Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation.

The skin's permeability barrier consists of stacked lipid sheets of splayed ceramides, cholesterol and free fatty acids, positioned intercellularly in the stratum corneum. We report here on the early stage of skin barrier formation taking place inside the tubuloreticular system in the secretory cells of the topmost viable epidermis and in the intercellular space between viable epidermis and stratum corneum. The barrier formation process was analysed in situ in its near-native state, using cryo-EM combined with molecular dynamics modeling and EM simulation. Stacks of lamellae appear towards the periphery of the tubuloreticular system and they are closely associated with granular regions. Only models based on a bicontinuous cubic phase organization proved compatible with the granular cryo-EM patterns. Only models based on a dehydrated lamellar phase organization agreed with the lamellar cryo-EM patterns. The data support that human skin barrier formation takes place via a cubic to lamellar lipid phase transition.

Simulation of transmission electron microscope images of biological specimens.

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated.

Packing and delivery of a genetic message.

Balbiani rings (BRs) 1 and 2 are two exceptionally large chromosomal puffs on chromosome IV in the salivary glands of the dipteran Chironomus tentans. The BR genes are 35-40 kb, contain four short introns, and encode salivary polypeptides of one million molecular weight. They have proven uniquely suited for visualization of the assembly and transport of a specific messenger ribonucleoprotein (RNP) particle. A BR transcript is packed with proteins into a thin RNP fibril, which is folded into a compact ring-like structure. The completed BR particle is released from the gene and moves randomly in the nucleoplasm before it becomes associated with the nuclear pore complex. The passage through the nuclear pore is a highly ordered process with a series of consecutive steps: initial binding, docking, unfolding, movement through the pore with the 5' end of the transcript in the lead, and exit into the cytoplasm. On the cytoplasmic side, the RNA becomes immediately engaged in protein synthesis. Recently, several major proteins in the BR particle have been identified and characterized. They are added to the BR RNA molecule concomitantly with transcription. During the ensuing RNA transport, the various proteins behave differently, some remaining in the nucleus, others entering the cytoplasm coupled to the RNA. The flow pattern of a given protein seems to be closely related to the specific function of the protein. The RNA-binding proteins are likely to play various active roles during gene expression rather than being solely packaging proteins. Finally, it is emphasized that the co-transcriptional loading of the transcript with proteins is probably a key process in gene expression that to a large extent determines the fate of an mRNA both in the nucleus and the cytoplasm.

Assembly and transport of a premessenger RNP particle.

Salivary gland cells in the larvae of the dipteran Chironomus tentans offer unique possibilities to visualize the assembly and nucleocytoplasmic transport of a specific transcription product. Each nucleus harbors four giant polytene chromosomes, whose transcription sites are expanded, or puffed. On chromosome IV, there are two puffs of exceptional size, Balbiani ring (BR) 1 and BR 2. A BR gene is 35-40 kb, contains four short introns, and encodes a 1-MDa salivary polypeptide. The BR transcript is packed with proteins into a ribonucleoprotein (RNP) fibril that is folded into a compact ring-like structure. The completed RNP particle is released into the nucleoplasm and transported to the nuclear pore, where the RNP fibril is gradually unfolded and passes through the pore. On the cytoplasmic side, the exiting extended RNP fibril becomes engaged in protein synthesis and the ensuing polysome is anchored to the endoplasmic reticulum. Several of the BR particle proteins have been characterized, and their fate during the assembly and transport of the BR particle has been elucidated. The proteins studied are all added cotranscriptionally to the pre-mRNA molecule. The various proteins behave differently during RNA transport, and the flow pattern of each protein is related to the particular function of the protein. Because the cotranscriptional assembly of the pre-mRNP particle involves proteins functioning in the nucleus as well as proteins functioning in the cytoplasm, it is concluded that the fate of the mRNA molecule is determined to a considerable extent already at the gene level.

Actin bound to the heterogeneous nuclear ribonucleoprotein hrp36 is associated with Balbiani ring mRNA from the gene to polysomes.

In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualized during its assembly on the gene and during its nucleocytoplasmic transport. We now show with immunoelectron microscopy that actin becomes associated with the BR particle concomitantly with transcription and is present in the particle in the nucleoplasm. DNase I affinity chromatography experiments with extracts from tissue culture cells indicate that both nuclear and cytoplasmic actin are bound to the heterogeneous RNP (hnRNP) protein hrp36, but not to the hnRNP proteins hrp23 and hrp45. The interaction is likely to be direct as purified actin binds to recombinant hrp36 in vitro. Furthermore, it is demonstrated by cross linking that nuclear as well as cytoplasmic actin are bound to hrp36 in vivo. It is known that hrp36 is added cotranscriptionally along the BR mRNA molecule and accompanies the RNA through the nuclear pores and into polysomes. We conclude that actin is likely to be bound to the BR transcript via hrp36 during the transfer of the mRNA from the gene all the way into polysomes.

Recovery of gel-separated proteins for in-solution digestion and mass spectrometry.

A protocol for mass spectrometry of gel-separated proteins resulting in significantly increased sequence coverage and in improved possibilities for detection and identification of posttranslational modifications was developed. In relation to the standard in-gel digestion procedure, the sequence coverage using a combination of matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry was on the average increased by 30%. The method involves electroblotting of the gel-separated proteins to a poly(vinylidene difluoride) membrane. The proteins are extracted from the membrane using a solution of 1% trifluoroacetic acid in 70% acetonitrile and lyophilized. After reconstitution of the protein extract in digestion buffer, proteolytic cleavage is carried out in-solution as opposed to the standard in-gel digestion procedure. This allows recovery of large and hydrophobic peptides for mass spectrometry and reduces the risk for entrapment of proteolytic peptides in the gel matrix. The method was applied to proteins in the 30-40-kDa range with highly different structural properties. The improved ability to localize and determine protein modifications is shown for N-terminal acetylation and methylation of a histidine residue. Furthermore, the method enables fast screening of homologous protein sequences.

The murine SCP3 gene is required for synaptonemal complex assembly, chromosome synapsis, and male fertility.

During meiosis, the homologous chromosomes pair and recombine. An evolutionarily conserved protein structure, the synaptonemal complex (SC), is located along the paired meiotic chromosomes. We have studied the function of a structural component in the axial/lateral element of the SC, the synaptonemal complex protein 3 (SCP3). A null mutation in the SCP3 gene was generated, and we noted that homozygous mutant males were sterile due to massive apoptotic cell death during meiotic prophase. The SCP3-deficient male mice failed to form axial/lateral elements and SCs, and the chromosomes in the mutant spermatocytes did not synapse. While the absence of SCP3 affected the nuclear distribution of DNA repair and recombination proteins (Rad51 and RPA), as well as synaptonemal complex protein 1 (SCP1), a residual chromatin organization remained in the mutant meiotic cells.

The intranuclear movement of Balbiani ring premessenger ribonucleoprotein particles.

Specific premessenger ribonucleoprotein (pre-mRNP) particles, the Balbiani ring (BR) granules in the salivary glands of the dipteran Chironomus tentans, can be visualized in the electron microscope when they assemble on the genes, move through nucleoplasm, and bind to and translocate through the nuclear pores. As shown by BrUTP labeling and immunoelectron microscopy, newly synthesized BR RNP particles, released from the BR genes, appear early in all nucleoplasmic regions of the cell nucleus and they saturate the nucleoplasmic pool of BR particles after 2 h of labelling. It is concluded that within the nucleus the BR particles move randomly. Furthermore, estimates of minimum diffusion coefficients for the BR particles are compatible with the view that the particles diffuse freely in the interchromosomal space, although it is not excluded that the random movement could be slightly retarded. Once the particles get bound to the nuclear pore complexes, they seem committed to translocation through the nuclear pores.

Pre-mRNP particles: From gene to nuclear pore.

It has been difficult to establish whether pre-messenger ribonucleoprotein (pre-mRNP) particles move from the gene towards the periphery of the nucleus in a directed or random manner. Two recent in vivo studies indicate that most pre-mRNP particles move randomly in the nucleus, apparently by free diffusion.

The hrp23 protein in the balbiani ring pre-mRNP particles is released just before or at the binding of the particles to the nuclear pore complex.

Balbiani ring (BR) pre-mRNP particles reside in the nuclei of salivary glands of the dipteran Chironomus tentans and carry the message for giant-sized salivary proteins. In the present study, we identify and characterize a new protein component in the BR ribonucleoprotein (RNP) particles, designated hrp23. The protein with a molecular mass of 20 kD has a single RNA-binding domain and a glycine-arginine-serine-rich auxiliary domain. As shown by immunoelectron microscopy, the hrp23 protein is added to the BR transcript concomitant with transcription, is still present in the BR particles in the nucleoplasm, but is absent from the BR particles that are bound to the nuclear pore complex or are translocating through the central channel of the complex. Thus, hrp23 is released just before or at the binding of the particles to the nuclear pore complex. It is noted that hrp23 behaves differently from two other BR RNP proteins earlier studied: hrp36 and hrp45. These proteins both reach the nuclear pore complex, and hrp36 even accompanies the RNA into the cytoplasm. It is concluded that each BR RNA-binding protein seems to have a specific flow pattern, probably related to the particular role of the protein in gene expression.

The synaptonemal complex protein SCP3 can form multistranded, cross-striated fibers in vivo.

The synaptonemal complex protein SCP3 is part of the lateral element of the synaptonemal complex, a meiosis-specific protein structure essential for synapsis of homologous chromosomes. We have investigated the fiber-forming properties of SCP3 to elucidate its role in the synaptonemal complex. By synthesis of SCP3 in cultured somatic cells, it has been shown that SCP3 can self-assemble into thick fibers and that this process requires the COOH-terminal coiled coil domain of SCP3, as well as the NH2-terminal nonhelical domain. We have further analyzed the thick SCP3 fibers by transmission electron microscopy and immunoelectron microscopy. We found that the fibers display a transversal striation with a periodicity of approximately 20 nm and consist of a large number of closely associated, thin fibers, 5-10 nm in diameter. These features suggest that the SCP3 fibers are structurally related to intermediate filaments. It is known that in some species the lateral elements of the synaptonemal complex show a highly ordered striated structure resembling that of the SCP3 fibers. We propose that SCP3 fibers constitute the core of the lateral elements of the synaptonemal complex and function as a molecular framework to which other proteins attach, regulating DNA binding to the chromatid axis, sister chromatid cohesion, synapsis, and recombination.

Evidence for close contact between recombination nodules and the central element of the synaptonemal complex.

During the first part of meiosis, homologous chromosomes pair and undergo genetic recombination. Two meiotic structures are involved in these processes: the synaptonemal complex (SC) is essential for synapsis of the chromosomes, and the recombination nodules (RNs) represent the sites for recombination. In the present investigation we have used conventional electron microscopy to study the association between the SCs and the RNs in the beetle Blaps cribrosa. This experimental material was chosen because the spermatocytes in B. cribrosa display both exceptionally well-defined SCs and distinct RNs. We find that the RNs are drop shaped, located on top of the SC and oriented in parallel with the ribbon-like SC. The most striking observation is that the RNs coalesce with the top layer of the central element of the SC. The RNs are also connected via fibres to the lateral elements of the SC. These and other structural observations suggest that the RNs could influence the synapsis of homologous chromosomes by affecting both early and late steps in the assembly of the SCs.

Evaluation of the sensitivity of the terminal deoxynucleotidyl transferase-immunogold technique on Balbani ring genes.

Recently, we developed the terminal deoxynucleotidyl transferase (TdT)-immunogold technique for in situ detection of DNA molecules. In this study the potential value and the limitations of the method were evaluated using the giant polytene chromosomes from Chironomus tentans salivary glands. Emphasis was put on the Balbiani rings (BRs), specialized chromosomal sites with exceptionally intense synthesis of large mRNA molecules. Immunolabeling was recorded not only over the bands and interbands of the polytene chromosomes but also over the BR structures. In the BRs, gold particles were present over segments of active transcription units, each with a central chromatin axis and a number of growing RNP products attached to the axis. One third of the transversely sectioned transcription units showed labeling in the central parts, i.e., where the unfolded chromatin axis is located, whereas the growing RNP fibers remained unlabeled. The absence of labeling of the RNP fibers is not likely to be due to lack of accessibility, because anti-RNA antibodies readily decorated the RNP fibers. The nuclear sap and cytoplasm displayed no significant label. These results clearly indicate that the TdT-immunogold technique is specific for DNA and detects not only DNA in compacted chromatin but also fully extended DNA. Its ability to efficiently label a single DNA molecule demonstrates the method's very high sensitivity.

Immunocytochemical evidence for a stepwise assembly of Balbiani ring premessenger ribonucleoprotein particles.

In the active Balbiani ring (BR) genes of the dipteran Chironomus tentans, the assembly of a specific pre-mRNP particle can be analyzed in situ, and the incorporation of hnRNP proteins into the nascent pre-mRNP can be directly visualized by immunoelectron microscopy. In the present study we have shown that hrp36, one of the major hnRNP proteins in Chironomus tentans, is continuously added to the nascent BR pre-mRNP particle throughout transcription and is localized along the entire BR RNP fiber. Interestingly, hrp36 becomes concealed during the structural transition that occurs during the formation of the mature BR RNP particle. This conclusion is based on the observation that hrp36 can be revealed by a monoclonal antibody during the initial assembly of the BR RNP fiber but becomes almost undetectable in the final packaging stage. The hrp36 protein, however, is not removed from the BR RNP particle since the ability of the monoclonal antibody to reveal hrp36 is restored by artificial relaxation of mature BR RNP particles. Another major hnRNP protein, hrp45, is also incorporated in a continuous manner into the nascent pre-mRNP fiber but remains accessible in mature BR RNP particles. Our results provide immunocytochemical evidence for drastic structural changes occurring in the final stage of BR pre-mRNP packaging, and suggest that different hnRNP proteins might be differently involved in the pre-mRNP assembly process.

A protein of the SR family of splicing factors binds extensively to exonic Balbiani ring pre-mRNA and accompanies the RNA from the gene to the nuclear pore.

We report on the molecular cloning and intracellular localization of a heterogeneous nuclear ribonucleoprotein (hnRNP), Ct-hrp45, one of the major components of pre-mRNP particles in Chironomus tentans. It is shown that hrp45 belongs to the SR family of splicing factors and exhibits high sequence similarity to Drosophila SRp55/B52 and human SF2/ASF. The distribution of hrp45 within the C. tentans salivary gland cells is studied by immunocytology. The hrp45 protein is found to be abundant in the nucleus, whereas it is undetectable in the cytoplasm. The fate of hrp45 in specific pre-mRNP particles, the Balbiani ring (BR) granules, is revealed by immunoelectron microscopy. It is observed that hrp45 is associated with the growing BR pre-mRNP particles and is being added continuously concomitant with the growth of the transcript, indicating that hrp45 is bound extensively to exon 4, which comprises 80-90% of the primary transcript. Furthermore, hrp45 remains bound to the BR RNP particles in the nucleoplasm and is not released until the particles translocate through the nuclear pore. Thus, hrp45 behaves as an hnRNP protein linked to exon RNA (and perhaps also to the introns) rather than as a spliceosome component connected to the assembly and disassembly of spliceosomes. It seems that hrp45, and possibly also other SR family proteins, is playing an important role in the structural organization of pre-mRNP particles and is perhaps participating not only in splicing but also in other intranuclear events.

RNP export is mediated by structural reorganization of the nuclear pore basket.

Messenger RNA leaves the cell nucleus as ribonucleoprotein (RNP) particles. The nucleocytoplasmic translocation of the particles takes place through the nuclear pore complex (NPC) and includes two steps: binding to the NPC and transit through its central channel. The NPC basket is a fishtrap-like component of NPC facing the nucleoplasm. Its position in the NPC strongly suggests that it has an important role in the initial steps of macromolecular export from the nucleus. Here we report a cyclic rearrangement of the basket structure in relation to the translocation of a specific messenger RNP (mRNP) of exceptional size, the Balbiani ring RNP particles in the salivary gland cells in Chironomus. We used field emission in-lens scanning electron microscopy (FEISEM), transmission electron microscopy (TEM), and immunocytochemistry to analyse the structural organization of the basket during the mRNP export. Our observations reveal five configurations of the basket which are presented in a model of basket reorganization related to the state of mRNP penetration into the NPC. We suggest that the functional role of the basket is to anchor the mRNP particle to the NPC and position it in correct orientation at the entrance to the central channel of the NPC.

Localization of the N-terminus of SCP1 to the central element of the synaptonemal complex and evidence for direct interactions between the N-termini of SCP1 molecules organized head-to-head.

The synaptonemal complex (SC) is a meiosis-specific, tripartite structure essential for synapsis of homologous chromosomes; it contains a central element positioned between two lateral elements and transversal filaments connecting the lateral elements. In mammals, a major constituent of the transversal filament is known: the SCP1 protein. It contains a long central coiled-coil motif and the molecules are probably organized as dimers, each forming a coiled-coil fiber. We have now developed a new sensitive procedure for immunoelectron microscopy of synaptonemal complex proteins and determined the exact localization of the two nonhelical ends of the SCP1 protein within the mouse synaptonemal complex. We found that the N-terminal end of the SCP1 protein is located within the central element of the synaptonemal complex, whereas the C-terminal end is close to or within the lateral element of the synaptonemal complex. This result supports the notion that SCP1 is an extended filamentous protein and that the two molecules of the putative SCP1 dimer are likely to have the same polarity. The observation that the N-termini are confined to the central element indicated that SCP1 dimers, anchored in opposite lateral elements, could establish contact with each other in the central element via their N-termini. To test this possibility we used the yeast two-hybrid system and found that the N-terminal end of the SCP1 protein indeed strongly interacted with itself, but not with other protein domains tested. We therefore suggest that a transversal filament consists of one or more pairs of SCP1 dimers, each pair being organized in a head-to-head arrangement with the C-termini anchored in the lateral elements and the two N-termini being joined in the central element.