMR-based approach to monitor aggregation of isotopically labeled samples, we demonstrate the incorporation of individual components into mixed vesicles. These experiments suggest that vesicles assembled in dilute, mixed solutions are depleted of the shorter-chain-length lipid species, a finding that carries implications for the composition of primitive cell membranes.     

Structural and functional role of the disulfide bridges in the hydrophobin SC3

Hydrophobins function in fungal development by self-assembly at hydrophobic-hydrophilic interfaces such as the interface between the fungal cell wall and the air or a hydrophobic solid. These proteins contain eight conserved cysteine residues that form four disulfide bonds. To study the effect of the disulfide bridges on the self-assembly, the disulfides of the SC3 hydrophobin were reduced with 1,4-dithiothreitol. The free thiols were then blocked with either iodoacetic acid (IAA) or iodoacetamide (IAM), introducing eight or zero negative charges, respectively. Circular dichroism and infrared spectroscopy showed that after opening of the disulfide bridges SC3 is initially unfolded. IAA-SC3 did not self-assemble at the air-water interface upon shaking an aqueous solution. Remarkably, after drying down IAA-SC3 or after exposing it to Teflon, it refolded into a structure similar to that observed for native SC3 at these interfaces. Iodoacetamide-SC3 on the other hand, which does not contain extra charges, spontaneously refolded in water in the amyloid-like beta-sheet conformation, characteristic for SC3 assembled at the water-air interface. From this we conclude that the disulfide bridges of SC3 are not directly involved in self-assembly but keep hydrophobin monomers soluble in the fungal cell or its aqueous environment, preventing premature self-assembly.     

Patterning of cells on functionalized poly(dimethylsiloxane) surface prepared by hydrophobin and collagen modification

Controllable cell growth on poly(dimethylsiloxzne) (PDMS) surface is important for its potential applications in biodevices. Herein, we developed a fully biocompatible approach for patterning of cells on the PDMS surface by hydrophobin (HFBI) and collagen modification. HFBI and collagen were immobilized on the PDMS surface one after another by using copper grids as a mask. HFBI self-assembly on PDMS surface converted the PDMS surface from hydrophobic to hydrophilic, which facilitated the following immobilization of collagen. Collagen had admirable ability to support cell adhesion and growth. Consequently, the HFBI/collagen-modified PDMS surface could promote cell adhesion and growth. What is more, the native PDMS surface did not support cell adhesion and growth. Patterning of cells was achieved by directly culturing 293T cells (the human embryonic kidney cell line) on the PDMS surface patterned with HFBI/collagen. Further studies by means of gene transfection experiment in vitro showed that the patterned cells were of good bioactivities. Herein, the biocompatible preparation of cell patterns on the PDMS surface could be of many applications in biosensor device fabrication.     

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

A requirement for concentrated and chemically homogeneous pools of molecular building blocks would severely restrict plausible scenarios for the origin of life. In the case of membrane self-assembly, models of prebiotic lipid synthesis yield primarily short, single-chain amphiphiles that can form bilayer vesicles only at very high concentrations. These high critical aggregation concentrations (cacs) pose significant obstacles for the self-assembly of single-chain lipid membranes. Here, we examine membrane self-assembly in mixtures of fatty acids with varying chain lengths, an expected feature of any abiotic lipid synthesis. We derive theoretical predictions for the cac of mixtures by adapting thermodynamic models developed for the analogous phenomenon of mixed micelle self-assembly. We then use several complementary methods to characterize aggregation experimentally, and find cac values in close agreement with our theoretical predictions. These measurements establish that the cac of fatty acid mixtures is dramatically lowered by minor fractions of long-chain species, thereby providing a plausible route for protocell membrane assembly. Using an NMR-based approach to monitor aggregation of isotopically labeled samples, we demonstrate the incorporation of individual components into mixed vesicles. These experiments suggest that vesicles assembled in dilute, mixed solutions are depleted of the shorter-chain-length lipid species, a finding that carries implications for the composition of primitive cell membranes.     

Structure and development of the cryptomonad periplast: A review

Summary The structure and development of the complex periplast, or cell covering, of cryptomonads is reviewed. The periplast consists of the plasma membrane (PM) plus an associated surface periplast component (SPC) and cytoplasmic or inner periplast component (IPC). The structure of the SPC and IPC, and their association with the PM, varies considerably between genera. This review, which concentrates on cryptomonads with an IPC of discrete plates, discusses relationships between periplast components and examines the development of this unique cell covering. Formation and growth of inner plates occurs throughout the cell cycle from specialized regions termed anamorphic zones. Crystalline surface plates, which comprise the SPC in many cryptomonad species, appear to form by self-assembly of disorganized subunits. InKomma caudata the subunits are composed of a high molecular weight glycoprotein that is produced within the endomembrane system and deposited onto the cell surface within anamorphic zones. The self-assembly of subunits into highly ordered surface plates appears closely associated with developmental changes in the underlying IPC and PM.     

The role of secondary structure in the entropically driven amelogenin self-assembly

Amelogenin, the major extracellular enamel matrix protein, plays critical roles in controlling enamel mineralization. This generally hydrophobic protein self-assembles to form nanosphere structures under certain solution conditions. To gain clearer insight into the mechanisms of amelogenin self-assembly, we first investigated the occurrences of secondary structures within its sequence. By applying isothermal titration calorimetry (ITC), we determined the thermodynamic parameters associated with protein-protein interactions and with conformational changes during self-assembly. The recombinant porcine full length (rP172) and a truncated amelogenin lacking the hydrophilic C-terminal (rP148) were used. Circular dichroism (CD) measurements performed at low concentrations (<5 microM) revealed the presence of the polyproline-type II (PPII) conformation in both amelogenins in addition to alpha-helix and unordered conformations. Structural transition from PPII/unordered to beta-sheet was observed for both proteins at higher concentrations (>62.5 microM) and upon self-assembly. ITC measurements indicated that the self-assembly of rP172 and rP148 is entropically driven (+DeltaS(A)) and energetically favorable (-DeltaG(A)). The magnitude of enthalpy (DeltaH(A)) and entropy changes of assembly (DeltaS(A)) were smaller for rP148 than rP172, whereas the Gibbs free energy change of assembly (DeltaG(A)) was not significantly different. It was found that rP172 had higher PPII content than rP148, and the monomer-multimer equilibrium for rP172 was observed in a narrower protein concentration range when compared to rP148. The large positive enthalpy and entropy changes in both cases are attributed to the release of ordered water molecules and the associated entropy gain (due to the hydrophobic effect). These findings suggest that PPII conformation plays an important role in amelogenin self-assembly and that rP172 assembly is more favorable than rP148. The data are direct evidence for the notion that hydrophobic interactions are the main driving force for amelogenin self-assembly.     

Microtubules: dissipative structures formed by self-assembly

Microtubules are hollow fibres that form the track upon which chromosomes or proteins, such as kinesins, are transported in the cell. They are formed by the self-assembly of the protein tubulin both in vitro and in vivo. In the cell, their appearance in time and space is strictly controlled by the presence of nucleation centres. Microtubules are very dynamic structures, a property that is obtained by coupling the self-assembly process to the hydrolysis of the nucleotide, guanosine 5′-triphosphate, (GTP). After assembly, GTP is hydrolysed and guanosine 5′-diphosphate, (GDP)-microtubule structure is formed which, although intrinsically very unstable, is stabilised by a small remaining tubulin-GTP-cap at both ends. As such, the ends of microtubules can be considered as gates for entry into the polymeric state. These gates can be blocked by sub-stoichiometric amounts of drugs such as colchicine.

As biological devices, microtubules differ considerably from man-made devices: they are dynamic dissipative structures, made by spontaneous self-assembly. It has been suggested that microtubules could play a role in the conduction and dynamic storage of information. This implies the existence of different conformational states of tubulin.