Archaeal signal peptides--a comparative survey at the genome level

The correct delivery of noncytoplasmic proteins to locations both within and outside the cell depends on the appropriate targeting signals. Protein translocation across the bacterial plasma membrane and the eukaryal endoplasmic reticulum membrane relies on cleavable N-terminal signal peptides. Although the signal peptides of secreted proteins in Bacteria and Eukarya have been extensively studied at the sequence, structure, and functional levels, little is known of the nature of archaeal signal peptides. In this report, genome-based analysis was performed in an attempt to define the amino acid composition, length, and cleavage sites of various signal peptide classes in a wide range of archaeal species. The results serve to present a picture of the archaeal signal peptide, revealing the incorporation of bacterial, eukaryal, and archaeal traits.

Detection and analysis of membrane interactions by a biomimetic colorimetric lipid/polydiacetylene assay

We describe applications of a colorimetric assay based on supramolecular assemblies of lipid-polydiacetylene vesicles for analysis and screening of membrane interactions of lipophilic enzymes, peptides, and ions and for study of the effects of lipid composition upon membrane properties. The lipid-polymer aggregates undergo visible and quantifiable blue-to-red transitions following interfacial interactions and perturbation by varied biochemical processes. Specifically, we show that the colorimetric assay can be tuned for selective detection of enzymes reacting with different lipid species. The experiments also demonstrate that the lipid/polymer platform facilitates screening of peptide-membrane interactions in multicomponent mixtures. The colorimetric vesicles can incorporate lipid species from different cellular sources facilitating analysis of the contribution of molecular components to membrane properties and lipid interactions.

Modelling the elastic scattering in diagnostic radiology: the importance of structure form factors

The importance of structure form factors in describing elastic scattering in diagnostic radiology was studied through a Monte Carlo code built to reproduce scattering in large water samples. The code, developed by us, considers all relevant interactions, including multiple scattering and interference due to scattering by the liquid structure. Geometrical conditions and energies similar to those found in radiology were used. The secondary to primary radiation ratio using the usual free atom approximation and the structure form factor was obtained and both approaches were compared. Calculations of radiological parameters such as the angular distribution of photons incident on the detector and the fraction of scattered photons stopped by anti-scattering grids were also performed considering mammography, thorax and abdomen radiography conditions. The results have shown that S(beta)/P depends on the experimental set-up, being more important for low momentum transfers and sample sizes for which the multiple scattering is not expected to be significant, as in the case of mammography. It was also verified that large samples increase the probability of multiple scattering, masking the structure peak in S(beta) and making the sample structure important just for relatively thin samples. Considering mammography-like geometry, the maximum of the S(beta)/P distribution considering structure form factors occurs around 15 degrees while the correspondent maximum without considering the structure factors occurs around 10 degrees for any sample thickness. S(beta)/P is almost independent of the irradiation field, with the maximum remaining at 15 degrees and 10 degrees for the SFF and FAFF, respectively. The cases studied in this paper stress some conditions in which it is mandatory to use SFF, but since it requires no further significant efforts, the SFF approach is recommended as a standard procedure when describing the elastic scattering process in radiology.

Evolution of the prokaryotic protein translocation complex: a comparison of archaeal and bacterial versions of SecDF

Protein translocation across the prokaryotic plasma membrane occurs at the translocon, an evolutionarily conserved membrane-embedded proteinaceous complex. Together with the core components SecYE, prokaryotic translocons also contain auxilliary proteins, such as SecDF. Alignment of bacterial and archaeal SecDF protein sequences reveals the presence of a similar number of homologous regions within each protein. Moreover, the conserved sequence domains in the archaeal proteins are located in similar positions as their bacterial counterparts. When these domains are, however, compared along Bacteria-Archaea lines, a much lower degree of similarity is detected. In Bacteria, SecDF are thought to modulate the membrane association of SecA, the ATPase that provides the driving force for bacterial protein secretion. As no archaeal version of SecA has been detected, the sequence differences reported here may reflect functional differences between bacterial and archaeal SecDF proteins, and by extension, between the bacterial and archaeal protein translocation processes. Moreover, the apparent absence of SecDF in several completed archaeal genomes suggests that differences may exist in the process of protein translocation within the archaeal domain itself.

Post-translational secretion of fusion proteins in the halophilic archaea Haloferax volcanii

Although protein secretion occurs post-translationally in bacteria and is mainly a cotranslational event in Eukarya, the relationship between the translation and translocation of secreted proteins in Archaea is not known. To address this question, the signal peptide-encoding region of the surface layer glycoprotein gene from the Haloarchaea Haloferax volcanii was fused either to the cellulose-binding domain of the Clostridium thermocellum cellulosome or to the cytoplasmic enzyme dihydrofolate reductase from H. volcanii. Signal peptide-cleaved mature versions of both the cellulose-binding domain and dihydrofolate reductase could be detected in the growth medium of transformed H. volcanii cells. Immunoblot analysis revealed, however, the presence of full-length signal peptide-bearing forms of both proteins inside the cytoplasm of the transformed cells. Proteinase accessibility assays confirmed that the presence of cell-associated signal peptide-bearing proteins was not due to medium contamination. Moreover, the pulse-radiolabeled signal peptide cellulose-binding domain chimera could be chased from the cytoplasm into the growth medium even following treatment with anisomycin, an antibiotic inhibitor of haloarchaeal protein translation. Thus, these results provide evidence that, in Archaea, at least some secreted proteins are first synthesized inside the cell and only then translocated across the plasma membrane into the medium.

Isolation of fusion proteins containing SecY and SecE, components of the protein translocation complex from the halophilic archaeon Haloferax volcanii

By exploiting the salt-insensitive interaction of the cellulose-binding domain (CBD) of the Clostridium thermocellum cellulosome with cellulose, purification of CBD-fused versions of SecY and SecE, components of the translocation apparatus of the halophilic archaeon Haloferax volcanii, was undertaken. Following transformation of Haloferax volcanii cells with CBD-SecY- or -SecE-encoding plasmids, cellulose-based purification led to the capture of stably expressed, membrane-bound 68 and 25 kDa proteins, respectively. Both fusion proteins were recognized by antibodies raised against the CBD. Thus, CBD-cellulose interactions can be employed as a salt-insensitive affinity purification system for the capture of complexes containing the Haloferax volcanii translocation apparatus components SecY and SecE.

Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii

The signal recognition particle (SRP) is a ribonucleoprotein complex involved in the recognition and targeting of nascent extracytoplasmic proteins in all three domains of life. In Archaea, SRP contains 7S RNA like its eukaryal counterpart, yet only includes two of the six protein subunits found in the eukaryal complex. To further our understanding of the archaeal SRP, 7S RNA, SRP19 and SRP54 of the halophilic archaeon Haloferax volcanii have been expressed and purified, and used to reconstitute the ternary SRP complex. The availability of SRP components from a haloarchaeon offers insight into the structure, assembly and function of this ribonucleoprotein complex at saturating salt conditions. While the amino acid sequences of H.volcanii SRP19 and SRP54 are modified presumably as an adaptation to their saline surroundings, the interactions between these halophilic SRP components and SRP RNA appear conserved, with the possibility of a few exceptions. Indeed, the H.volcanii SRP can assemble in the absence of high salt. As reported with other archaeal SRPs, the limited binding of H.volcanii SRP54 to SRP RNA is enhanced in the presence of SRP19. Finally, immunolocalization reveals that H.volcanii SRP54 is found in the cytosolic fraction, where it is associated with the ribosomal fraction of the cell.

Lipid modification of proteins in Archaea: attachment of a mevalonic acid-based lipid moiety to the surface-layer glycoprotein of Haloferax volcanii follows protein translocation

Once the newly synthesized surface (S)-layer glycoprotein of the halophilic archaeaon Haloferax volcanii has traversed the plasma membrane, the protein undergoes a membrane-related, Mg(2+)-dependent maturation event, revealed as an increase in the apparent molecular mass and hydrophobicity of the protein. To test whether lipid modification of the S-layer glycoprotein could explain these observations, H. volcanii cells were incubated with a radiolabelled precursor of isoprene, [(3)H]mevalonic acid. In Archaea, isoprenoids serve as the major hydrophobic component of archaeal membrane lipids and have been shown to modify other haloarchaeal S-layer glycoproteins, although little is known of the mechanism, site or purpose of such modification. In the present study we report that the H. volcanii S-layer glycoprotein is modified by a derivative of mevalonic acid and that maturation of the protein was prevented upon treatment with mevinolin (lovastatin), an inhibitor of mevalonic acid biosynthesis. These findings suggest that lipid modification of S-layer glycoproteins is a general property of halophilic archaea and, like S-layer glycoprotein glycosylation, lipid-modification of the S-layer glycoproteins takes place on the external cell surface, i.e. following protein translocation across the membrane.

Protein glycosylation in Haloferax volcanii: partial characterization of a 98-kDa glycoprotein

The plasma membrane of Haloferax volcanii contains several glycoproteins, including a 98-kDa species. Using lectin-based chromatography, the glycoprotein was isolated and partially characterized. Sequence comparison, based on antibody binding as well as one-dimensional peptide maps show that the 98-kDa glycoprotein is distinct from the S-layer glycoprotein, the major glycoprotein in H. volcanii. The 98-kDa glycoprotein can be further distinguished from the S-layer glycoprotein on the basis of membrane attachment. Unlike the S-layer glycoprotein, the 98-kDa glycoprotein is not associated with the membrane in a Mg2+-dependent manner. Both proteins, however, apparently rely on a similar mechanism of glycosylation, since neither was affected by treatment with bacitracin or tunicamycin, agents known to interfere with protein glycosylation in other species. Finally, the pattern of glycosylation of the 98-kDa glycoprotein is not shared by a 95-kDa glycoprotein of the related Haloferax mediterranei strain.

[Introduction to tissue optics and optical dosimetry]

The spatial distribution of radiation during medical laser application is determined by the characteristics of the beam (power, time, beam geometry) and the optical properties of the tissue. The irradiance E (in W/m2) describes the primary laser beam. Scattered radiation, in turn, is taken into account by the fluence rate phi (also in W/m2). The basic parameters of tissue optics are the absorption coefficient mu a, the scattering coefficient mu s and the anisotropy factor g. In addition, derived parameters are also used, i.e., total attenuation coefficient mu t, reduced scattering coefficient mu s', effective attenuation coefficient mu eff, mean free path of a photon d and penetration depth delta. Further tissue properties are the diffuse reflectance Rd and the back-scattering factor k. In an one-dimensional model the fluence rate phi in tissue is a nearly exponential function characterized by the penetration depth delta. At the tissue surface, the relationship exists phi = kE. This model is compared with the results of a computer program based on the finite element method.

Characterization of inverted membrane vesicles from the halophilic archaeon Haloferax volcanii

Membrane-related processes in archaea, the third and most-recently described domain of life, are in general only poorly understood. One obstacle to a functional understanding of archaeal membrane-associated activities corresponds to a lack of archaeal model membrane systems. In the following, characterization of inverted archaeal membrane vesicles, prepared from the halophilic archaeon Haloferax volcanii, is presented. The inverted topology of the vesicles was revealed by defining the orientation of membrane-bound enzymes that in intact cells normally face the cytoplasm or of other protein markers, known to face the exterior medium in intact cells. Electron microscopy, protease protection assays and lectin-binding experiments confirmed the sealed nature of the vesicles. Upon alkalinization of the external medium, the vesicles were able to generate ATP, reflecting the functional nature of the membrane preparation. The availability of preparative scale amounts of inverted archaeal membrane vesicles provides a platform for the study of various membrane-related phenomena in archaea.

Post-translational modification of the S-layer glycoprotein occurs following translocation across the plasma membrane of the haloarchaeon Haloferax volcanii

The halophilic archaeon Haloferax volcanii is surrounded by a protein shell solely comprised of the S-layer glycoprotein. While the gene sequence and glycosylation pattern of the protein and indeed the three-dimensional structure of the surface layer formed by the protein have been described, little is known of the biosynthesis of the S-layer glycoprotein. In the following, pulse-chase radiolabeling and cell-fractionation studies were employed to reveal that newly synthesized S-layer glycoprotein undergoes a maturation step following translocation of the protein across the plasma membrane. The processing step, detected as an increase in the apparent molecular mass of the S-layer glycoprotein, is unaffected by inhibition of protein synthesis and is apparently unrelated to glycosylation of the protein. Maturation requires the presence of magnesium ions, involved in membrane association of the S-layer glycoprotein, and results in increased hydrophobicity of the protein as revealed by enhanced detergent binding. Thus, along with protein glycosylation, additional post-translational modifications apparently occur on the external face of the haloarchaeal plasma membrane, the proposed topological homologue of the lumenal face of the eukaryal endoplasmic reticulum membrane.

Influence of pulse duration on ultrashort laser pulse ablation of biological tissues

Ablation characteristics of ultrashort laser pulses were investigated for pulse durations in the range of 130 fs-10 ps. Tissue samples used in the study were dental hard tissue (dentin) and water. We observed differences in ablation crater morphology for craters generated with pulse durations in the 130 fs-1 ps and the 5 ps-10 ps range. For the water experiment, the surface ablation and subsequent propagation of stress waves were monitored using Mach-Zehnder interferometry. For 130 fs-1 ps, energy is deposited on the surface while for longer pulses the beam penetrates into the sample. Both studies indicate that a transition occurs between 1 and 5 ps.

The signal recognition particle of Archaea

It is becoming increasingly clear that similarities exist in the manner in which extracytoplasmic proteins are targeted to complexes responsible for translocating these proteins across membranes in each of the three domains of life. In Eukarya and Bacteria, the signal recognition particle (SRP) directs nascent polypeptides to membrane-embedded translocation sites. In Archaea, the SRP protein targeting pathway apparently represents an intermediate between the bacterial and eukaryal systems. Understanding the archaeal SRP pathway could therefore reveal universal aspects of targeting not detected in current comparisons of the eukaryal and bacterial systems while possibly identifying aspects of the process either not previously reported or unique to Archaea.

Collagen structure and nonlinear susceptibility: effects of heat, glycation, and enzymatic cleavage on second harmonic signal intensity

BACKGROUND AND OBJECTIVE

Helical macromolecules such as collagen and DNA are characterized by nonlinear optical properties, including nonlinear susceptibility. Because collagen is the predominant component of most biological tissues, as well as the major source of second harmonic generation (SHG), it is reasonable to assume that changes in harmonic signal can be attributed to structural changes in collagen. The purpose of this study is to determine whether various modifications of collagen structure affect second harmonic intensity.

STUDY DESIGN/MATERIALS AND METHODS

SHG was measured in tissues from cows, humans, and chickens. The effects of beam polarization, thermal denaturation, glyco-oxidative damage, and enzymatic cleavage of tissues on second harmonic intensity was studied.

RESULTS

The second harmonic intensity differed considerably among different tissues, as did the effect of the incident beam polarization. In structurally modified collagen, SHG was significantly degraded from SHG in intact collagen.

CONCLUSION

These structural modifications are representative of changes that occur in pathophysiologic conditions such as thermal injury, diabetes, tumor invasion, and abnormal wound healing. The ability to assess these changes rapidly and noninvasively has considerable clinical applicability. SHG analysis might provide a unique tool for monitoring these structural changes of collagen.

Near-threshold photoionization of hydrogenlike uranium studied in ion-atom collisions via the time-reversed process

Radiative electron capture, the time-reversed photoionization process occurring in ion-atom collisions, provides presently the only access to photoionization studies for very highly charged ions. By applying the deceleration mode of the ESR storage ring, we studied this process in low-energy collisions of bare uranium ions with low- Z target atoms. This technique allows us to extend the current information about photoionization to much lower energies than those accessible for neutral heavy elements in the direct reaction channel. The results prove that for high- Z systems, higher-order multipole contributions and magnetic corrections persist even at energies close to the threshold.

[In vitro experiments with Nd:YAG laser surgery on the turbinates]

BACKGROUND

Turbinate surgery is a therapeutic method for the treatment of the obstruction of nasal respiration. In this paper the dimensions of the laser lesions are described. In addition macro- and microscopical findings after laser surgery are given.

METHODS

10 human lower and 4 middle turbinates in vitro were treated with the Nd:YAG-laser in the non-contact mode (1064 nm, 2.5-25 W, cw). Stripe-like lesion with 3 cm length were produced. In addition the posterior end of the lower turbinates and the head of the middle turbinates were vaporized.

RESULTS

Width, depth and volume of the lesions are given in dependence of laser power and irradiation time. The histological changes immediately after laser treatment are described.

CONCLUSIONS

The energy doses for a clinical relevant stripe-like laser lesion of 3-4 cm in length of the lower turbinate is about 1500 Ws using Nd:YAG-laser. For evaporation of a posterior end of the lower turbinate 360 Ws are required using Nd:YAG-laser. For evaporation of the head of the middle turbinate a doses of about 1500 Ws are required using Nd:YAG-laser.

Archaeal protein translocation crossing membranes in the third domain of life

Proper cell function relies on correct protein localization. As a first step in the delivery of extracytoplasmic proteins to their ultimate destinations, the hydrophobic barrier presented by lipid-based membranes must be overcome. In contrast to the well-defined bacterial and eukaryotic protein translocation systems, little is known about how proteins cross the membranes of archaea, the third and most recently described domain of life. In bacteria and eukaryotes, protein translocation occurs at proteinaceous sites comprised of evolutionarily conserved core components acting in concert with other, domain-specific elements. Examination of available archaeal genomes as well as cloning of individual genes from other archaeal strains reveals the presence of homologues to selected elements of the bacterial or eukaryotic translocation machines. Archaeal genomic searches, however, also reveal an apparent absence of other, important components of these two systems. Archaeal translocation may therefore represent a hybrid of the bacterial and eukaryotic models yet may also rely on components or themes particular to this domain of life. Indeed, considering the unique chemical composition of the archaeal membrane as well as the extreme conditions in which archaea thrive, the involvement of archaeal-specific translocation elements could be expected. Thus, understanding archaeal protein translocation could reveal the universal nature of certain features of protein translocation which, in some cases, may not be readily obvious from current comparisons of bacterial and eukaryotic systems. Alternatively, elucidation of archaeal translocation could uncover facets of the translocation process either not yet identified in bacteria or eukaryotes, or which are unique to archaea. In the following, the current status of our understanding of protein translocation in archaea is reviewed.

Temperature distribution for combined laser hyperthermia-photodynamic therapy in the esophagus

In recent years photodynamic laser therapy (PDT) has been tested in animal and clinical studies for treatment of esophageal cancer. In several animal experiments a synergistic effect was found by simultaneously applying PDT and hyperthermia (HT). In this paper an optical fibre system is described which can be used in the esophagus for combined PDT with a 1 W dye laser and HT with a 15 W Nd:YAG laser. A phantom was built simulating the geometry of the esophagus using cow muscle. The spatial temperature field during HT was measured versus irradiation time. The results were compared with calculations using a coupled Monte Carlo laser transport/finite difference heat transport model using the LATIS computer program. Measurements and calculations yield a realistic description of the temperature distribution during HT under various experimental conditions. The LATIS program allows the prediction of the effects of blood perfusion for in vivo situations. The results show that perfusion has considerable influence on the temperature field, reducing the effective depth in tissue for HT.